Authenticity and the argument from testability: a bottom-up approach : Author

Jesper Ahlin Marceta published an article in this journal in which he formulated his "argument from testability", stating that it is impossible, at least practically, to operationalize procedural authenticity. That is, using procedural accounts of authenticity, one cannot reliably differentiate between authentic and inauthentic desires. There are roughly two ways to respond to the argument from testability: top-down and bottom-up. Several authors have endeavored the top-down approach by trying to show that some conceptions of authenticity might be operationalizable after all. At present, however, the bottom-up approach has not been put to the test. That is, no attempt has been made to use a currently existing assessment tool to guide the development of an account of authenticity. In this paper, I will investigate what it means to develop an account of authenticity bottom-up based on measures of concordance. More specifically, I will investigate the following three research questions. First, how do concordance and authenticity relate at a conceptual level? As crucial similarities exist between these concepts, concordance measures seem to offer a good starting point for the bottom-up approach. Second, how do judgements of concordance differ from judgements of authenticity? Both their scope and the way they are justified will turn out to be different. This suggests novel ways to react to Marceta's argument from testability. Third, should we develop a theory of concordance? The positive answer to this question will point towards a central limitation of the bottom-up approach.

Comparison of middle- and bottom-up mass spectrometry in forced degradation studies of bevacizumab and infliximab

Monoclonal antibodies (mAbs) used as therapeutics need comprehensive characterization for appropriate quality assurance. For analysis, cost-effective methods are of high importance, especially when it comes to biosimilar development which is based on extended physicochemical characterization. The use of forced degradation to study the occurrence of modifications for analysis is well established in drug development and may be used for the evaluation of critical quality attributes (CQAs). For mAb analysis different procedures of liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses are commonly applied. In this study the middle-up approach is compared to the more expensive bottom-up analysis in a forced oxidation biosimilar comparability study. Bevacizumab and infliximab as well as biosimilar candidates for the two mAbs were forcefully oxidized by H2O2 for 24, 48 and 72 h. For bottom-up, the reduced and alkylated trypsin or Lys-C digested samples were analysed by LC-MS with quadrupole time-of-flight mass analyser (LC-QTOF-MS) to detect susceptible residues. By middle-up analysis several species of every subunit (Fc/2, light chain and Fd') were detected which differed in the number of oxidations. For the most abundant species, results from middle-up were in line with results from bottom-up analysis, confirming the strength of middle-up analysis. However, for less abundant species of some subunits, results differed between the two approaches. In both mAbs, the Fc was extensively oxidized. In infliximab, additional extensive oxidation was found in the Fab. Assignment to specific amino acid residues was finally possible using the results from bottom-up analyses. Interestingly, the C-terminal cysteine of the light chain was partially found triply oxidized in both mAbs. The comparison of susceptibility to oxidation showed high similarity between the reference products and their biosimilar candidates. It is suggested that the findings of middle-up experiments should be complemented by bottom-up analysis to confirm the assignments of the localization of modifications. Once the consistency of results has been established, middle-up analyses are sufficient in extended forced degradation biosimilar studies.

Synthetic routes to theranostic applications of carbon-based quantum dots

Background and Purpose

Modern technologies are making advanced paths to address emerging issues. The development of carbon dots (CDs) technology at a tiny level has been researched to have made impeccable strides in advancing the modern scientific field, especially in nanomedicine.

Experimental Approach

Researchers have gained much attention on CDs of their unique properties in the synthesis, easy surface modifications, excellent optical properties, low toxicity, and water solubility. Doping carbon dots with other elements makes them more convenient for their use in the medical sector.

Key Results

The manuscript provides a detailed discussion of the two main methods, including the hydrothermal pathway. CDs are synthesized bottom-up by building up molecules at the atomic scale and top-down by transforming large carbon particles into nanoscale dimensions.

Conclusion

The present article discussed the role, importance, and recent advancements in the synthesis of CDs, by using various approaches giving importance to the hydrothermal process. Recent investigations, their mechanism, and theranostic applications have also been reported.

Determination of the Number of Tissue Groups of Kinetically Distinct Transit Time in Whole-Body Physiologically Based Pharmacokinetic (PBPK) Models I: Theoretical Consideration of Bottom-Up Approach of Lumping Tissues in Whole-Body PBPK

