Transmission in near‐infrared optical windows for deep brain imaging

Near‐infrared (NIR) radiation has been employed using one‐ and two‐photon excitation of fluorescence imaging at wavelengths 650–950 nm (optical window I) for deep brain imaging; however, longer wavelengths in NIR have been overlooked due to a lack of suitable NIR‐low band gap semiconductor imaging detectors and/or femtosecond laser sources. This research introduces three new optical windows in NIR and demonstrates their potential for deep brain tissue imaging. The transmittances are measured in rat brain tissue in the second (II, 1,100–1,350 nm), third (III, 1,600–1,870 nm), and fourth (IV, centered at 2,200 nm) NIR optical tissue windows. The relationship between transmission and tissue thickness is measured and compared with the theory. Due to a reduction in scattering and minimal absorption, window III is shown to be the best for deep brain imaging, and windows II and IV show similar but better potential for deep imaging than window I.

     

Proteomic changes in response to crystal formation in Drosophila Malpighian tubules

Kidney stone disease is a major health burden with a complex and poorly understood pathophysiology. Drosophila Malpighian tubules have been shown to resemble human renal tubules in their physiological function. Herein, we have used Drosophila as a model to study the proteomic response to crystal formation induced by dietary manipulation in Malpighian tubules. Wild-type male flies were reared in parallel groups on standard medium supplemented with lithogenic agents: control, Sodium Oxalate (NaOx) and Ethylene Glycol (EG). Malpighian tubules were dissected after 2 weeks to visualize crystals with polarized light microscopy. The parallel group was dissected for protein extraction. A new method of Gel Assisted Sample Preparation (GASP) was used for protein extraction. Differentially abundant proteins (p<0.05) were identified by label-free quantitative proteomic analysis in flies fed with NaOx and EG diet compared with control. Their molecular functions were further screened for transmembrane ion transporter, calcium or zinc ion binder. Among these, 11 candidate proteins were shortlisted in NaOx diet and 16 proteins in EG diet. We concluded that GASP is a proteomic sample preparation method that can be applied to individual Drosophila Malpighian tubules. Our results may further increase the understanding of the pathophysiology of human kidney stone disease.     

Dynamical characterization of inactivation path in voltage-gated Na+ ion channel by non-equilibrium response spectroscopy

Inactivation path of voltage gated sodium channel has been studied here under various voltage protocols as it is the main governing factor for the periodic occurrence and shape of the action potential. These voltage protocols actually serve as non-equilibrium response spectroscopic tools to study the ion channel in non-equilibrium environment. In contrast to a lot of effort in finding the crystal structure based molecular mechanism of closed-state(CSI) and open-state inactivation(OSI); here our approach is to understand the dynamical characterization of inactivation. The kinetic flux as well as energetic contribution of the closed and open- state inactivation path is compared here for voltage protocols, namely constant, pulsed and oscillating. The non-equilibrium thermodynamic quantities used in response to these voltage protocols serve as improved characterization tools for theoretical understanding which not only agrees with the previously known kinetic measurements but also predict the energetically optimum processes to sustain the auto-regulatory mechanism of action potential and the consequent inactivation steps needed. The time dependent voltage pattern governs the population of the conformational states which when couple with characteristic rate parameters, the CSI and OSI selectivity arise dynamically to control the inactivation path. Using constant, pulsed and continuous oscillating voltage protocols we have shown that during depolarization the OSI path is more favored path of inactivation however, in the hyper-polarized situation the CSI is favored. It is also shown that the re-factorisation of inactivated sodium channel to resting state occurs via CSI path. Here we have shown how the subtle energetic and entropic cost due to the change in the depolarization magnitude determines the optimum path of inactivation. It is shown that an efficient CSI and OSI dynamical profile in principle can characterize the open-state drug blocking phenomena.     

Bulked sample analysis in genetics,genomics and crop improvement

Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high‐throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker‐assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.     

