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Abstract Anti-microbial stewardship program (AMSP) is practiced only in tertiary hospitals in India, though, the lower tier hospitals remain the first point of contact in patient care. This study was conducted in lower tier hospitals to calculate antibiotic and multiple antibiotic prescription rate (APR, MPR) for common infections and finding existing strength of health system for optimizing antibiotic prescription. We conducted a cross sectional convergent parallel mix-method study in eight lower tier hospitals of three districts of West Bengal, India. Six hundred OPD prescriptions of UTI, ARI, AUFI, ADD were evaluated. Qualitative data collected through in-depth interviews of medical officers/officers in administrative positions, infection control nurses were analyzed using content analysis method. APR was 63.8% in primary tier hospitals and 60.8% in secondary tier hospitals. The MPR was higher in secondary tier hospital (23.8%). Presence of infection control committee, designated nursing staff, initiation of prescription audit, increased monitoring were identified as few facilitators for future implementation of AMSP in lower tier hospitals. The routine infection control activities of lower tier hospitals are currently delinked from AMR containment measures and thus, customized AMSP needs to be established in these hospitals catering two third of the population of India.

Abstract We have previously engineered E. coli transketolase (TK) enzyme variants that accept new substrates such as aliphatic or aromatic aldehydes, and also with improved thermal stability. Irreversible aggregation is the primary mechanism of deactivation for TK in the buffers used for biocatalysis, and so we were interested in determining the extent to which this remains true in more complex media, crude cell lysates or even in vivo. Such understanding would better guide future protein engineering efforts. NMR offers a potential approach to probe protein structure changes, aggregation, and diffusion, and19F-labelled amino acids are a useful NMR probe for complex systems with little or no background signal from the rest of the protein or their environment. Here we labelled E. coli TK with two different19F probes, trifluoromethyl-L-phenylalanine (tfm-Phe), and 4-fluoro phenylalanine (4 F-Phe), through site specific non-natural amino acid incorporation. We targeted them to residue K316, a highly solvent exposed site located at the furthest point from the enzyme active sites. Characterisation of the19F-labelled TK variants revealed surprising effects of these mutations on stability, and to some extent on activity. While variant TK-tfm-Phe led to a 7.5 °C increase in the thermal transition midpoint (T m) for denaturation, the TK-4 F-Phe variant largely abolished the aggregation of the enzyme when incubated at 50 °C19. F-NMR revealed different behaviours in response to temperature increases for the two TK variants, displaying opposite temperature gradient chemical shifts, and diverging motion regimes, suggesting that the mutations affected differently both the local environment at this site, and its temperature-induced dynamics. A similar incubation of TK at 40–55 °C is also known to induce higher cofactor-binding affinities, leading to an apparent heat activation under low cofactor concentration conditions. We have hypothesised previously that a heat-inducible conformational change in TK leads to this effect1. H-NMR revealed a temperature-dependent re-structuring of methyl groups, also at 30–50 °C, which may be linked to the heat activation. While our kinetic studies were not expected to observe the heat activation event due to the high cofactor concentrations used, this was not the case for TK-4 F-Phe, which did appear to heat activate slightly at 45 °C. This implied that the mutations at K316 could influence cofactor-binding, despite their location at 47 Å from either active site. Such long-distance effects of mutations are not unprecedented, and indeed we have previously shown how distant mutations can influence active-site loop stability and function in TK, mediated via dynamically coupled networks of residues. Molecular dynamics simulations of the two19F containing variants similarly revealed networks of residues that could couple the changes in dynamics at residue K316, through to changes in active site dynamics. These results independently highlight the sensitivity of active-site function to distant mutations coupled through correlated dynamic networks of residues. They also highlight the potential influence of surface-incorporated probes on protein stability and function, and the need to characterise them well prior to further studies.