Minimal physiologically based pharmacokinetic (mPBPK) models, consisting of system-specific (e.g., tissue volume and blood flow) and drug-related (e.g., tissue-to-plasma partition coefficient) parameters, are practically useful for pharmacokinetic analyses. However, biopharmaceutical principles were not clear on how peripheral tissues, adopted in whole-body physiologically based pharmacokinetic (WB-PBPK) models, could be kinetically consolidated into one or two tissue groups in the mPBPK models. In this theoretical examination, we studied the relationship between the progressive tissue lumping in the direction from the longest mean transit time (MTT_max) to the shorter one(s) and the slopes of the terminal (λ_ter)/distributional phases, assuming tissues with comparable MTTs are kinetically combined. The appropriateness of lumping was ascertained by evaluating the impact of difference in tissue MTTs during the lumping on the analytical solution of WB-PBPK models. We found that the ratio of MTT_max to the mean residence time in the body, viz., K_det, is related to the change in λ_ter by the progressive lumping and can serve as an index for the robustness of λ_ter. Calculations with two extreme cases revealed that, for caffeine at K_det < 0.03, the change in λ_ter was minimal even when all peripheral tissues were collectively lumped, whereas for artesunic acid at K_det > 50, the tissue of MTT_max could not be kinetically combined even with the tissue having the second-longest MTT without significantly affecting λ_ter. Therefore, we proposed K_det as an index for the robustness of λ_ter during tissue lumping and for the number of tissue groups with distinct transit times in WB-PBPK.

Determination of the Number of Tissue Groups of Kinetically Distinct Transit Time in Whole-Body Physiologically Based Pharmacokinetic (PBPK) Models II: Practical Application of Tissue Lumping Theories for Pharmacokinetics of Various Compounds

In our companion paper, we described the theoretical basis for tissue lumping in whole-body physiologically based pharmacokinetic (WB-PBPK) models and found that K_det, a coefficient for determining the number of tissue groups of distinct transit time in WB-PBPK models, was related to the fractional change in the terminal slope (FCT) when tissues were progressively lumped from the longest transit time to shorter ones. This study was conducted to identify the practical threshold of K_det by applying the lumping theory to plasma/blood concentration-time relationships of 113 model compounds collected from the literature. We found that drugs having K_det < 0.3 were associated with FCT < 0.1 even when all peripheral tissues were lumped, resulting in comparable plasma concentration-time profiles between one-tissue minimal PBPK (mPBPK) and WB-PBPK models. For drugs with K_det ≥ 1, WB-PBPK profiles appeared similar with two-tissue mPBPK models by applying the rule of FCT < 0.1 for lumping slowly equilibrating tissues. The two-tissue mPBPK model also appeared appropriate in terms of concentration-time profiles for drugs with 0.3 ≤ K_det < 1, although, some compounds (15.9% of the total cases), but not all, in this range showed a slight (maximum of 18.9% of the total AUC) deviation from WB-PBPK models, indicating that the two-tissue model, with caution, could still be used for those cases. Comparison of kinetic parameters between traditional (model-fitting) and current (theoretical calculation) mPBPK analyses revealed their significant correlations. Collectively, these observations suggest that the number of tissue groups could be determined based on the K_det/FCT criteria, and plasma concentration-time profiles from WB-PBPK could be calculated using equations significantly less complex.

A locally relevant framework for assessing the risk of sea level rise under changing temperature conditions: Application in New Caledonia, Pacific Ocean

Sea level rise is a key feature in a warmer world and its impact can be seen globally. Assessing climate change-induced sea level rise, therefore, is urgently needed particularly in small island nations, where the threats of sea level rise are immediate, but the level of preparedness is low. Here, we propose a stochastic simulator to link changes in Mean Annual Temperature (MAT) to Mean Annual Sea Level (MASEL) at the local scale. This is through what-if scenarios that are developed based on the association between local temperature and sea level. The model can provide a basis for a bottom-up impact assessment by addressing limitations of applying large-scale projections in small islands and facilitating the accessibility of the impact assessment to stakeholders. For this purpose, we decompose the MAT and MASEL signals into their linear trend and autocorrelation components as well as independent and identically distributed residual terms. We further explore the association between trend and residual terms of MAT and MASEL. If such dependencies exist, scenarios of sea level can be synthesized based on the trend and residual terms of temperature. We use linear regression to link trends of MAT and MASEL, and copulas to formulate dependencies between residuals. This allows stochastic sampling of MASEL conditioned to trend and random variability in MAT. This framework is used for retrospective and prospective simulations of MASEL in Nouméa, the capital city of New Caledonia, the Pacific. We set up six different model configurations for developing the stochastic sampler, each including various parametric options. By selecting the best setup from each configuration, we provide a multi-model stochastic projection of MASEL, assuming the persistence in current long-term trend in MAT and MASEL. We demonstrate how such simulations can be used for a risk-based impact assessments and discuss sources of uncertainty in future projections.

