Molecular detection of Orientia tsutsugamushi in ectoparasites & their small mammal hosts captured from scrub typhus endemic areas in Madurai district, India

BACKGROUND OBJECTIVES

Scrub typhus, caused by Orientia tsutsugamushi present in small mammals harbouring the ectoparasites. A study was undertaken to detect the pathogen present in small mammals and its ectoparasites in the scrub typhus-reported areas.

METHODS

The small mammals (rodents/shrews) and its ectoparasites were screened for O. tsutsugamushi using nested PCR amplification of the groEL gene. Small mammals were collected by trapping and screened for ectoparasites (mites, ticks and fleas) by combing method.

RESULTS

All the chigger mites collected were tested negative for O. tsutsugamushi . Interestingly, adult non-trombiculid mites ( Oribatida sp., Dermanyssus gallinae ), fleas ( Xenopsylla astia, X. cheopis, Ctenophalides felis and Ctenophalides sp.) and ticks ( Rhipicephalus sanguineus , R. haemaphysaloides ) screened were found to be positive for O. tsutsugamushi , which the authors believe is the first report on these species globally. Bandicota bengalensis with O. tsutsugamushi infection is reported for the first time in India. The O. tsutsugamushi groEL sequences from the positive samples were similar to the reference strains, Karp and Ikeda and phylogenetically clustered in clade IV with less evolutionary divergence. The blood samples of Rattus rattus , Suncus murinus and B. bengalensis collected from this area were tested positive for O. tsutsugamushi ; interestingly, the sequence similarity was much pronounced with their ectoparasites indicating the transmission of the pathogen to host or vice versa .

INTERPRETATION CONCLUSIONS

The outcome of the present investigations widened our scope on the pathogens present in ectoparasites and rodents/shrews from this area. This will help to formulate the required vector control methods to combat zoonotic diseases.

Persistence of foliar applied and pre-storage seed-treated insecticides in rice and its processed products

A field study was conducted to investigate the persistence of foliar-applied thiamethoxam 25% WG at a rate of 25 g ai ha-1 and chlorantraniliprole 18.5% SC at 30 g ai ha-1 in various parts of rice plants, including whole grain rice, brown rice, bran, husk, straw, and cooked rice. Liquid Chromatography-Mass spectrometry/Mass spectrometry was used for sample analysis. Chlorantraniliprole residues were found to persist in whole grains, bran, husk, and straw at the time of harvest, while thiamethoxam residue was not detected in harvested grains, processed products, or straw. The study concluded that foliar-applied chlorantraniliprole and thiamethoxam did not pose any dietary risk in cooked rice. In a pre-storage seed treatment study, thiamethoxam 30% FS at 3 mL kg-1 was evaluated against Angoumois grain moth infestation during storage. The seeds remained unharmed for nine months and exhibited significantly less moth damage (2.0%) even after twelve months of storage. Thiamethoxam residues persisted for more than one year in whole rice grain, brown rice, bran, and husk with seed treatment, with higher residue levels observed in bran and husk. Parboiling and cooking led to the degradation of thiamethoxam residues.

Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda

BACKGROUND

Paenibacillus thiaminolyticus may be an underdiagnosed cause of neonatal sepsis.

METHODS

We prospectively enrolled a cohort of 800 full-term neonates presenting with a clinical diagnosis of sepsis at 2 Ugandan hospitals. Quantitative polymerase chain reaction specific to P. thiaminolyticus and to the Paenibacillus genus were performed on the blood and cerebrospinal fluid (CSF) of 631 neonates who had both specimen types available. Neonates with Paenibacillus genus or species detected in either specimen type were considered to potentially have paenibacilliosis, (37/631, 6%). We described antenatal, perinatal, and neonatal characteristics, presenting signs, and 12-month developmental outcomes for neonates with paenibacilliosis versus clinical sepsis due to other causes.

RESULTS

Median age at presentation was 3 days (interquartile range 1, 7). Fever (92%), irritability (84%), and clinical signs of seizures (51%) were common. Eleven (30%) had an adverse outcome: 5 (14%) neonates died during the first year of life; 5 of 32 (16%) survivors developed postinfectious hydrocephalus (PIH) and 1 (3%) additional survivor had neurodevelopmental impairment without hydrocephalus.

CONCLUSIONS

Paenibacillus species was identified in 6% of neonates with signs of sepsis who presented to 2 Ugandan referral hospitals; 70% were P. thiaminolyticus. Improved diagnostics for neonatal sepsis are urgently needed. Optimal antibiotic treatment for this infection is unknown but ampicillin and vancomycin will be ineffective in many cases. These results highlight the need to consider local pathogen prevalence and the possibility of unusual pathogens when determining antibiotic choice for neonatal sepsis.

Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study

BACKGROUND

Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis, meningitis, and postinfectious hydrocephalus, we aimed to complete three separate studies of Ugandan infants. The first study was on peripartum prevalence of Paenibacillus in mother-newborn pairs. The second study assessed Paenibacillus in blood and cerebrospinal fluid (CSF) from neonates with sepsis. The third study assessed Paenibacillus in CSF from infants with hydrocephalus.

METHODS

In this observational study, we recruited mother-newborn pairs with and without maternal fever (mother-newborn cohort), neonates (aged ≤28 days) with sepsis (sepsis cohort), and infants (aged ≤90 days) with hydrocephalus with and without a history of neonatal sepsis and meningitis (hydrocephalus cohort) from three hospitals in Uganda between Jan 13, 2016 and Oct 2, 2019. We collected maternal blood, vaginal swabs, and placental samples and the cord from the mother-newborn pairs, and blood and CSF from neonates and infants. Bacterial content of infant CSF was characterised by 16S rDNA sequencing. We analysed all samples using quantitative PCR (qPCR) targeting either the Paenibacillus genus or Paenibacillus thiaminolyticus spp. We collected cranial ultrasound and computed tomography images in the subset of participants represented in more than one cohort.