Abstract The severity of autism spectrum disorder (ASD) shows wide variations, though the reason remains unclear. Vitamin D (VitD) deficiency is considered a risk factor for ASD and its supplementation was reported to reduce symptom severity. Since VitD, either synthesized in the skin or absorbed from the food, is transported to the liver by the vitamin D binding protein (DBP), we have analyzed DBP genetic polymorphisms [rs7041 (A/C), rs4588 (G/T), and rs3755967 (C/T)] affecting DBP function [Case = 411; Control = 397], levels of plasma 25(OH)D and DBP [Case = 25; Control = 26], and DBP mRNA expression [Case = 74; Control = 44] in a group of Indo-Caucasoid ASD probands and neurotypical subjects. ASD probands with rs7041’CC’, rs4588 ‘TT’, and rs3755967 ‘TT’ genotypes exhibited higher scores for a few traits. Scores for Imitation and Listening response were also higher in the presence of the “A-T” haplotype (rs7041–rs4588). Plasma 25(OH)D and DBP levels as well as DBP mRNA expressions were significantly lower in the ASD probands as compared to the neurotypical subjects. We infer that DBP deficiency, in the presence of risk genetic variants, could be one of the reasons for the reported 25(OH)D deficiency of the ASD probands.

Abstract There is a lot of confusion and ambiguity regarding the quantification of the Quality of Service (QoS) of a system, especially for cyber-physical systems (CPS) involved in automating or controlling the operations in built environments and critical urban infrastructures, such as office buildings, factories, transportation systems, smart cities, etc. In these cases, the QoS, as experienced by human users, depends on the context in which they (i.e., humans) interact with these systems. Traditionally, the QoS of a CPS has been defined in terms of absolute metrics. Such measures are unable to take into account the variations in performance due to contextual factors arising out of different kinds of human interactions. Further, the QoS of a CPS has typically been evaluated by comparing the performance of the actual, fully realized system with the given QoS constraints only after the actual system has been completely developed. In the case of faults in the design exposed by observed deviations from the QoS constraints due to unpredicted variations in the contextual factors, the system needs to be re-designed and re-developed from scratch. Due to the above-mentioned reason, the validation approach associated with the traditional QoS makes the design of CPS systems prohibitively expensive, impractical, as well as infeasible in numerous application areas, such as civil and engineering works, since it may not be possible to modify the system once developed beyond a certain extent. To that end, we propose a context-aware definition of QoS of a CPS which facilitates the design of robust systems as elaborated below. In this paper, we define QoS as a function of contextual factors. A CPS designed according to our QoS specifications would always satisfy the QoS irrespective of any possible changes in contextual factors resulting from many different human interactions that may occur during operation of the system. We also present QACDes - a novel framework that provides a formal mechanism for validating the design of a CPS with respect to the specified QoS constraints at the design phase as well as after the realization of the actual system. QACDes can validate any given CPS, irrespective of its application domain, against a QoS guarantee: (A) as early as even before the design phase by comparing the proposed model with a baseline model, or (B) after the realization of the actual system based on logs collected from running the actual system. We consider a lighting control system that manages the light switches - switching it on/off depending on contextual factors, such as the presence of occupants and time of the day. Using the lighting control system in a building as a use case, we analyze and demonstrate the effectiveness of our QoS definition as well as the QACDes framework against the performance metric measured in an actual fully-realized CPS.

Abstract The large compositional space of high entropy alloys (HEA) often presents significant challenges in comprehensively deducing the critical influence of atomic composition on their mechanical responses. We propose an efficient nonparametric kernel-based probabilistic computational mapping to obtain the optimal composition of HEAs under ballistic conditions by exploiting the emerging capabilities of machine learning (ML) coupled with molecular-level simulations. Compared to conventional ML models, the present Gaussian approach is a Bayesian paradigm that can have several advantages, including small training datasets concerning computationally intensive simulations and the ability to provide uncertainty measurements of molecular dynamics simulations therein. The data-driven analysis reveals that a lower concentration of Ni with a higher concentration of Al leads to higher dissipation of kinetic energy and lower residual velocity, but with higher penetration depth of the projectile. To deal with such conflicting computationally intensive functional objectives, the ML-based simulation framework is further extended in conjunction with multi-objective genetic algorithm for identifying the critical elemental compositions to enhance kinetic energy dissipation with minimal penetration depth and residual velocity of the projectile simultaneously. The computational framework proposed here is generic in nature, and it can be extended to other HEAs with a range of non-aligned multi-physical property demands.