Graphene quantum dots: synthesis, properties, and applications to the development of optical and electrochemical sensors for chemical sensing

GQDs exhibits exceptional electrochemical activity owing to their active edge sites that make them very attractive for biosensing applications. However, their use in the design of new biosensing devices for application to the detection and quantification of toxins, pathogens, and clinical biomarkers has so far not investigated in detail. In this regard, herein we provide a detailed review on various methodologies employed for the synthesis of GQDs, including bottom-up and top-down approaches, with a special focus on their applications in biosensing via fluorescence, photoluminescence, chemiluminescence, electrochemiluminescence, fluorescence resonance energy transfer, and electrochemical techniques. We believe that this review will shed light on the critical issues and widen the applications of GQDs for the design of biosensors with improved analytical response for future applications. HIGHLIGHTS: • Properties of GQDs play a critical role in biosensing applications. • Synthesis of GQDs using top-down and bottom-up approaches is discussed comprehensively. • Overview of advancements in GQD-based sensors over the last decade. • Methods for the design of selective and sensitive GQD-based sensors. • Challenges and opportunities for future GQD-based sensors.

Dying in hospital in Germany - optimising care in the dying phase: study protocol for a multi-centre bottom-up intervention on ward level

Background

Hospitals are globally an important place of care for dying people and the most frequent place of death in Germany (47%), but at the same time, the least preferred one – for both patients and their relatives. Important indicators and outcome variables indexing quality of care in the dying phase are available, and various proposals to achieve corresponding quality objectives exist. However, they are not yet sufficiently adapted to the heterogeneous needs of individual hospital wards.

Methods

This multi-centre single-arm pre-post study aims at the development and implementation of context-specific measures in everyday clinical practice, followed by evaluating this approach. Therefore, (1) already existing measures regarding optimal care in the dying phase are identified applying a systematic literature review as well as an online survey and a symposium with experts. Supported by the thereby generated collection of measures, (2) a stratified sample of ten teams of different wards from two university hospitals select suitable measures and implement them in their everyday clinical practice. Circumstances of patients’ deaths on the selected wards are recorded twice, at baseline before application of the self-chosen measures and afterwards in a follow-up survey. Retrospective file analysis of deceased persons, quantitative staff surveys as well as qualitative multi-professional focus groups and interviews with relatives form the data basis of the pre-post evaluation. (3) Results are reviewed regarding their transferability to other hospitals and disseminated (inter-)nationally.

Discussion

Measures that are easy to implement and appropriate to the specific situation are supposed to significantly improve the quality of care during the dying phase in hospitals and contribute to the well-being of dying patients and their relatives. Successful implementation of those measures requires consideration of the individual conditions and needs of patients and their relatives—but also of the health professionals—on the different hospital wards. Therefore, a bottom-up approach, in which the ward-specific situation is first analysed in detail and then the staff itself selects and implements measures to improve care, appears most promising for optimising care in the dying phase in hospitals.

Trial registration

The study is registered in the German Clinical Trials Register (DRKS00025405).

Spatiotemporal high-resolution prediction and mapping: methodology and application to dengue disease

Dengue disease has become a major public health problem. Accurate and precise identification, prediction and mapping of high-risk areas are crucial elements of an effective and efficient early warning system in countering the spread of dengue disease. In this paper, we present the fusion area-cell spatiotemporal generalized geoadditive-Gaussian Markov random field (FGG-GMRF) framework for joint estimation of an area-cell model, involving temporally varying coefficients, spatially and temporally structured and unstructured random effects, and spatiotemporal interaction of the random effects. The spatiotemporal Gaussian field is applied to determine the unobserved relative risk at cell level. It is transformed to a Gaussian Markov random field using the finite element method and the linear stochastic partial differential equation approach to solve the "big n" problem. Sub-area relative risk estimates are obtained as block averages of the cell outcomes within each sub-area boundary. The FGG-GMRF model is estimated by applying Bayesian Integrated Nested Laplace Approximation. In the application to Bandung city, Indonesia, we combine low-resolution area level (district) spatiotemporal data on population at risk and incidence and high-resolution cell level data on weather variables to obtain predictions of relative risk at subdistrict level. The predicted dengue relative risk at subdistrict level suggests significant fine-scale heterogeneities which are not apparent when examining the area level. The relative risk varies considerably across subdistricts and time, with the latter showing an increase in the period January-July and a decrease in the period August-December.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10109-021-00368-0.

Identification of conditions for efficient cell-sized liposome preparation using commercially available reconstituted in vitro transcription-translation system

Attempts to create complex molecular systems that mimic parts of cellular systems using a bottom-up approach have become important in the field of biology. Among various molecular systems, in vitro protein synthesis inside lipid vesicles (liposomes), which we refer to as the artificial cell, has become an attractive system because it possesses two fundamental features of living cells: central dogma, and compartmentalization. Here, we investigated the effect of altering the amount or concentration of four constituents of the artificial cell consisting of a commercially available reconstituted in vitro transcription-translation (IVTT) system. As this IVTT system is available worldwide, the results will be useful to the scientific community when shared, unlike those from a lab-made IVTT system. We succeeded in revealing the effect and trend of altering each parameter and identified a suitable condition for preparing liposomes that are unilamellar and can synthesize proteins equally as well as the original IVTT system. Because the commercially available reconstituted IVTT system is an important standardization tool and the constituents can be adjusted as desired, our results will be useful for the bottom-up creation of more complex molecular systems.