A thermodynamic approach for assessing agroecosystem sustainability

By revisiting theoretical concepts in biogeography and the importance of thermodynamic laws in biosphere-atmosphere interactions, ecological sustainability in agricultural systems may be better defined. In this case study, we employed a multidisciplinary methodology for exploring agroecosystem sustainability by using eddy covariance (EC) data to compute thermodynamic entropy production (σ) and relate it to water, energy and carbon cycling in croplands and grasslands of the Central US. From 2002 to 2012, the biophysical metric of σ was compared across AmeriFlux sites, each with site-specific land management practices of irrigation, crop rotation, and tillage. Results show that σ is most correlated with net ecosystem exchange (NEE) of carbon, and when cropland and grassland sites are close to being carbon neutral, σ values range from 0.51–1.0 W K⁻¹ m⁻² for grasslands, 0.81–1.0 W K⁻¹ m⁻² for rainfed croplands, and 0.81–1.1 W K⁻¹ m⁻² for irrigated croplands. Irrigated maize stressed by hydrologic and high temperature anomalies associated with the 2012 drought exhibit the greatest increase in σ, indicating the possibility of decreased sustainability compared to rainfed croplands and grasslands. These results suggest that maximizing carbon uptake with irrigation and fertilizer use tends to move agroecosystems further away from thermodynamic equilibrium, which has implications for ecological sustainability and greenhouse gas (GHG) mitigation in climate-smart agriculture. The underlying theoretical concepts, multidisciplinary methodology, and use of eddy covariance data for biophysical indicators in this study contribute to a unique understanding of ecological sustainability in agricultural systems.     

Calculating the local nonequilibrium configurational entropy in quasi-one-dimensional heat conduction

In a quasi-one-dimensional (QOD) system the particles remain ordered from left to right allowing the association of a volume element to the particle which on average resides there. Thus the properties of that single particle give the local densities in the volume element. With reservoirs of different temperatures connected to each end of the system a steady heat current with an anomalous thermal conductivity results. The largest contribution to the local configurational entropy density is calculated from two-particle correlation functions which vary locally within the nonequilibrium system. This contribution to the local configurational entropy is calculated for a QOD system in a nonequilibrium steady state.     

Factor scoring models of the Pittsburgh Sleep Quality Index: a comparative confirmatory factor analysis

The Pittsburgh Sleep Quality Index (PSQI) is a rigorously validated questionnaire with extensive use in sleep assessment. Findings from numerous factor analytic studies of the PSQI have been interpreted to support a heterogeneous factor structure model for the test. Nevertheless, the literature continues to lack a focused evaluation of whether this heterogeneous factor structure is justified. A consideration of this issue led to a conclusion that a closer analysis of the PSQI’s factor structure was merited. To address this need a comparative confirmatory factor analysis for assessing the performance of the accepted factors models of the PSQI was conducted. A sample of university students (n = 418), age = 20.92 ± 1.81 years, BMI = 23.30 ± 2.57 kg/m² completed the multi-structured sleep survey at Jamia Millia Islamia, New Delhi, India. Seventeen putative factor structures (three 1-Factor, eight 2-Factor, and six 3-Factor) of the PSQI from the existing literature were selected for analysis. Fourteen models (82.35%) had almost similar values for model fit indices. Two models were misfits, and one model was a poor fit. The two misfit models incorporated gender and age as covariates. The third poor fit model was used to produce a unique path diagram, which made it distinct from the remaining 16 models. The overlapping values in the fit range of the model fit indices did not support the often projected heterogeneous factor structures of the PSQI for the vast majority of the models.     

Assessment of physical activity of the human body considering the thermodynamic system

Correctly dosed physical activity is the basis of a vital and healthy life, but the measurement of physical activity is certainly rather empirical resulting in limited individual and custom activity recommendations. Certainly, very accurate three-dimensional models of the cardiovascular system exist, however, requiring the numeric solution of the Navier–Stokes equations of the flow in blood vessels. These models are suitable for the research of cardiac diseases, but computationally very expensive. Direct measurements are expensive and often not applicable outside laboratories. This paper offers a new approach to assess physical activity using thermodynamical systems and its leading quantity of entropy production which is a compromise between computation time and precise prediction of pressure, volume, and flow variables in blood vessels. Based on a simplified (one-dimensional) model of the cardiovascular system of the human body, we develop and evaluate a setup calculating entropy production of the heart to determine the intensity of human physical activity in a more precise way than previous parameters, e.g. frequently used energy considerations. The knowledge resulting from the precise real-time physical activity provides the basis for an intelligent human–technology interaction allowing to steadily adjust the degree of physical activity according to the actual individual performance level and thus to improve training and activity recommendations.