FINDINGS

No Paenibacillus spp were detected in vaginal, maternal blood, placental, or cord blood specimens from the mother-newborn cohort by qPCR. Paenibacillus spp was detected in 6% (37 of 631 neonates) in the sepsis cohort and, of these, 14% (5 of 37 neonates) developed postinfectious hydrocephalus. Paenibacillus was the most enriched bacterial genera in postinfectious hydrocephalus CSF (91 [44%] of 209 patients) from the hydrocephalus cohort, with 16S showing 94% accuracy when validated by qPCR. Imaging showed progression from Paenibacillus spp-related meningitis to postinfectious hydrocephalus over 1-3 months. Patients with postinfectious hydrocephalus with Paenibacillus spp infections were geographically clustered.

INTERPRETATION

Paenibacillus spp causes neonatal sepsis and meningitis in Uganda and is the dominant cause of subsequent postinfectious hydrocephalus. There was no evidence of transplacental transmission, and geographical evidence was consistent with an environmental source of neonatal infection. Further work is needed to identify routes of infection and optimise treatment of neonatal Paenibacillus spp infection to lessen the burden of morbidity and mortality.

FUNDING

National Institutes of Health and Boston Children's Hospital Office of Faculty Development.

NUCLEAR MEDICINE PROCEDURE VOLUME AND ESTIMATION OF COLLECTIVE EFFECTIVE DOSE IN TAMIL NADU TOWARDS THE ESTABLISHMENT OF DIAGNOSTIC REFERENCE LEVEL

With an objective to establish adult diagnostic reference levels in the practice of nuclear medicine (NM) in the state of Tamil Nadu (TN), data on the predominant NM procedures carried out in the state are analyzed. In this study, data on total NM diagnostic procedures during the years 2015-19 along with patient-specific diagnostic NM procedure data for the period April-June 2021 from all centers in Tamil Nadu are collected and analyzed using SPSS statistical software. Nine predominant types of NM scans are analyzed. Collective effective dose from NM scans and per capita dose for the TN population are estimated. The 75th percentile of the distribution and average administered activity (AAA) has been derived and local reference levels are reported. Based on the statistical analysis, it is observed that the whole-body positron emission tomography (PET), renal diethylenetriamine pentaacetate (DTPA) scan, bone methylene diphosphonate (MDP) scan, iodine-131 whole body scan, thyroid studies using Technetium per technetate, renal dimercaptosuccinic acid (DMSA), myocardial perfusion methoxyisobutyl isonitrile sestamibi (MIBI), mebrofenin, Galium-68 prostate-specific membrane antigen (PSMA) are the most common procedure covering >90% of the practices carried out. The collective effective dose is 410 man-Sv in the year 2019, leading to a mean effective dose of 0.006 mSv per capita of the TN state population. The 75th percentile of the distribution of AA is slightly higher than diagnostic reference level (DRL) as compared with Australian DRL (310 MBq). It is also observed that F-18 PET procedures are primarily responsible for most of the collective effective dose, local DRL is 316 MBq and it is important to establish national DRLs for NM diagnostic scans to optimize the NM examinations.

1328. Paenibacillosis: An Emerging Cause of Neonatal Sepsis and Postinfectious Hydrocephalus

Background

The etiology of neonatal sepsis is often not identified. Molecular methods can identify pathogens that culture-based methods miss. Most cases of neonatal sepsis globally are treated empirically per WHO guidelines with intravenous ampicillin and gentamicin, which may not be the best regimen for all pathogens.

Methods

We prospectively enrolled 800 neonates presenting with signs of sepsis to two Ugandan hospitals. Blood and cerebrospinal fluid were subjected to 16S rRNA sequencing, which identified Paenibacillus thiaminolyticus in 33/800 (4%) neonates. We confirmed the presence of P. thiaminolyticus by quantitative polymerase chain reaction (PCR). We describe neonatal and birth characteristics, presenting signs, and 12-month developmental outcomes for neonates with paenibacillosis. We performed antibiotic susceptibility testing and genomic analyses on three clinical isolates successfully grown in the laboratory.

Results

Neonates presented at a median age of 3 (1, 7) days. Fever (86%), irritability (78%) and seizures (52%) were common presenting signs (Figure). Most neonates were born vaginally (73%) at a medical facility (79%). Twelve (36%) had an adverse outcome: 5 (15%) neonates died; 4 (14%) survivors developed postinfectious hydrocephalus and three (9%) additional survivors had neurodevelopmental impairment.

All three isolates were resistant to vancomycin, two were resistant to penicillin and ampicillin and one was unlikely to be sensitive to ceftriaxone; all were susceptible to gentamicin and meropenem. The genomes of all three strains contained multiple beta-lactamase genes and a cluster of genes that encodes a type IV pilus.

Clinical signs at presentation for neonates with good and poor outcomes followng paenibacillosis

Conclusion

Molecular methods such as 16S rRNA sequencing and PCR can be used to improve the identification of pathogens causing neonatal sepsis. Paenibacillosis is an important emerging cause of neonatal sepsis in Uganda and is likely an underrecognized cause of postinfectious hydrocephalus in the region and possibly elsewhere. Antibiotics commonly used for neonatal sepsis may be inadequate for the treatment of paenibacillosis. Additional studies to understand the pathophysiology and optimal treatment of this novel infection are urgently needed to prevent neonatal mortality and morbidity including postinfectious hydrocephalus.

Disclosures

Jessica E. Ericson, MD, MPH, Abbvie: Advisor/Consultant Abhaya Kulkarni, MD, MSc, PhD, Medtronic: Advisor/Consultant.

Differential richness inference for 16S rRNA marker gene surveys

Background

Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is essential. While microbiome data generated using high-throughput 16S rRNA marker gene surveys are appealing for this purpose, 16S surveys also generate a plethora of spurious microbial taxa.

Results

When this artificial inflation in the observed number of taxa is ignored, we find that changes in the abundance of detected taxa confound current methods for inferring differences in richness. Experimental evidence, theory-guided exploratory data analyses, and existing literature support the conclusion that most sub-genus discoveries are spurious artifacts of clustering 16S sequencing reads. We proceed to model a 16S survey’s systematic patterns of sub-genus taxa generation as a function of genus abundance to derive a robust control for false taxa accumulation. These controls unlock classical regression approaches for highly flexible differential richness inference at various levels of the surveyed microbial assemblage: from sample groups to specific taxa collections. The proposed methodology for differential richness inference is available through an R package, Prokounter.