Absolute quantification of senescence mediators in cells using multiple reaction monitoring liquid chromatography-Tandem mass spectrometry

BACKGROUND

The identification of unique senescence markers remains challenging. Current hallmarks of senescent cells, including increased senescence-associated β-galactosidase activity, increased levels of cell cycle regulators such as p16^INK4a, p27, and p53, and altered levels of sirtuins and lamins, are detected commonly by Western blot and immunohistochemistry methods. Mass spectrometry outperforms these conventional quantification methods in terms of high throughput, specificity, and reproducibility.

OBJECTIVES

To develop multiple reaction monitoring-based tandem mass spectrometric senescence assay for simultaneous measuring of p16^INK4a, p27, p53, p53-β, the seven proteins of the sirtuins family and the four transcript variants of lamins proteins in aging cell model and cancerous cell lines.

METHODOLOGY

Multiple reaction monitoring-tandem mass transitions per protein were developed for each signature peptide(s) and stable isotope-labeled internal standard. The developed assay was validated in a matrix using breast cancer MCF7 cell lines according to the US-FDA guidelines for bioanalytical assays.

RESULTS

The analytes chromatographic peaks were baseline separated and showed linear behavior in a wide dynamic range with r² ≥ 0.98. The method for all proteins has passed the inter/intra-day precision and accuracy validation using three levels of quality control samples. The accuracy and the precision for most analytes were 80-120% and ≤20%, respectively. The method's sensitivity for the panels' signature peptides ranged from 1 ng μL^-1 to 1 μg mL^-1. Extraction recovery assessed in two quality control levels was >60% for most analytes. This LC-MS-MS validated senescence assay showed reduced lamin A, lamin A△10, lamin A△50, SIRT1, SIRT3, SIRT5, p53, and p16^INK4a, as well as p53-β induction, are implicated in replicative senescence. Meanwhile, increased lamin C: lamin A ratio was evident and can diagnose breast carcinogenesis. Moreover, in breast cancer metastasis, reduced SIRT2 and p27 and elevated levels of lamin A△50, SIRT5, SIRT7, and p53-β are evident.

CONCLUSION

LC-MS/MS is a potent alternative tool to the currently available assays. The high throughput method established can study senescence's role in different pathophysiological processes.

Cancer: An unknown territory; rethinking before going ahead

Cancer is a disease of altered signaling and metabolism, causing uncontrolled division and survival of transformed cells. A host of molecules, factors, and conditions have been designated as underlying causes for the inception and progression of the disease. An enormous amount of data is available, system-wide interaction networks of the genes and proteins are generated over the years and have now reached up to a level of saturation, where we need to shift our focus to the more advanced and comprehensive methods and approaches of data analysis and visualization. Even with the availability of enormous literature on this one of the most pressing pathological conditions, a successful cure of the disease seems to be obscure. New treatment plans, like immunotherapy and precision medicine, are being employed for different studies. Nevertheless, their actual benefits to the patients would be known only after the evaluation of clinical data over the next few years. Therefore, we need to look at few fundamental challenges that should be addressed in more depth before we could devise better, rigorous, and comprehensive treatment plans and may successfully reach a possible cure of the disease. This article aims at bringing attention towards some fundamental gaps in our approach towards the disease that leads to failure in devising successful therapeutics.

Factors affecting adult intensive care units costs by using the bottom-up and top-down costing methodology in OECD countries: A systematic review

OBJECTIVES

To review the studies, which calculated the total intensive care unit costs and indicated the main cost drivers in the intensive care by using either top-down, bottom-up approach or the combination of them.

RESEARCH METHODOLOGY/DESIGNS

A systematic review of papers published until October 2020 was conducted. Search was performed on PubMed, Medline, Scopus and Science Direct databases.

SETTING

This review i examined costs in adult intensive care units, in countries belonging to the Organisation for Economic Co-operation and Development (OECD) (medical, surgical or general adult , paediatric and neonatal were not included).

MAIN OUTCOME MEASURES

Eighteen articles were included in the review.

RESULTS

Eight of the studies used the top-down costing methodology, six of them used the bottom-up approach and four of them used both of them. The mean total patient cost per day ranged from €200.75 to €4321.91 (all costs are presented in 2020 values for euro). Human resources were identified as the largest proportion of total costs. Length of stay, mechanical ventilation, continuous haemodialysis and severe illness are the main cost drivers of intensive care unit total costs.

CONCLUSION

There are a variety of methods and study designs used to calculate costs of an intensive care unit stay.t It is necessary to evolve standardised costing methods in order to make comparisons and succeed in cost-effective management.