Abstract Studies on the neural correlates of navigation in 3D environments are plagued by several issues that need to be solved. For example, experimental studies show markedly different place cell responses in rats and bats, both navigating in 3D environments. In this study, we focus on modelling the spatial cells in rodents in a 3D environment. We propose a deep autoencoder network to model the place and grid cells in a simulated agent navigating in a 3D environment. The input layer to the autoencoder network model is the HD layer, which encodes the agent’s HD in terms of azimuth (θ) and pitch angles (ϕ). The output of this layer is given as input to the Path Integration (PI) layer, which computes displacement in all the preferred directions. The bottleneck layer of the autoencoder model encodes the spatial cell-like responses. Both grid cell and place cell-like responses are observed. The proposed model is verified using two experimental studies with two 3D environments. This model paves the way for a holistic approach using deep neural networks to model spatial cells in 3D navigation.

Abstract In quantum computing there are quite a few universal gate sets, each having their own characteristics. In this paper we study the Clifford+CS universal fault-tolerant gate set. The CS gate is used is many applications and this gate set is an important alternative to Clifford+T. We introduce a generating set in order to represent any unitary implementable by this gate set and with this we derive a bound on the CS-count of arbitrary multi-qubit unitaries. Analysing the channel representation of the generating set elements, we infer $${\mathcal {J}}_n^{CS}\subset {\mathcal {J}}_n^T$$ J n CS ⊂ J n T , where $${\mathcal {J}}_n^{CS}$$ J n CS and $${\mathcal {J}}_n^T$$ J n T are the set of unitaries exactly implementable by the Clifford+CS and Clifford+T gate sets, respectively. We develop CS-count optimal synthesis algorithms for both approximately and exactly implementable multi-qubit unitaries. With the help of these we derive a CS-count-optimal circuit for Toffoli, implying $${\mathcal {J}}_n^{Tof}={\mathcal {J}}_n^{CS}$$ J n Tof = J n CS , where $${\mathcal {J}}_n^{Tof}$$ J n Tof is the set of unitaries exactly implementable by the Clifford+Toffoli gate set. Such conclusions can have an important impact on resource estimates of quantum algorithms.

Abstract The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected additional 12% Shigella and 13% ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.

Abstract Glutamate (Glu) is important for memory and learning. Hence, Glu imbalance is speculated to affect autism spectrum disorder (ASD) pathophysiology. The action of Glu is mediated through receptors and we analyzed four metabotropic Glu receptors (mGluR/GRM) in Indo-Caucasoid families with ASD probands and controls. The trait scores of the ASD probands were assessed using the Childhood Autism Rating Scale2-ST. Peripheral blood was collected, genomic DNA isolated, and GRM5 rs905646, GRM6 rs762724 & rs2067011, and GRM7 rs3792452 were analyzed by PCR/RFLP or Taqman assay. Expression of mGluRs was measured in the peripheral blood by qPCR. Significantly higher frequencies of rs2067011 ‘A’ allele/ AA’ genotype were detected in the probands. rs905646 ‘A ‘exhibited significantly higher parental transmission. Genetic variants showed independent as well as interactive effects in the probands. Receptor expression was down-regulated in the probands, especially in the presence of rs905646 ‘AA’, rs762724 ‘TT’, rs2067011 ‘GG’, and rs3792452 ‘CC’. Trait scores were higher in the presence of rs762724 ‘T’ and rs2067011 ‘G’. Therefore, in the presence of risk genetic variants, down-regulated mGluR expression may increase autistic trait scores. Since our investigation was confined to the peripheral system, in-depth exploration involving peripheral as well as central nervous systems may validate our observation.

