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Harnessing the evolutionary information on oxygen binding proteins through Support Vector Machines based modules
(BioMed Central Ltd, 2018-12-01) Muthukrishnan S; Puri M
Objectives: The arrival of free oxygen on the globe, aerobic life is becoming possible. However, it has become very clear that the oxygen binding proteins are widespread in the biosphere and are found in all groups of organisms, including prokaryotes, eukaryotes as well as in fungi, plants, and animals. The exponential growth and availability of fresh annotated protein sequences in the databases motivated us to develop an improved version of "Oxypred" for identifying oxygen-binding proteins.
Results: In this study, we have proposed a method for identifying oxy-proteins with two different sequence similarity cutoffs 50 and 90%. A different amino acid composition based Support Vector Machines models was developed, including the evolutionary profiles in the form position-specific scoring matrix (PSSM). The fivefold cross-validation techniques were applied to evaluate the prediction performance. Also, we compared with existing methods, which shows nearly 97% recognition, but, our newly developed models were able to recognize almost 99.99 and 100% in both oxy-50 and 90% similarity models respectively. Our result shows that our approaches are faster and achieve a better prediction performance over the existing methods. The web-server Oxypred2 was developed for an alternative method for identifying oxy-proteins with more additional modules including PSSM, available at http://bioinfo.imtech.res.in/servers/muthu/oxypred2/home.html.
Harvesting optimization and Omega-3 recovery improvement from Schizochytrium DT3 using surfactant-aided dispersed air flotation: Response surface methodology
(Elsevier B.V., 2024-06) Alhattab M; Puri M
Microalgae's potential to produce high value bioactives is contingent on the cost-effective harvesting of algal biomass. The use of CTAB (cetyl trimethylammonium bromide) assisted dispersed air flotation as a harvesting technique for Schizochytrium biomass, was optimized as a cost-effective means for recovery (R) and concentration factor (CF) using Response Surface Methodology. To the best of our knowledge, this is the first study to employ surfactant assisted dispersed air flotation (SDAF) in the recovery of a heterotrophic thraustochytrid strain. A Box-Behnken design of experiment investigating the operating parameters of CTAB amount, air flow rate and volume on Schizochytrium was employed. Initially, both responses were analyzed individually and then used to simultaneously maximize both variables. The optimized conditions of CTAB (500 mg/L), air flow of 2 L/min and volume of 600 mL resulted in a R of 91 % and CF of 19 times. Although a secondary step is necessary for further concentration, this technique utilizes 70 times less energy as compared to conventional centrifugation techniques which are used to recover Schizochytrium sp. This is significant as this technique can be easily adapted to existing bioreactors, as they are already equipped with gas spargers. In addition, the presence of surfactant carried through demonstrated an improvement in the recovery of long chain poly unsaturated fatty acid (PUFA) by 6 %, particularly in DHA and DPA which was not observed in washed biomass.
Nutritive value of fodder beet for broilers chickens
(Elsevier B V, 2026-01-15) Ganraj K; David LS; Morel PCH
An experiment was conducted to determine the apparent metabolisable energy (AME), nitrogen-corrected AME (AMEn) and the standardised ileal digestible content of amino acids in fodder beet (FB). Three maize-soybean-based diets were formulated, a basal diet (FB0), the basal diet supplemented with 12.5 % of FB (FB12.5), and the basal diet supplemented with 25 % of FB (FB25). Each diet was randomly allocated to six replicate cages with six birds per cage and fed from days 14–21. Titanium dioxide (4 g/kg) was included in all diets as an indigestible marker for the measurement of marker-based AME and ileal nutrient digestibility. The total collection (TC) method was also used for the measurement of AME. A regression method was used to determine the nutritive value of FB. The AME and AMEn of FB were determined to be 9.63 MJ/kg and 9.36 MJ/kg, respectively, using the TC method, and 7.97 MJ/kg, 7.79 MJ/kg, respectively, using the marker method. The apparent ileal crude protein (CP) and gross energy (GE) content of FB were 56.4 g/kg and 11.2 MJ/kg, respectively. Standardised ileal digestible amino acid content was higher for glutamic acid (21.1 g/kg) while it was lower for sulfur containing amino acids (-0.1 to −0.4 g/kg). In conclusion, nutritive value of FB was determined for 14–21 day old broilers using regression method. Further studies are needed to validate the current findings, and to determine the optimal inclusion level of FB in poultry diets.
Modeling the role of institutional trust to improve vaccine confidence: The New Zealand case
(Taylor and Francis Group, 2025-07-03) Diers-Lawson A; Ashwell D; Murray N
This study explores how institutional trust influences vaccine confidence during public health crises, using New Zealand’s COVID-19 response as a high-trust case study. Applying the Stakeholder Relationship Management (SRM) framework, the research investigates how demographic, value-based, health, institutional, and informational factors shape vaccine attitudes across varying levels of institutional trust. Results demonstrate that institutional trust is a critical predictor of both vaccine confidence and skepticism, with trust in science and reliance on official sources driving confidence, and social media reliance correlating with skepticism. Segmenting participants by trust levels revealed distinct patterns, highlighting the importance of tailoring communication strategies to trust-based subgroups. The findings reposition vaccine hesitancy as a crisis and risk communication challenge—rooted not solely in individual traits but in institutional relationships and the complex information environment. The study advocates for integrating strategic communication principles into public health risk communication, emphasizing long-term trust-building, credibility, and message alignment across platforms. This research offers a model for cross-contextual testing and underscores the need for governments and health authorities to engage low-trust communities more effectively, particularly through strategic use of social media during health emergencies.
Testing and adapting dietary habits and food security questions for a national nutrition survey using cognitive interviews and expert consultation
(Cambridge University Press on behalf of The Nutrition Society, 2025-10-06) Follong B; Haliburton C; Grey J; Maiquez M; Mackay S; Te Morenga L; Mhurchu CN
Objective: To cognitively test questions for inclusion in a national nutrition survey, ensuring the questions are interpreted as intended and to inform further improvements.
Design: A draft nutrition survey questionnaire was developed based on existing questionnaires and expert input. Twelve questions on dietary habits and food security were selected for cognitive testing as these were newly developed, amended from existing questions, or identified to no longer reflect the current food environment or concepts. Cognitive interviews were conducted using both think-aloud and probing techniques to capture respondents’ thought processes used to arrive at an answer. Interviews were audio recorded and transcribed verbatim. Qualitative data were analysed for recurring patterns and unique discoveries across the survey questions.
Setting: New Zealand.
Participants: Sixty-eight participants aged 11 years and older representing diverse sociodemographics including gender, ethnicity, and education level.
Results: Three main cognitive challenges were identified: 1) interpreting ambiguous terms, 2) understanding of dietary or technical terms, and 3) following complex or unclear instructions. Questions were refined based on the study findings and further advice from experts in nutrition and survey design to enhance participant understanding and accuracy.
Conclusion: The cognitive testing findings and expert input led to the refinement and potential improvement of selected questions for inclusion in a national nutrition survey. Changes included simplified terminology, clearer instructions, improved examples, and better question order. Our methodological approach and findings may be valuable for those designing similar questions for dietary surveys.