Conclusions

False species discoveries bias richness estimation and confound differential richness inference. In the case of 16S microbiome surveys, supporting evidence indicate that most sub-genus taxa are spurious. Based on this finding, a flexible method is proposed and is shown to overcome the confounding problem noted with current approaches for differential richness inference.

Package availability: https://github.com/mskb01/prokounter

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02722-x.

Analysis of mobility based COVID-19 epidemic model using Federated Multitask Learning

Aggregating a massive amount of disease-related data from heterogeneous devices, a distributed learning framework called Federated Learning(FL) is employed. But, FL suffers in distributing the global model, due to the heterogeneity of local data distributions. To overcome this issue, personalized models can be learned by using Federated multitask learning(FMTL). Due to the heterogeneous data from distributed environment, we propose a personalized model learned by federated multitask learning (FMTL) to predict the updated infection rate of COVID-19 in the USA using a mobility-based SEIR model. Furthermore, using a mobility-based SEIR model with an additional constraint we can analyze the availability of beds. We have used the real-time mobility data sets in various states of the USA during the years 2020 and 2021. We have chosen five states for the study and we observe that there exists a correlation among the number of COVID-19 infected cases even though the rate of spread in each case is different. We have considered each US state as a node in the federated learning environment and a linear regression model is built at each node. Our experimental results show that the root-mean-square percentage error for the actual and prediction of COVID-19 cases is low for Colorado state and high for Minnesota state. Using a mobility-based SEIR simulation model, we conclude that it will take at least 400 days to reach extinction when there is no proper vaccination or social distance.

Automated Multimodal Fusion Based Hyperparameter Tuned Deep Learning Model for Brain Tumor Diagnosis

As medical image processing research has progressed, image fusion has emerged as a realistic solution, automatically extracting relevant data from many images before fusing them into a single, unified image. Medical imaging techniques, such as Computed Tomography (CT), Magnetic Resonance Imaging (MRI), etc., play a crucial role in the diagnosis and classification of brain tumors (BT). A single imaging technique is not sufficient for correct diagnosis of the disease. In case the scans are ambiguous, it can lead doctors to incorrect diagnoses, which can be unsafe to the patient. The solution to this problem is fusing images from different scans containing complementary information to generate accurate images with minimum uncertainty. This research presents a novel method for the automated identification and classification of brain tumors using multi-modal deep learning (AMDL-BTDC). The proposed AMDL-BTDC model initially performs image pre-processing using bilateral filtering (BF) technique. Next, feature vectors are generated using a pair of pre-trained deep learning models called EfficientNet and SqueezeNet. Slime Mold Algorithm is used to acquire the DL models’ optimal hyperparameter settings (SMA). In the end, an autoencoder (AE) model is used for BT classification once features have been fused. The suggested model’s superior performance over other techniques under diverse measures was validated by extensive testing on the benchmark medical imaging dataset.

Onychomadesis- A Late Manifestation of Hand, Foot and Mouth Disease: A Case Series

Hand Foot Mouth Disease (HFMD) is one of the most common viral illness that is characterised by fever below 38.3°C, painful oral lesions on the tongue and buccal mucosa and macular, maculopapular or vesicular skin lesions on the soles and palms. Many viruses are implicated in HFMD, such as Coxsackievirus A5, A6, A7, A9, A10, A16 (most common), B1, B2, B3, B5, Echoviruses E3, E4, E9 and Enterovirus 71. The illness is usually mild and self-limiting. HFMD due to Enterovirus 71, is associated with a severe illness complicated by aseptic meningitis, acute flaccid paralysis, pulmonary oedema and heart failure. Onychomadesis is a very rare complication of HFMD, typically occurring three to eight week of onset of illness. This is characterised by the detachment of the nail plate from the proximal nail fold by a full thickness sulcus. It is postulated that viral infection causes inflammation around the nail matrix either due to direct effect or due to the deposition of immune complexes secondary to distal thromboembolism. Here, authors report six children of different age groups who were affected with onychomadesis during an outbreak of HFMD in the month of February to May 2022 in Chennai, Tamil Nadu, India. All these six children developed onychomadesis following HFMD, after a couple of weeks. Both upper and lower limb nails were involved. Other causes of onychomadesis like chronic illness, nutritional deficiencies, drug ingestion, periungual dermatitis, trauma were ruled out. Children were given supportive care and were followed-up. The changes in nails spontaneously regressed after a couple of weeks.

Comparitive Study of Formulated Herbal Mosquito Repellent Incense Sticks with Market Product

The mosquito repellent formulations that are available on the market are causing irritations like coughing, sneezing, allergic reactions and respiratory disorders to human.The mosquito repellents available in the market are in various forms like colis,mats,sprays and fast cards. So the present study was carried out to formulate mosquito repellent incense sticks using herbals like Vitex negundo, Neem, Holy basil, and Garlic. The poly herbal mosquito repellent formulation are made by hand rolling method.The solid formulation containing binders and additives are rolled in the form of incense sticks and dried for 24 hrs. After drying its evaluated and compared with the market formulation. The prepared herbal mosquito incense sticks are potent, safe with more duration of time and less cost.

Genetic structure and connectivity among Aedes aegypti populations within Madurai city in Southern India

We investigated the genetic variability and differentiation among 12 Ae. aegypti populations collected within the Madurai city in Tamil Nadu state of Southern India. Genotyping of 12 microsatellite markers in 353 individual samples showed moderate levels of genetic diversity among 12 populations. UPGMA tree, hierarchical clustering, Bayesian clustering and Discriminant Analysis on Principal Components roughly divided these populations into two genetic clusters: main city populations and the populations located at the border of the corporation limit. Significant positive correlation between genetic and geographic distance was observed among 12 populations, however, the correlation was non-significant within each genetic cluster. Population assignment and divMigrate graph depicted less migration between two groups. Overall, the findings of this study provided an overview of Ae. aegypti population structure within an urban setting in India that have implications in effective implementation of vector control in the city area.