The study was aimed to evaluate the performance of a newly developed spectroscopy-based non-invasive and noncontact device (SAMIRA) for the simultaneous measurement of hemoglobin, bilirubin and oxygen saturation as an alternative to the invasive biochemical method of blood sampling. The accuracy of the device was assessed in 4318 neonates having incidences of either anemia, jaundice, or hypoxia. Transcutaneous bilirubin, hemoglobin and blood saturation values were obtained by the newly developed instrument which was corroborated with the biochemical blood tests by expert clinicians. The instrument is trained using Artificial Neural Network Analysis to increase the acceptability of the data. The artificial intelligence incorporated within the instrument determines the disease condition of the neonate. The Pearson's correlation coefficient, r was found to be 0.987 for hemoglobin estimation and 0.988 for bilirubin and blood gas saturation respectively. The bias and the limits of agreement for the measurement of all the three parameters were within the clinically acceptance limit.

Abstract The evaluation of Weather Research and Forecasting (WRF) model has been performed for simulating episodic Heat Wave (HW) events of 2015 and 2016 with varied horizontal resolutions of 27 km for the entire India (d01), 9 km for the North West (NW (d02)) and South East (SE (d03)) domain. Study compares the maximum temperature (Tmax) simulated by WRF model, using six different combination of parameterization schemes, with observations from the India Meteorological Department (IMD) during the HW events. Among the six experiments, Exp2 (i.e., combination of WSM6 microphysics (MP) together with radiation parameterization CAM, Yonsei (PBL), NOAH land surface and Grell-3D convective schemes) is found closest to the observations in reproducing the temperature. The model exhibits an uncertainty of ± 2 °C in maximum temperature (Tmax) for both the regions, suggesting regional temperature is influenced by the location and complex orography. Overall, statistical results reveal that the best performance is achieved with Exp2. Further, to understand the dynamics of rising HW intensity, two case studies of HW days along with influencing parameters like Tmax, RH and prevailing wind distribution have been simulated. Model simulated Tmax during 2015 reaches up to 44 °C in NW and SE part of India. In 2016, HW is more prevailing towards NW, while in SE region Tmax reaches upto 34–38 °C with high RH (60–85%). The comparative research made it abundantly evident that these episodic events are unique in terms of duration and geographical spread which can be used to assess the WRF performance for future projections of HW.

Abstract Improving the range of substrates accepted by enzymes with high catalytic activity remains an important goal for the industrialisation of biocatalysis. Many enzymes catalyse two-substrate reactions which increases the complexity in engineering them for the synthesis of alternative products. Often mutations are found independently that can improve the acceptance of alternatives to each of the two substrates. Ideally, we would be able to combine mutations identified for each of the two alternative substrates, and so reprogramme new enzyme variants that synthesise specific products from their respective two-substrate combinations. However, as we have previously observed for E. coli transketolase, the mutations that improved activity towards aromatic acceptor aldehydes, did not successfully recombine with mutations that switched the donor substrate to pyruvate. This likely results from several active site residues having multiple roles that can affect both of the substrates, as well as structural interactions between the mutations themselves. Here, we have designed small libraries, including both natural and non-natural amino acids, based on the previous mutational sites that impact on acceptance of the two substrates, to achieve up to 630× increases in k cat for the reaction with 3-formylbenzoic acid (3-FBA) and pyruvate. Computational docking was able to determine how the mutations shaped the active site to improve the proximity of the 3-FBA substrate relative to the enamine-TPP intermediate, formed after the initial reaction with pyruvate. This work opens the way for small libraries to rapidly reprogramme enzyme active sites in a plug and play approach to catalyse new combinations of two-substrate reactions.