Measurement uncertainty in quantifying delta-9-tetrahydrocannabinol (THC) in blood using SPE and LC/MS/MS

A method for the quantitative analysis of delta-9-tetrahydrocannabinol (THC, the main active ingredient of cannabis) in whole blood using solid phase extraction and LC/MS/MS has been developed. A bottom-up approach with method validation data was used to evaluate and estimate the measurement uncertainty (MU) of the analytical method. The sources of uncertainty were identified using a cause and effect diagram. The contribution of each uncertainty component was estimated and were combined to derive the overall uncertainty of the analytical method. The combined uncertainty was estimated to be 0.131 μg/L (<7%). At a 99.7% confidence level, the expanded uncertainty was 0.393 μg/L for a THC concentration of 2 μg/L in a whole blood sample. The calculations not only enable the laboratory to quantify the uncertainty associated with a quantitative result, but can also be used to identify the sources of uncertainty and determine if the analytical method can be improved. An open access Measurement Uncertainty Calculator (MUCalc) software has been developed using the method described in this paper.

The cost of inpatient burn management in Nepal

INTRODUCTION

The management of burns is costly and complex with inpatient burns accounting for a high proportion of the costs associated with burn care. We conducted a study to estimate the cost of inpatient burn management in Nepal. Our objectives were to identify the resource and cost components of the inpatient burn care pathways and to estimate direct and overhead costs in two specialist burn units in tertiary hospitals in Nepal.

METHODS

We conducted fieldwork at two tertiary hospitals to identify the cost of burns management in a specialist setting. Data were collected through semi-structured in-depth interviews (IDIs) and focus group discussions (FGDs) with burn experts; unit cost data was collected from hospital finance departments, laboratories and pharmacies. The study focused on acute inpatient burn cases admitted to specialist burn centres within a hospital-setting.

RESULTS

Experts divided inpatient burn care pathways into three categories: superficial partial-thickness burns (SPT), mixed depth partial-thickness burns (MDPT) and full thickness burns (FT). These pathways were confirmed in the FGDs. A 'typical' burns patient was identified for each pathway. Total resource use and total direct costs along with overhead costs were estimated for acute inpatient burn patients. The average per patient pathway costs were estimated at NRs 102,194 (US$ 896.4), NRs 196,666 (US$ 1725), NRs 481,951 (US$ 4,227.6) for SPT, MDPT and FT patients respectively. The largest cost contributors were surgery, dressings and bed charges respectively.

CONCLUSION

This study is a first step towards a comprehensive estimate of the costs of severe burns in Nepal.

Estimation of the uncertainty of values assigned to calibration materials prepared in-house: An example for hydroxychloroquine calibrators in blood-hemolysate-based matrix

Background

Hydroxychloroquine is an antimalarial drug that has been prescribed for the treatment of patients with COVID-19 infection. To assist in clinician decision-making, several clinical laboratories have developed and validated measurement procedures in-house based on HPLC or HPLC-MS/MS to measure the mass concentration of hydroxychloroquine in different biological fluids. In these cases, laboratories produce their calibration materials but rarely estimate the measurement uncertainty of their assigned values. Thus, we aimed to show how this uncertainty can be calculated, using the preparation of hydroxychloroquine calibrators in blood-hemolysate-based matrix as an example.

Methods

A bottom-up approach was used to estimate the uncertainty related to the values assigned to end-user calibration materials prepared in-house. First, a specification of the measurand and a measurement equation were proposed. Then, different sources of uncertainty related to the preparation of hydroxychloroquine calibration materials were identified and quantified. Afterwards, the combined uncertainty was calculated using the law for the propagation of uncertainty resulting in the final expanded uncertainty.

Results

In this study, the most significant source of uncertainty was that associated with the hydroxychloroquine’s reference material mass obtained via balance, while the smallest contribution was from the uncertainty associated with the hydroxychloroquine reference material purity.

Conclusions

A simple procedure to estimate the measurement uncertainty of values assigned to calibration materials is presented here, which would be easy to implement in clinical laboratories. Also, it could be put into practice for other pharmacological quantities measured by in-house HPLC or HPLC-MS/MS procedures commonly used in clinical laboratories.

Real world-like simulations show efficient predictive power of in vitro skin corrosion tests used as stand-alone and in combination and how can toxicologists take advantage of them

Historically, performance of in vitro toxicology test methods has been evaluated and considered for regulatory purposes based on sensitivity & specificity values derived from validation studies. Other indicators are however useful to evaluate in vitro tests such as positive & negative predictive values (PPV & NPV), likelihood ratios (LRs) or odds ratio (OR). These indicators, which are routinely used in diagnostic tests, if adapted and adequately applied to in vitro tests would help determine their realistic predictive power in real world-like situation and help risk assessors know how they can rely on in vitro tests used for their safety assessments. This paper performs a series of simulations considering the actual distribution in ECHA C&L inventory of skin corrosive chemicals to calculate several of these indicators of performance (PPV, NPV, LRs, OR). It shows applied examples of predictive power on EpiSkin™ and SkinEthic™ RHE two validated in vitro skin corrosive tests, explains how to build testing strategies based on these examples, compares so called 'bottom-up' and 'top-down' approaches, and demonstrates the number of tests required, and how risk assessors can practically take advantage of this.