A Novel Variable Weight Grey Wolf Optimization Algorithm in Medical Image Fusion

Medical image fusion (MIF) is essential in clinical domain that integrates the multi-modal medical features to a unique frame known as fused image which finds utility in diagnosis process. Scaling based approaches are the commonly used multimodal MIF model where the generalized scaling has a stationary scale value selection that enhances the fusion quality Discrete Wavelet Transform (db4)-based approaches give a maximum amount of approximation in multi-modal medical image fusion, while using less edge features. For generating efficient edge features, Laplacian filtering (LF) approach is employed. This paper introduces an optimized Laplacian Wavelet Mask (OLWM) based fusion model for multi-modal MIF using Variable Weight Grey Wolf Optimization (VW-GWO). An enhanced GWO algorithm with variable weights (VW-GWO) is faced with the idea of using the social hierarchy of the grey wolves to locate the searching positions. Besides, to minimize the possibility of trapping into local optima, an efficient parameter control mechanism is employed. The VW-GWO algorithm has the capability to choose the control variables of the GWO algorithm in an automated way. A set of medical images, including MR-SPECT, MR-PET, MR-CT and MR: T1–T2 of brain scans, validates the proposed VW-GWO algorithm. The simulation outcome showed that the effectiveness of the VW-GWO algorithm seems to be much higher over the compared methods under various dimensions.

Structural and Optical Properties of Self-Assembled Epitaxially Grown GaN Nanorods and Nanoporous Film on Sapphire (0001) Using Laser Molecular Beam Epitaxy

The GaN nanoporous-film (NPF) and nanorods (NRs) were grown on sapphire (0001) using laserassisted molecular beam epitaxy (LMBE) technique by laser ablating solid GaN target at different laser energy density. The interconnected GaN NPF was grown at low laser energy density of ˜4 J/cm² whereas vertically aligned GaN NRs was obtained at high laser energy density of ˜7 J/cm². The pore size of the GaN NPF structure is in range of 40-120 nm. The GaN NRs possess hexagonal shape with six sidewall facets and truncated top facet. The length, width and density of GaN NRs are 600-900 nm, 150-250 nm and ˜2.5×10⁷ cm^-2, respectively. The X-ray rocking curve full width at half maximum values along GaN (0002) and (1012) planes for GaN NRs obtained to be 0.41 and 0.53°, respectively. The biaxial stress in hetero-epitaxially grown GaN was investigated with Raman spectroscopy and it was found that GaN NRs possesses a very low in-plane compressive biaxial stress of 0.09 GPa. The photoluminescence study exhibits a sharp band-to-band emission at 3.4 eV with a peak line width of 140 meV, signifying the good optical quality of the LMBE grown GaN NRs on sapphire (0001).

Excitation Density Dependent Photoluminescence Studies on Homo-Epitaxial GaN Nanowall Networks Grown by Laser Assisted Molecular Beam Epitaxy

The optical properties of laser-assisted molecular beam epitaxy grown homo-epitaxialGaN nanowall networks (NWNs) were investigated using power dependent photoluminescence (PL) spectroscopy and compared with homo-epitaxial GaN thin film. The pore size and tip width of GaN NWN sample is ˜120-180 nm and 10-15 nm, respectively. The ultraviolet-visible spectroscopy study shows that the GaN NWNs have low optical light reflection and minimum Fabry-Perot cavity effect than GaN film. The room temperature PL spectroscopy reveals that the GaN NWNs possesses enhanced band gap of 3.51 eV with blue shift of 90 meV than the GaN film (3.42 eV). The excitation density dependent PL spectroscopy measurements reveal that the GaN NWNs nanowall and near band emission (NBE) peak position and its linewidth invariant. The intensity of NBE peak for GaN film and nanowalls varies linearly whereas NBE to defect related yellow luminescence peak intensity ratio shows a non-linear variation on the excitation density. The excitation density in PL measurements plays a key role when the sample quality compared on the basis of PL data.

Structural and Optical Properties of GaN Film on Copper and Graphene/Copper Metal Foils Grown by Laser Molecular Beam Epitaxy

We report the direct growth of crystalline GaN on bare copper (Cu) and monolayer-graphene/Cu metal foils using laser molecular beam epitaxy technique at growth temperature of 700 °C. The surface morphology investigated with field emission scanning electron microscopy revealed that the size of GaN grains for film grown on bare Cu falls in range of 90 to 160 nm whereas large grains with size of ˜200 to 600 nm was obtained for GaN grown on graphene/Cu foil under similar growth condition. The transverse optical mode of cubic GaN and E₂ (high) phonon mode for wurtzite GaN phases were obtained on the GaN film grown on Cu and graphene/Cu metal foils as deduced by Raman spectroscopy. The photoluminescence (PL) spectroscopy studies showed that the near band edge emission peaks for GaN on Cu and graphene/Cu consist two major peaks at 3.26 and 3.4 eV, corresponding to cubic and wurtzite GaN, respectively. The Raman and PL studies disclosed that the mixed phase growth of GaN occurs on these foils and better structural and optical quality for GaN on graphene/Cu foil. The direct growth of GaN on two dimensional graphene on polycrystalline metal foils is beneficial various transferrable and flexible opto-electronics device applications.

Self-Induced Growth of GaN Nanowall Structure on Si (111) by Laser Molecular Beam Epitaxy

Evolution of GaN nanostructure grown on Si (111) substrate has been studied systematically using laser molecular beam epitaxial process. The in-situ reflection high energy electron diffraction and ex-situ high resolution X-ray diffraction studies reveal that the GaN nanostructures have a hexagonal-wurtzite phase and grow along c-axis. The GaN morphology changes from compact granular layer to faceted pyramids to nanowall structure as a function of laser ablation frequency of the KrF excimer laser and radio frequency nitrogen plasma condition. It is observed that GaN nanowall structure is formed on Si (111) when grown under strong nitrogen-rich flux at a higher growth rate and growth temperature. The crystalline and optical quality of the GaN nanostructures significantly improved with increase of laser ablation frequency. The nanowall structure shows good optical emission properties with an intense, sharp near-band edge emission and a negligible deep band luminescence.