Abstract Diabetes mellitus (DM) is the third most common chronic condition associated with frequent hospital readmissions. Predictors of the number of readmissions within 1 year among patients with DM are less often studied compared with those of 30-day readmission. This study aims to identify predictors of number of readmissions within 1 year amongst adult patients with DM and compare different count regression models with respect to model fit. Data from 2008 to 2015 were extracted from the electronic medical records of the National University Hospital, Singapore. Inpatients aged ≥ 18 years at the time of index admission with a hospital stay > 24 h and survived until discharge were included. The zero-inflated negative binomial (ZINB) model was fitted and compared with three other count models (Poisson, zero-inflated Poisson and negative binomial) in terms of predicted probabilities, misclassification proportions and model fit. Adjusted for other variables in the model, the expected number of readmissions was 1.42 (95% confidence interval [CI] 1.07 to 1.90) for peripheral vascular disease, 1.60 (95% CI 1.34 to 1.92) for renal disease and 2.37 (95% CI 1.67 to 3.35) for Singapore residency. Number of emergency visits, number of drugs and age were other significant predictors, with length of stay fitted as a zero-inflated component. Model comparisons suggested that ZINB provides better prediction than the other three count models. The ZINB model identified five patient characteristics and two comorbidities associated with number of readmissions. It outperformed other count regression models but should be validated before clinical adoption.

Abstract Thermal Power Plant generates FGD gypsum as by-product during coal combustion. This study evaluates the characterization (spectroscopic and elemental), potentially toxic elements (PTEs) distribution, and environmental risk assessment of FGD gypsum for safe and sustainable use in agriculture. The XRD and SEM analysis confirmed the dominance of crystalline CaSO4·2H2O in FGD gypsum. The order of concentrations of PTEs in FGD gypsum was Fe > Al > Mn > Zn > Ni > Co. The residual fraction was the dominant pool, sharing 80–90% of the total PTEs. The heavy metals (HMs) were below the toxic range in the leachates. The Co, Ni, Al, Fe Mn, Zn had low (

Abstract Attention deficit hyperactivity disorder (ADHD), a childhood-onset neurobehavioral disorder, often perturbs scholastic achievement and peer-relationship. The pivotal role of glutamate (Glu) in learning and memory indicated an influence of Glu in ADHD, leading to the exploration of Glu in different brain regions of ADHD subjects. We for the first time analyzed GluR genetic variations, Glu levels, as well as expression of Glu receptors (GluR) in the peripheral blood of eastern Indian ADHD probands to find out the relevance of Glu in ADHD prognosis. After obtaining informed written consent for participation, peripheral blood was collected for analyzing the genetic variants, Glu level, and expression of target genes. Since ADHD probands are often treated with methylphenidate or atomoxetine for providing symptomatic remediation, we have also tested post-therapeutic improvement in the ADHD trait scores in the presence of different GluR genotypes. Two variants, GRM7 rs3749380 “T” and GRIA1 rs2195450 “C”, exhibited associations with ADHD (P ≤ 0.05). A few GluR genetic variants showed significant association with higher trait severity, low IQ, lower plasma Glu level, down-regulated GluR mRNA expression, and poor response to medications. This indicates that down-regulated glutamatergic system may have an effect on ADHD etiology and treatment efficacy warranting further in-depth investigation.