Recent advances in robotic protein sample preparation for clinical analysis and other biomedical applications

Discovery of new protein biomarker candidates has become a major research goal in the areas of clinical chemistry, analytical chemistry, and biomedicine. These important species constitute the molecular target when it comes to diagnosis, prognosis, and further monitoring of disease. However, their analysis requires powerful, selective and high-throughput sample preparation and product (analyte) characterisation approaches. In general, manual sample processing is tedious, complex and time-consuming, especially when large numbers of samples have to be processed (e.g., in clinical studies). Automation via microtiter-plate platforms involving robotics has brought improvements in high-throughput performance while comparable or even better precisions and repeatability (intra-day, inter-day) were achieved. At the same time, waste production and exposure of laboratory personnel to hazards were reduced. In comprehensive protein analysis workflows (e.g., liquid chromatography-tandem mass spectrometry analysis), sample preparation is an unavoidable step. This review surveys the recent achievements in automation of bottom-up and top-down protein and/or proteomics approaches. Emphasis is put on high-end multi-well plate robotic platforms developed for clinical analysis and other biomedical applications. The literature from 2013 to date has been covered.

Evaluation of climate change impacts and adaptation strategies on rainfed rice production in Songkhram River Basin, Thailand

This study investigates rice yield and evaluates potential adaptation measures on field management practices for rainfed rice production under climate change scenarios in the Songkhram River Basin, Thailand. The top-down and bottom-up approaches are combined to evaluate the future climate conditions in the Songkhram River Basin and identify adaptation strategies respectively. An ensemble of four Regional Climate Models (RCMs) bias-corrected using the Quantile Mapping technique was used to project the future climate under two climate change scenarios (RCP4.5 and RCP8.5). The DSSAT crop simulation model was used to simulate rice yield and evaluate the impacts of climate change on rice yield, as well as the feasibility of four adaptation options, which were solicited from four hundred farmers through questionnaire surveys in the basin. The strategies include (i) change in planting date, (ii) change in fertiliser application date, (iii) change in fertiliser application dose, and (iv) supplying irrigation water. Based on the model results, future maximum and minimum temperatures are expected to increase by 2.8 and 3.2 °C respectively under RCP8.5 scenario for 2080s. Although annual rainfall may be unchanged, rainfall patterns will shift earlier in future. Evaluation of adaptation strategies suggest that supplying irrigation water under RCP4.5 and RCP8.5 scenarios respectively are the best strategies to increase rice yield under climate change scenarios. Change in fertiliser application date and change in planting date can increase the future rice yield by 12 and 8%, respectively under RCP4.5 scenario for 2080s. Adjusting the fertiliser application dose may however reduce future rice yield. Although supplying irrigation water can aid the production of rainfed rice, other concerns such as the source of water are involved. The feasibility of adaptation actions would depend largely on available resources and mindset of farmers. Further work is warranted in exploring a combination of adaptation strategies and management plans to combat the adverse impacts of climate change.

Drivers and barriers of adaptation initiatives - How societal transformation affects natural hazard management and risk mitigation in Europe

A key challenge of hazard risk management is finding novel ways to respond to future extremes amid increasing vulnerability. Societal transformation in the context of multi-functional protection schemes offers potential in this regard. However, the drivers and barriers of societal transformation in hazard management are poorly understood. Here we interrogate drivers and barriers of societal transformation in natural hazard management through case studies in Austria, France and Ireland focusing on attempts to integrate multi-functional protection schemes in the context of flood and avalanche hazards. We conducted qualitative semi-structured interviews with key stakeholders connected to proposed transformative strategies in the selected case studies. We find that transformative approaches have been mainly supported by local initiatives instigated by local governments, residents, or NGOs with the aim of complementing conventional hazard management policies. Our analysis shows that local actors and stakeholders often pursue initiatives to address local problems or to seize local opportunities rather than to contribute to a broader societal transformation. According to our findings, key drivers of community-based initiatives with multiple functionality and use include: (i) lack of funding, (ii) lack of legal protection or (iii) lack of space, where classical risk management measures can no longer respond to new circumstances. In contrast, key barriers relate to: (i) lack of local capacities, (ii) lack of local political support and (iii) technological challenges in the implementation phase. These insights support European regions currently working on the implementation of climate change adaptation strategies arising from natural hazards.