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures

BACKGROUND

There are a variety of bioinformatic pipelines and downstream analysis methods for analyzing 16S rRNA marker-gene surveys. However, appropriate assessment datasets and metrics are needed as there is limited guidance to decide between available analysis methods. Mixtures of environmental samples are useful for assessing analysis methods as one can evaluate methods based on calculated expected values using unmixed sample measurements and the mixture design. Previous studies have used mixtures of environmental samples to assess other sequencing methods such as RNAseq. But no studies have used mixtures of environmental to assess 16S rRNA sequencing.

RESULTS

We developed a framework for assessing 16S rRNA sequencing analysis methods which utilizes a novel two-sample titration mixture dataset and metrics to evaluate qualitative and quantitative characteristics of count tables. Our qualitative assessment evaluates feature presence/absence exploiting features only present in unmixed samples or titrations by testing if random sampling can account for their observed relative abundance. Our quantitative assessment evaluates feature relative and differential abundance by comparing observed and expected values. We demonstrated the framework by evaluating count tables generated with three commonly used bioinformatic pipelines: (i) DADA2 a sequence inference method, (ii) Mothur a de novo clustering method, and (iii) QIIME an open-reference clustering method. The qualitative assessment results indicated that the majority of Mothur and QIIME features only present in unmixed samples or titrations were accounted for by random sampling alone, but this was not the case for DADA2 features. Combined with count table sparsity (proportion of zero-valued cells in a count table), these results indicate DADA2 has a higher false-negative rate whereas Mothur and QIIME have higher false-positive rates. The quantitative assessment results indicated the observed relative abundance and differential abundance values were consistent with expected values for all three pipelines.

CONCLUSIONS

We developed a novel framework for assessing 16S rRNA marker-gene survey methods and demonstrated the framework by evaluating count tables generated with three bioinformatic pipelines. This framework is a valuable community resource for assessing 16S rRNA marker-gene survey bioinformatic methods and will help scientists identify appropriate analysis methods for their marker-gene surveys.

Effect of surface modification and laser repetition rate on growth, structural, electronic and optical properties of GaN nanorods on flexible Ti metal foil

The effect of flexible Ti metal foil surface modification and laser repetition rate in laser molecular beam epitaxy growth process on the evolution of GaN nanorods and their structural, electronic and optical properties has been investigated. The GaN nanostructures were grown on bare- and pre-nitridated Ti foil substrates at 700 °C for different laser repetition rates (10–30 Hz). It is found that the low repetition rate (10 Hz) promotes sparse growth of three-dimensional inverted-cone like GaN nanostructures on pre-nitridated Ti surface whereas the entire Ti foil substrate is nearly covered with film-like GaN consisting of large-sized grains for 30 Hz growth. In case of the GaN growth at 20 Hz, uniformly-aligned, dense (∼8 × 10⁹ cm⁻²) GaN nanorods are successfully grown on pre-nitridated Ti foil whereas sparse vertical GaN nanorods have been obtained on bare Ti foil under similar growth conditions for both 20 and 30 Hz. X-ray photoemission spectroscopy (XPS) has been utilized to elucidate the electronic structure of GaN nanorods grown under various experimental conditions on Ti foil. It confirms Ga–N bonding in the grown structures, and the calculated chemical composition turns out to be Ga rich for the GaN nanorods grown on pre-nitridated Ti foil. For bare Ti substrates, a preferred reaction between Ti and N is noticed as compared to Ga and N leading to sparse growth of GaN nanorods. Hence, the nitridation of Ti foil is a prerequisite to achieve the growth of dense and aligned GaN nanorod arrays. The X-ray diffraction, high resolution transmission electron microscopy and Raman studies revealed the c-axis growth of wurtzite GaN nanorods on Ti metal foil with good crystallinity and structural quality. The photoluminescence spectroscopy showed that the dense GaN nanorod possesses a near band edge emission at 3.42 eV with a full width at half maximum of 98 meV at room temperature. The density-controlled growth of GaN nanorods on a flexible substrate with high structural and optical quality holds promise for potential applications in futuristic flexible GaN based optoelectronics and sensor devices.

The effect of flexible Ti metal foil surface modification and laser repetition rate in laser molecular beam epitaxy growth process on the evolution of GaN nanorods and their structural, electronic and optical properties has been investigated.

Effect of Implant Abutment Acid Etching on the Retention of Crowns Luted with Different Cements: An In Vitro Comparative Evaluation

Background:

Air abrasion of the implant abutment surface improves the bond strength of luting agents. However, the effect of acid etching and combination of air abrasion and acid etching on the bond strength of various luting agents under masticatory load is yet to be documented.

Purpose:

The purpose of this study was to evaluate the effect of implant abutment surface modifications on the tensile bond strength (TBS) of cast metal copings (CMCs) luted with different luting agents, subjected to cyclic fatigue loads.

Materials and Methods:

A total of 150 Ni-Cr CMCs were made on commercially pure titanium (Cp-Ti) laboratory analogues. The samples were categorized into three groups based on surface modifications and five subgroups for luting agents. The CMCs were cemented to the respective surface-modified groups, stored in distilled water at 37°C for 24 hours, and then subjected to load cycling, followed by tensile loading. One-way analysis of variance (ANOVA) was used to compare the mean bond strength between luting agents.

Results:

Self-adhesive resin cement showed the highest TBS followed by resin-modified glass ionomer cement, zinc polycarboxylate, and zinc phosphate cement. Non-eugenol temporary cement showed least TBS values on all modified abutment surfaces.

Conclusion:

Air abrasion + acid etching (HY) provided the greatest TBS followed by acid-etched (AE) surface only. Air-abraded (AA) surface yielded the least TBS for luting agents.

Prevalence of Iron Deficiency Anemia in Children with Severe Early Childhood Caries

Dental caries is an international public health challenge, especially amongst young children. Early childhood caries (ECC) is a serious public health problem in both developing and industrialised countries. ECC can begin early in life, progresses rapidly in those who are at high risk, and often goes untreated. Its consequences can affect the immediate and long-term quality of life of the child's family and can have significant social and economic consequences beyond the immediate family as well. ECC can be a particularly virulent form of caries, beginning soon after dental eruption, developing on smooth surfaces, progressing rapidly, and having a lasting detrimental impact on the dentition. Children experiencing caries as infants or toddlers have a much greater probability of subsequent caries in both the primary and permanent dentitions. Iron deficiency being the most common nutritional deficiency in childhood is often seen associated with severe caries destruction. Lack of iron is one of the most common dietary deficiency observed worldwide particularly in developing countries. In some instances this deficiency is alleviated by supplementary foods with added iron salts. In many countries where the iron deficiency is apparent, the prevalence of dental caries is high.