Engineered cyanobacterium Synechococcus elongatus can use light and CO2 to produce sucrose, making it a promising candidate for use in co-cultures with heterotrophic workhorses. However, this process is challenged by the mutual stresses generated from the multispecies microbial culture. Here we demonstrate an ecosystem where S. elongatus is freely grown in a photo-bioreactor (PBR) containing an engineered heterotrophic workhorse (either β-carotene-producing Yarrowia lipolytica or indigoidine-producing Pseudomonas putida) encapsulated in calcium-alginate hydrogel beads. The encapsulation prevents growth interference, allowing the cyanobacterial culture to produce high sucrose concentrations enabling the production of indigoidine and β-carotene in the heterotroph. Our experimental PBRs yielded an indigoidine titer of 7.5 g/L hydrogel and a β-carotene titer of 1.3 g/L hydrogel, amounts 15-22-fold higher than in a comparable co-culture without encapsulation. Moreover, 13C-metabolite analysis and protein overexpression tests indicated that the hydrogel beads provided a favorable microenvironment where the cell metabolism inside the hydrogel was comparable to that in a free culture. Finally, the heterotroph-containing hydrogels were easily harvested and dissolved by EDTA for product recovery, while the cyanobacterial culture itself could be reused for the next batch of immobilized heterotrophs. This co-cultivation and hydrogel encapsulation system is a successful demonstration of bioprocess optimization under photobioreactor conditions.

In this report, we systematically characterize 32 response regulators (RRs) from a metal tolerant groundwater isolate, Pseudomonas stutzeri RCH2 to assess the impact of host-derived post-translational phosphorylation. As observed by distinct shifted bands in a phos-tag gel, 12 of the 24 detected RRs show homogenous mixtures of phosphorylated proteins or heterogenous mixtures of unphosphorylated and phosphorylated proteins. By evaluating the phosphorylation state of CzcR and CopR II under varying assay parameters, we found that changes to pH and exogenous addition of phospho-donors (e.g. acetyl phosphate) have little to no effect on phosphorylation state. By applying protein production conditions that decrease the pool of intracellular acetyl-phosphate in E. coli, we found a reduction in the phosphorylated population of CopR II when magnesium was added to the medium, but observed no change in phosphorylated population when CopR II is expressed in E. coli BL21 (DE3) ∆pta, a mutant with a metabolic disruption to the acetyl-phosphate pathway. Therefore, the specific mechanism of post-translational phosphorylation of RRs in E. coli remains obscure. These findings show the importance of characterizing the phosphorylation state of proteins when heterologously expressed, since their biochemical and physiological properties can be dependent on post-translational modification.

Abstract As the enthusiasm surrounding Deep Learning grows, both medical practitioners and regulatory bodies are exploring ways to safely introduce image segmentation in clinical practice. One frontier to overcome when translating promising research into the clinical open world is the shift from static to continual learning. Continual learning, the practice of training models throughout their lifecycle, is seeing growing interest but is still in its infancy in healthcare. We present Lifelong nnU-Net, a standardized framework that places continual segmentation at the hands of researchers and clinicians. Built on top of the nnU-Net—widely regarded as the best-performing segmenter for multiple medical applications—and equipped with all necessary modules for training and testing models sequentially, we ensure broad applicability and lower the barrier to evaluating new methods in a continual fashion. Our benchmark results across three medical segmentation use cases and five continual learning methods give a comprehensive outlook on the current state of the field and signify a first reproducible benchmark.

Elafin is an antimicrobial and anti-inflammatory protein. We hypothesize that elafin expression correlates with diabetes. Among non-diabetic and prediabetic groups, men have significantly higher serum elafin levels than women. Men with type 2 diabetes mellitus (T2DM) have significantly lower serum elafin levels than men without T2DM. Serum elafin levels are inversely correlated with fasting blood glucose and hemoglobin A1c levels in men with T2DM, but not women with T2DM. Lentiviral elafin overexpression inhibited obesity, hyperglycemia, and liver steatosis in high-fat diet (HFD)-treated male mice. Elafin-overexpressing HFD-treated male mice had increased serum leptin levels, and serum exosomal miR181b-5p and miR219-5p expression. Transplantation of splenocytes and serum exosomes from elafin-overexpressing HFD-treated donor mice reduced food consumption and fat mass, and increased adipose tissue leptin mRNA expression in HFD-treated recipient mice. Elafin improved leptin sensitivity via reduced interferon-gamma expression and induced adipose leptin expression via increased miR181b-5p and miR219-5p expression. Subcutaneous and oral administration of modified elafin inhibited obesity, hyperglycemia, and liver steatosis in the HFD-treated mice. Circulating elafin levels are associated with hyperglycemia in men with T2DM. Elafin, via immune-derived miRNAs and cytokine, activates leptin sensitivity and expression that subsequently inhibit food consumption, obesity, hyperglycemia, and liver steatosis in HFD-treated male mice.