Working on Womanhood (WOW): A participatory formative evaluation of a community-developed intervention

The well-documented disparities in availability, accessibility, and quality of behavioral health services suggest the need for innovative programs to address the needs of ethnic minority youth. The current study aimed to conduct a participatory, formative evaluation of "Working on Womanhood" (WOW), a community-developed, multifaceted, school-based intervention serving primarily ethnic minority girls living in underserved urban communities. Specifically, the current study aimed to examine the feasibility, acceptability, and initial promise of WOW using community-based participatory research (CBPR) and represented the third phase of a community-academic partnership. Qualitative and quantitative data were collected from 960 WOW participants in 21 urban public schools, as well as WOW counselors, parents, and school staff over the course of one academic year. Results demonstrated evidence of acceptability of WOW and noteworthy improvements for WOW participants in targeted outcomes, including mental health, emotion regulation, and academic engagement. Findings also indicated several challenges to implementation feasibility and acceptability, including screening and enrollment processes and curriculum length. Additionally, we discuss how, consistent with participatory and formative research, findings were used by program implementers to inform program improvements, including modifications to screening processes, timelines, curriculum, and trainings - all in preparation for a rigorous effectiveness evaluation.

Environmental impacts of food waste in Europe

Approximately 88 Million tonnes (Mt) of food is wasted in the European Union each year and the environmental impacts of these losses throughout the food supply chain are widely recognised. This study illustrates the impacts of food waste in relation to the total food utilised, including the impact from food waste management based on available data at the European level. The impacts are calculated for the Global Warming Potential, the Acidification Potential and the Eutrophication Potential using a bottom-up approach using more than 134 existing LCA studies on nine representative products (apple, tomato, potato, bread, milk, beef, pork, chicken, white fish). Results show that 186 Mt CO₂-eq, 1.7 Mt SO₂-eq. and 0.7 Mt PO₄-eq can be attributed to food waste in Europe. This is 15 to 16% of the total impact of the entire food supply chain. In general, the study confirmed that most of the environmental impacts are derived from the primary production step of the chain. That is why animal-containing food shows most of the food waste related impacts when it is extrapolated to total food waste even if cereals are higher in mass. Nearly three quarters of all food waste-related impacts for Global Warming originate from greenhouse gas emissions during the production step. Emissions by food processing activities contribute 6%, retail and distribution 7%, food consumption, 8% and food disposal, 6% to food waste related impacts. Even though the results are subject to certain data and scenario uncertainties, the study serves as a baseline assessment, based on current food waste data, and can be expanded as more knowledge on the type and amount of food waste becomes available. Nevertheless, the importance of food waste prevention is underlined by the results of this study, as most of the impacts originate from the production step. Through food waste prevention, those impacts can be avoided as less food needs to be produced.

Chemical Crosslinking: Role in Protein and Peptide Science

BACKGROUND

Chemical crosslinking refers to intermolecular or intramolecular joining of two or more molecules by a covalent bond. The reagents that are used for the purpose are referred to as 'crosslinking reagents' or 'crosslinkers'. Based on factors like reactivity and spacer length these are classified into different types, each having its own specific function and application. In recent times, chemical crosslinking has emerged as an efficient tool for the study of biomolecules like proteins. It finds its application in various studies including the attachment of proteins to a solid support for the study of membrane receptors, protein-protein complexes, protein-DNA complexes, and others. When coupled with techniques like mass spectroscopy, it has been used not only for the determination of three dimensional structures of proteins but also for the study of protein-protein interactions and determination of interesting sites. This combination of mass spectrometry techniques and bioinformatics, added yet another dimension to our present day understanding of protein chemistry. Thus, chemical crosslinking has multitude uses that it can be put to.

METHODS

We undertook a systematic search of bibliographic databases and search engine such as Google Scholar, Scifinder, Scopus, Mendeley etc for review of research literature. We excluded research paper which only reported synthesis of crosslinker molecules and did not involve any mass spectrometry studies.

RESULTS

Sixty-four papers were included in the review. The majority of references were taken from last ten years as there has been an immense progress in this area in the recent years. Eleven classical papers in this field were included which talk about basic of this methodology. Thirty-two papers discussed about various types of organic groups used for designing chemical cross-linkers and various methodologies which were used to enhance the crosslinking efficiency. These papers also highlight various strategies used to enhance detection of cross-linked proteins and various computer software used to detect cross-linking sites from mass data. Twenty-one papers showed the proof concept application of this methodology to detect protein crosslinking in-vivo and in-vitro.

CONCLUSION

The findings of this review confirm the importance chemical crosslinking combined with mass spectroscopy as a low cost alternative to understand protein-protein interaction. The information generated by this methodology can help in better understating of various diseases and for the development of better drugs for them.