Laser molecular beam epitaxy of vertically self-assembled GaN nanorods on Ta metal foil: role of growth temperature and laser repetition rate

Self-aligned GaN nanorod assembly directly grown on metal foil substrates is very attractive for developing flexible devices.

Analysis and correction of compositional bias in sparse sequencing count data

BACKGROUND

Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count data is compositional, measuring relative and not absolute abundances of the assayed features. This compositional bias confounds inference of absolute abundances. Commonly used count data normalization approaches like library size scaling/rarefaction/subsampling cannot correct for compositional or any other relevant technical bias that is uncorrelated with library size.

RESULTS

We demonstrate that existing techniques for estimating compositional bias fail with sparse metagenomic 16S count data and propose an empirical Bayes normalization approach to overcome this problem. In addition, we clarify the assumptions underlying frequently used scaling normalization methods in light of compositional bias, including scaling methods that were not designed directly to address it.

CONCLUSIONS

Compositional bias, induced by the sequencing machine, confounds inferences of absolute abundances. We present a normalization technique for compositional bias correction in sparse sequencing count data, and demonstrate its improved performance in metagenomic 16s survey data. Based on the distribution of technical bias estimates arising from several publicly available large scale 16s count datasets, we argue that detailed experiments specifically addressing the influence of compositional bias in metagenomics are needed.

Negative-capacitance and bulk photovoltaic phenomena in gallium nitride nanorods network

An enhanced self-powered near-ultraviolet photodetection phenomenon was observed in epitaxial gallium nitride (GaN) nanorods network grown on an intermediate layer of N:GaN on a nitridated HfO₂(N:HfO₂)/SiO₂/p-Si substrate. The fabricated Au/GaN/N:GaN/N:HfO₂/Ag heterostructure exhibited a giant change (OFF/ON ratio > 50 without applying any external electrical field) in its conductance when illuminated by a very weak (25 mW cm^-2) near-UV monochromatic light with a low dark current (nearly 20 nA). The presented near-UV photodetector offers photoresponsivity of ∼2.4 mA W^-1 at an applied voltage of 1 V. We observed an optically generated internal open circuit voltage of ∼155 mV and short circuit current ∼430 nA, which can be attributed to the quantum confinement of free charge carriers in the nanorod matrix. Interestingly, it also shows a negative capacitance after near-UV illumination. It has great potential as a self-powered UV photodetector and in metamaterial applications.

Fe-Dy Nanogranular Thin Films: Investigation of Structural, Microstructural and Magnetic Properties

A series of Fe100-xDyx thin films with the concentration range x = 6 to 35 were fabricated by dc magnetron sputtering process. X-ray diffraction and TEM studies revealed that films have separate Fe and Dy nanograins and that there is no intermixing of Fe and Dy thus forming nanogranular films. This unmixed behaviour in our thin films is very different from the bulk Fe-Dy alloys where several stoichiometric compounds can be formed. Magnetic properties of the films have been systematically studied. The contribution to the total magnetization is due to the Fe grains and the Dy grains are paramagnetic down to 4 K. The saturation magnetization of all the samples is significantly lower than that of bulk Fe due to the existence of superparamagnetic Fe grains. Upon increasing x, the in-plane magnetic anisotropy is found to decrease and the samples become isotropic. The zero field cooled and field cooled magnetization measurements also confirmed the presence of the superparamagnetic Fe grains.

Directly observed therapy of sofosbuvir/ribavirin +/- peginterferon with minimal monitoring for the treatment of chronic hepatitis C in people with a history of drug use in Chennai, India (C-DOT)

We assessed the feasibility of field-based directly observed therapy (DOT) with minimal monitoring to deliver HCV treatment to people with a history of drug use in Chennai, India. Fifty participants were randomized 1:1 to sofosbuvir+peginterferon alfa 2a+ribavirin (SOF+PR) for 12 weeks (Arm 1) vs sofosbuvir+ribavirin (SOF+R) for 24 weeks (Arm 2). SOF+R was delivered daily at participant chosen venues and weekly peginterferon injections at the study clinic. HCV RNA testing was performed to confirm active HCV infection and sustained virologic response 12 weeks after treatment completion (SVR12). No baseline genotyping or on-treatment viral loads were performed. Median age was 46 years. All were male and 20% had significant fibrosis/cirrhosis. All self-reported history of injection drug use, 18% recent noninjection drug use and 38% alcohol dependence. Six discontinued treatment (88% completed treatment in each arm). Of 22 who completed SOF+PR, all achieved SVR12 (22/25=88%); 15 of 22 who completed SOF+R achieved SVR12 (15/25=60%; P=.05). Among those completing SOF+R, SVR12 was significantly less common in participants reporting ongoing substance use (36% vs 100%) and missed doses. Active substance use and missed doses did not impact SVR with SOF+PR. Field-based DOT of HCV therapy without real-time HCV RNA monitoring was feasible; however, achieving 100% adherence was challenging. SOF+PR appeared superior to SOF+R in achieving SVR12, even when doses were missed with no discontinuations due to side effects. Further exploration of short duration treatment with peginterferon plus direct-acting antivirals is warranted.

Effect of surfactants and hydrophilic polymers on the stability of an antihypertensive drug candesartan cilexetil: Evaluation by HPLC

OBJECTIVES

The objective of this study is to investigate the effect of surfactants (polysorbate 80 and sodium lauryl sulphate) and hydrophilic polymers (polyvinylpyrrolidone and polyethylene glycol 6000) on the stability of candesartan cilexetil under isothermal stress conditions (100°C, 48h).

METHODS

HPLC method was employed to evaluate the drug content and formation of degradation products in stress samples. Drug and degradation products were separated on Hypersil BDS C18 (250×4.6mm, 5μ) column using acetonitrile-water (pH 2.8) in the ratio of 85:15% v/v as a mobile phase.