Abstract Aberrant expression of xenobiotic metabolism and DNA repair genes is critical to lung cancer pathogenesis. This study aims to identify the cis-regulatory variants of the genes modulating lung cancer risk among tobacco smokers and altering their chemotherapy responses. From a list of 2984 SNVs, prioritization and functional annotation revealed 22 cis-eQTLs of 14 genes within the gene expression-correlated DNase I hypersensitive sites using lung tissue-specific ENCODE, GTEx, Roadmap Epigenomics, and TCGA datasets. The 22 cis-regulatory variants predictably alter the binding of 44 transcription factors (TFs) expressed in lung tissue. Interestingly, 6 reported lung cancer-associated variants were found in linkage disequilibrium (LD) with 5 prioritized cis-eQTLs from our study. A case–control study with 3 promoter cis-eQTLs (p

Abstract The study was aimed to evaluate the performance of a newly developed spectroscopy-based non-invasive and noncontact device (SAMIRA) for the simultaneous measurement of hemoglobin, bilirubin and oxygen saturation as an alternative to the invasive biochemical method of blood sampling. The accuracy of the device was assessed in 4318 neonates having incidences of either anemia, jaundice, or hypoxia. Transcutaneous bilirubin, hemoglobin and blood saturation values were obtained by the newly developed instrument which was corroborated with the biochemical blood tests by expert clinicians. The instrument is trained using Artificial Neural Network Analysis to increase the acceptability of the data. The artificial intelligence incorporated within the instrument determines the disease condition of the neonate. The Pearson’s correlation coefficient, r was found to be 0.987 for hemoglobin estimation and 0.988 for bilirubin and blood gas saturation respectively. The bias and the limits of agreement for the measurement of all the three parameters were within the clinically acceptance limit.

Abstract Gram-negative bacterial septicemia is mediated through binding of lipopolysaccharide (LPS) to mammalian toll-like receptor protein 4 (TLR4). TLR4 and its cognate protein, myeloid differentiation factor 2 (MD2) form a heterodimeric complex after binding LPS. This complex induces a cascade of reactions that results in increased proinflammatory cytokine gene expression, including TNFα, which leads to activation of innate immunity. In horses, the immune response to LPS varies widely. To determine if this variation is due to differences in TLR4 or MD2, DNA from 15 healthy adult horses with different TNFα dynamics after experimental intravenous LPS infusion was sequenced across exons of TLR4 and MD2. Haplotypes were constructed for both genes using all identified variants. Four haplotypes were observed for each gene. No significant associations were found between either TNFα baseline concentrations or response to LPS and haplotype; however, there was a significant association (P value = 0.0460) between the baseline TNFα concentration and one MD2 missense variant. Three-dimensional structures of the equine TLR4-MD2-LPS complex were built according to haplotype combinations observed in the study horses, and the implications of missense variants on LPS binding were modeled. Although the sample size was small, there was no evidence that variation in TLR4 or MD2 explains the variability in TNFα response observed after LPS exposure in horses.