Development, validation and different approaches for the measurement uncertainty of a multi-class veterinary drugs residues LC-MS method for feeds

A sensitive method for the simultaneous residues analysis of 62 veterinary drugs in feeds by liquid chromatography-tandem mass spectrometry has been developed and validated in accordance to Commission Decision 657/2002/EC. Additionally, limits of detection (LOD), limits of quantitation (LOQ), matrix effects and measurement uncertainty were also assessed. Extraction was performed for all analytes and respective internal standards in a single step and chromatographic separation was achieved in only 12min. LOQ were set to 0.63-5.00μgkg^-1 (amphenicols), 0.63-30.00μgkg^-1 (avermectins), 0.63μgkg^-1 (benzimidazoles), 0.25-200.00μgkg^-1 (coccidiostats), 0.63-200.00μgkg^-1 (lincosamides and macrolides), 0.25-5.00μgkg^-1 (nitrofurans), 0.63-20.00μgkg^-1 (fluoroquinolones and quinolones), 15.00μgkg^-1 (quinoxaline), 0.63-7.50μgkg^-1 (sulfonamides), 0.63-20.00μgkg^-1 (tetracyclines), 0.25μgkg^-1 (β-agonists), and 30.00μgkg^-1 (β-lactams). The top-down approach was adequate for the calculation of measurement uncertainty for all analytes, except the banned substances, which should be rather assessed by the bottom-up approach. Routine analysis of different types of feeds was then carried out. An interesting profile of residues of veterinary drugs among samples was revealed, enlightening the need for stricter control in producing animals. Among the total of 27 feed samples, 20 analytes could be detected/quantified, ranging from trace levels to very high concentrations. A high throughput screening/confirmatory method for the residue analysis of several veterinary drugs in feeds was proposed as a helpful control tool.

The bottom-up approach to bounding potential low-dose cancer risks from formaldehyde: An update

In 2013, we proposed a novel bottom-up approach to bounding low-dose cancer risks that may result from small exogenous exposures to chemicals that are always present in the body as a result of normal biological processes. The approach utilizes the background cancer risk and the background (endogenous) concentration of a cancer-related exposure biomarker in specific target tissues. After allowing for statistical uncertainty in these two parameters, the ratio of the background risk to background exposure provides a conservative slope factor estimate that can be utilized to bound the added risk that may be associated with incremental exogenous exposures. Our original bottom-up estimates were markedly smaller than those obtained previously by the US Environmental Protection Agency (USEPA) with a conventional top-down approach to modeling nasopharyngeal cancer and leukemia mortality data from a US worker cohort. Herein we provide updated bottom-up estimates of risk for these two cancers that are smaller still, and rely upon more robust estimates of endogenous and exogenous formaldehyde-DNA adducts in monkeys and a more robust estimate of the DNA adduct elimination half-life in rats, both obtained very recently. We also re-examine the worker mortality data used by USEPA in developing its estimate of human leukemia incidence from lifetime exposure to 1 ppm airborne formaldehyde. Finally, we compare a new bottom-up slope estimate of the risk of rat nasal cancer with conventional top-down estimates obtained with empirical dose-response modeling of rat nasal cancer bioassay data.

Child malnutrition and the Millennium Development Goals: much haste but less speed?

The Millennium Development Goals (MDGs) provide a framework for measuring the progress of nations. Several of these goals relate to child malnutrition, which remains an important contributor to child morbidity and mortality, accounting for approximately 45% of child deaths globally. A high proportion of undernourished children still live in Africa and parts of Asia, and the uneven rate of reduction in the prevalence of various types of child malnutrition among different income groups worldwide is worrying. Attempts to reduce child malnutrition should therefore begin from the grassroots by improving primary healthcare services in developing countries with particular focus on basic requirements. Adequate nutrition should be provided from birth, through infancy, preschool and early childhood to adolescence. The overall strategy should be one of careful and meticulous planning involving all development sectors with an emphasis on a bottom-up approach within a stable and disciplined polity; the MDGs will be only be useful if they are seen not as narrow objectives with unidirectional interventions but as multifaceted and co-ordinated. The setting of deadlines, whether 2015 or 2035, should not be emphasised so as to avoid hasty decision making. The top priority should be the implementation of the essential social services of basic education, primary healthcare, nutrition, reproductive health care, water and sanitation in partnership with the developed economies.

Potential for reducing air-pollutants while achieving 2 °C global temperature change limit target

This study analyzes the potential to reduce air pollutants while achieving the 2 °C global temperature change limit target above pre-industrial levels, by using the bottom-up optimization model, AIM/Enduse[Global]. This study focuses on; 1) estimating mitigation potentials and costs for achieving 2 °C, 2.5 °C, and 3 °C target scenarios, 2) assessing co-benefits of reducing air pollutants such as NOx, SO2, BC, PM, and 3) analyzing features of sectoral attributions in Annex I and Non-Annex I groups of countries. The carbon tax scenario at 50 US$/tCO2-eq in 2050 can reduce GHG emissions more than the 3 °C target scenario, but a higher carbon price around 400 US$/tCO2-eq in 2050 is required to achieve the 2 °C target scenario. However, there is also a co-benefit of large reduction potential of air pollutants, in the range of 60-80% reductions in 2050 from the reference scenario while achieving the 2 °C target.