RESULT

Similar degradation behaviour of drug was observed with polyvinylpyrrolidone, polyethylene glycol 6000 and polysorbate 80; four common degradation peaks were observed at the retention time of 3.7, 4.5, 7.8 and 11minutes. One extra common degradation peak of very low intensity was also observed with polyethylene glycol 6000 and polysorbate 80 at the retention time of 4.2min. The drug was eluting at the retention time of 5.4min. In the case of sodium lauryl sulphate, two prominent degradation peaks were observed at the retention time of 3.7 and 13.25min along with few very low-intensity degradation peaks.

CONCLUSION

The drug showed 41%, 64%, 72% and 98% degradation in presence of polyvinylpyrrolidone, polyethylene glycol 6000, polysorbate 80 and sodium lauryl sulphate, respectively.

Evaluating the Correlation between Anteroposterior and Mediolateral Compensatory Curves and their Influence on Dentoskeletal Morphology-An In vitro CBCT Study

INTRODUCTION

To date, many orthodontist corrects malocclusion based on patients aesthetic concern and fails to correct the compensatory curves. This scenario is due to less insight on understanding relationship of compensatory curves and its correlation in treatment prognosis.

AIM

The purpose of this study was to evaluate the correlation between the curve of Spee, curve of Monson and curve of Wilson, their influence on dentoskeletal morphology and their contribution to occlusal stability.

MATERIALS AND METHODS

This study included 104 non-orthodontic models. The study casts were subdivided into two groups, Group-I consist 52 non- orthodontic models with Class-I molar relationship and Group-II consist of 52 non- orthodontic models with Class-II molar relationship. Curve of Spee was measured with digital vernier caliper, curve of Monson estimated using specially made sphere (7″inch, 8″ inch and 9″inch) and curve of Wilson was evaluated using Cone Beam Computed Technology (CBCT).

RESULTS

Mean value for curve of Spee obtained for Group I and Group II is 1.844 mm and 3.188 mm. For curve of Monson, the mean value obtained for Group I and Group-II is 7.65 inches and 7.40 inches. The mean degree obtained for the curve of Wilson for Group I and Group-II is 12.05 and 16.49. The result showed positive correlation between curve of Spee and curve of Wilson and no correlation between curve of Monson and curve of Wilson and no correlation between curve of Spee and curve of Monson. The Pearson correlation coefficient analysis from the study confirmed these results.

CONCLUSION

The results showed positive correlation between curve of spee and curve of Wilson. The data found in this study can be applied clinically for Class I and Class II malocclusion patients on diagnosis and treatment planning.

Color Stability Assessment of Two Different Composite Resins with Variable Immersion Time Using Various Beverages: An In vitro Study

Purpose of the Study:

The aim of the study was to evaluate the difference in the color of microhybrid (MH) and nanofilled (NF) composite resins after 24 and 48 h in beverages such as red wine (RW), Coca-Cola, and distilled water. The specific objective of this study was to investigate the cumulative effect of the colorant solutions on the dental composites.

Materials and Methods:

MH and NF composite resins (A2 shade) were used in this current study. Sixty disk-shaped material specimens (10 mm in diameter × 2 mm in thickness) were prepared using a fiber mold (ring), with the desired dimensions. The specimen surfaces were polished using super-snap polishing system. Sixty specimens were divided into two groups of 30 each (Group I: MH resin composite; Group II: NF resin composite). Both the groups divided into six subgroups (Subgroup I: RW for 24 h [RW-24]; Subgroup II: RW for 48 h; Subgroup III: Coca-Cola for 24 h [CC-24]; Subgroup IV: Coca-Cola for 48 h [CC-48]; Subgroup V: Distilled water for 24 h [DW-24]; Subgroup VI: Distilled water for 48 h [DW-48]). All the samples were immersed in respective drinks for a period of 24 h, and color differences were measured using ultraviolet spectrophotometer. Once again, all the samples were immersed for another 24 h in the same drinks. After 48 h, the color change of the samples was measured. Measurements were made according to the CIE L × a × b × color space relative to the CIE standard illuminant D65. The color changes of the specimens were evaluated using the following formula: Statistical analysis was performed. The data were analyzed using the one-way ANOVA and t-test at a significance level of 0.05.

Conclusion:

Color stability of MH composite resin was found to be inferior than the NF resin composite irrespective of immersion medium and time. In RW, the color change observed was maximum for both composite resins followed by Coca-Cola. Immersing the resin composites in distilled water for 24 and 48 h had negligible color change. A 48-h immersion of both composite resins in all three immersion mediums showed greater color change than 24 h immersion.

Evaluating the Type of Light Transmittance in Mono Crystalline, Poly Crystalline and Sapphire Brackets- An Invitro Spectrofluorometer Study

INTRODUCTION

Most of the patients seek orthodontic treatment to improve the smile, which improves the facial profile by means of fixed appliances i.e., brackets and wires. The brackets are of different types like stainless steel and ceramic. Ceramic brackets were considered as aesthetic appliance which was divided into mono-crystalline, polycrystalline and sapphire brackets. The light transmittance might influence the degree of curing adhesive material in mono crystalline, polycrystalline and sapphire brackets.

AIM

The aim of the present study was to evaluate the translucency and intensity of three different aesthetic brackets (mono crystalline, poly crystalline and sapphire ceramic brackets) and to determine their influence on shear bond strength of the brackets. The adhesive remnant index was also measured after debonding of the brackets from the tooth surface.

MATERIALS AND METHODS

Twenty six samples each of monocrystalline, polycrystalline and sapphire brackets (total 78 ceramic brackets) were used for the study. The bracket samples were subjected to optical fluorescence test using spectrofluorometer to measure the intensity of the brackets. Seventy eight extracted premolar teeth were procured and divided into 3 groups. The brackets were then bonded to the tooth using Transbond XT (3M Unitek) light cure composite material and cured with new light cure unit (Light Emitting Diode) of wood pecker company (400-450nm) for 30 seconds, and these samples were subjected to shear bond strength test with Instron Universal Testing Machine (UNITEK-94100) with a load range between 0 to 100 KN with a maximum cross head speed of 0.5mm/min. ARI (Adhesive Remnant Index) scores were evaluated according to Artun and Bergland scoring system using stereomicroscope at 20x magnification.