Abstract Reference genes are obligatory for accurate normalization of mRNA transcript levels across samples and experimental conditions in Real Time-polymerase chain reaction (qRT-PCR) based quantitative gene expression assays. Selection of stably expressed reference genes is therefore crucial for ensuring reproducibility of such assays. However, there is a complete dearth of data on stability of commonly used reference genes in Peripheral Blood Mononuclear Cells (PBMCs) from Type 2 diabetes mellitus (T2DM) patients. We have evaluated the gene expression stability of 4 widely used reference genes (Beta-actin, ACTB; Peptidylprolyl Isomerase B, PPIB; Tyrosine 3 Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Zeta, YWHAZ; and Glyceraldehyde-3-Phosphate Dehydrogenase, GAPDH); in PBMCs from 39 T2DM patients and 47 normoglycemic (NGT) subjects. ACTB and YWHAZ were found to be the most stable genes in PBMCs from T2DM patients and therefore, can be recommended as suitable reference genes in similar contexts. GAPDH and PPIB expressions were not stable in PBMCs from T2DM patients. On using ACTB and YWHAZ as reference genes for measuring relative expression of GAPDH and PPIB in these subjects, relative GAPDH expression was found to be significantly lower in female T2DM patients, compared to female NGT subjects [GAPDH relative normalization unit (RNU): female T2DM (n = 19), median (Q1, Q3): 9.0 (8.1, 9.9); female NGT (n = 18): median (Q1, Q3): 10.1 (9.1, 11.0); P = 0.034]. Dysregulation of GAPDH in PBMCs from female T2DM patients could be associated with sex-specific differences in pathogenesis and outcomes of T2DM.

Abstract Pathological cardiac remodeling as an aftermath of a severe cardiac injury can lead to ventricular dysfunction and subsequent heart failure. Adamts4, a metalloproteinase, and disintegrin with thrombospondin-like motif, involved in the turnover of certain extracellular matrix molecules and pathogenesis of osteoarthritis, also plays a role in cardiac remodeling although little is presently known about its expression and function in the heart. Here, we have investigated the dynamic expression pattern of Adamts4 during cardiogenesis and also in the adult heart. To our surprise, adult cardiac injury reactivated Adamts4 expression concomitant with fibrosis induction. To better understand the mechanism, cultured H9c2 cardiomyocyte cells were subjected to ROS injury and Hypoxia. Moreover, through combinatorial treatment with SB431542 (an inhibitor of Tgf-β1), and Adamts4 siRNA mediated gene knockdown, we were able to decipher a regulatory hierarchy to the signal cascade being at the heart of Tgf-β regulation. Besides the hallmark expression of Adamts4 and Tgf-β1, expression of other fibrosis-related markers like Collagen-III, alpha-SMA and Periostin were also assessed. Finally, increased levels of Adamts4 and alpha-SMA proteins in cardiac patients also resonated well with our animal and cell culture studies. Overall, in this study, we highlight, Adamts4 as a novel biomarker of adult cardiac injury.

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pSC101 is a narrow host range, low-copy plasmid commonly used for genetically manipulating Escherichia coli. As a byproduct of a genetic screen for a more sensitive lactam biosensor, we identified multiple novel mutations that increase the copy number of plasmids with the pSC101 origin. All mutations identified in this study occurred on plasmids which also contained at least one mutation localized to the RepA protein encoded within the origin. Homology modelling predicts that many of these mutations occur within the dimerization interface of RepA. Mutant RepA resulted in plasmid copy numbers between ~31 and ~113 copies/cell, relative to ~5 copies/cell in wild-type pSC101 plasmids. Combining the mutations that were predicted to disrupt multiple contacts on the dimerization interface resulted in copy numbers of ~500 copies/cell, while also attenuating growth in host strains. Fluorescent protein production expressed from an arabinose-inducible promoter on mutant origin derived plasmids did correlate with copy number. Plasmids harboring RepA with one of two mutations, E83K and N99D, resulted in fluorescent protein production similar to that from p15a- (~20 copies/cell) and ColE1- (~31 copies/cell) based plasmids, respectively. The mutant copy number variants retained compatibility with p15a, pBBR, and ColE1 origins of replication. These pSC101 variants may be useful in future metabolic engineering efforts that require medium or high-copy vectors compatible with p15a- and ColE1-based plasmids.