RESULTS

The light absorption values obtained from spectrofluorometeric study were 3300000-3500000 cps for group 1 (monocrystalline ceramic brackets), 6000000-6500000 cps for Group 2 (polycrystalline ceramic brackets) and 2700000 -3000000 cps for Group 3 (sapphire ceramic brackets) i.e., Group 2 showed the highest light absorption and the least translucency followed by groups 1 and 3. Shear bond strength results were 2.4 mpa, 1.9 mpa and 3.6 mpa for groups 1,2 and 3 respectively. Superior shear bond strength was recorded in group 3 (sapphire ceramic brackets). ARI results showed that group 3 had increased bond between bracket adhesive interfaces when compared to the other 2 groups.

CONCLUSION

From this study, it has been concluded that sapphire ceramic brackets (Group 3) was superior in translucency and shear bond strength followed by monocrystalline and polycrystalline ceramic brackets.

A comparative evaluation of two rotary Ni-Ti instruments in the removal of gutta-percha during retreatment

AIM

The purpose of this study is to achieve an effective method to remove root canal filling material from the root canal system. The study, thus, aims to evaluate the efficacy of the cleaning ability of two different rotary Ni-Ti systems; ProTaper Retreatment files and RaCe System compared to hand instrumentation with Hedstrom files for the removal of gutta-percha during retreatment.

MATERIALS AND METHODS

Thirty mandibular premolars with one single straight canal were decoronated and instrumented with ProTaper files and filled with thermoplastic gutta-percha. After 30 days, the samples were divided into three groups and gutta-percha was removed with the test instruments. The postoperative radiographs were evaluated with known criteria by dividing the root into cervical third, middle third, and apical third. The results were tabulated and Statistical Package for Social Sciences Software (IBM Corporation) was used for analysis.

RESULTS

The mean deviation of the results were first calculated and then t-test and analysis of variance test (two-tailed P value) were evaluated for establishing significant differences. The rotary instruments were effective in removing the gutta-percha from the canals. Therefore, significant difference was observed between the efficacies of the two rotary systems used. The rotary instruments showed effective gutta-percha removal in the cervical and middle one third. (P > 0.05). However, apical debridement was effective with Hedstrom files.

CONCLUSION

The study concluded the use of both rotary and hand instrumentation for effective removal of gutta-percha for retreatment.

Molecular identification of multi drug resistant bacteria from urinary tract infected urine samples

Urinary tract infections (UTIs) are of great concern in both developing and developed countries all over the world. Even though the infections are more common in women and children, they are at a considerable rate in men and of all ages. The uropathogens causing the infections are spread through various routes. The treatment generally recommended by the physicians is antibiotic usage. But, most of the uropathogens have evolved antibiotic resistance mechanisms. This makes the present situation hectic in control and prevention of UTIs. The present study aims to illustrate the multidrug resistance patterns among isolated bacterial strains from infected urine samples in Odisha state, India. Four bacterial strains were isolated and identified as Proteus sp. SK3, Pseudomonas sp. ADMK77, Proteus sp. BLKB2 and Enterobacter hormaechei strain CW-3 by 16S rRNA gene sequencing. Phylogenetc analysis indicated the strains belong to three various genera namely, Proteus, Pseudomonas and Enterobacter. The evolutionary timeline of the bacteria was studied by constructing phylogenetic trees by Neighborhood Joining method. The presence of ESBL gene and biofilm forming capability were studied for the four strains. Antibiotic susceptibility patterns of the isolates were studied toward the commonly recommended antibiotics. Both the Proteus strains were found commonly susceptible to aminoglycoside and sulphonamide groups. Pseudomonas strain was found to be susceptible to cephems, aminoglycosides and fluoroquinolones. Enterobacter sp was found to be resistant to almost all antibiotic groups and susceptible to only sulphonamides group. The antibiotic susceptibility patterns of the bacteria help in choosing the empirical antibiotic treatment for UTI.

Evaluating the Surface Characteristics of Stainless Steel, TMA, Timolium, and Titanium-niobium Wires: An in vivo Scanning Electron Microscope Study

BACKGROUND

Recent metallurgical research and advancement in material science has benefited orthodontists in the selection of an appropriate wire size and alloy type, which is necessary to provide an optimum and predictable treatment results. The purpose of the study was to clinically evaluate and compare the surface characteristics of 16 x 22 stainless steel, Titanium molybdenum alloy, timolium, and titanium-niobium before and after placing them in a patient's mouth for 3 months using a scanning electron microscope (SEM).

MATERIALS AND METHODS

The total sample size was 40, which were divided into four groups (group 1 - stainless steel wires, 10 samples, group 2 - TMA wires, 10 samples, group 3 - timolium wires, 10 samples, and group 4 - titanium-niobium wires, 10 samples), and these were further subdivided into 5 each. The first subgroup of five samples was placed in the patient's mouth and was evaluated under SEM, and another subgroup of five samples was directly subjected to the SEM.

RESULTS

Scanning electron microscopic evaluation of surface characteristics of unused 16 x 22 rectangular stainless steel wire under 500 x magnification showed an overall smooth surface. Stainless steel wire samples placed in the patient's mouth showed black hazy patches, which may be interoperated as areas of stress. TMA unused wires showed multiple small voids of areas and small craters with fewer elevated regions. The TMA wire samples placed in the patient's mouth showed black hazy patches and prominent ridges, making the wire rougher. Timolium unused archwires showed heavy roughness and voids, whereas wires tested in the patient's mouth showed homogeneous distribution of deep cracks and craters. Unused titanium-niobium archwires showed uniform prominent striations and ridges with occasional voids, whereas wires used in the patient's mouth showed prominent huge voids that could be interpreted as maximum stress areas.

CONCLUSION

Stainless steel (group 1) used and unused wires showed smooth surface characteristics when compared with all the other three groups followed by timolium, which was superior to titanium-niobium wires and TMA wires.

CLINICAL SIGNIFICANCE

Timolium wires are superior to titanium-niobium wires and TMA wires.

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution

CRISPRs offer adaptive immunity in prokaryotes by acquiring genomic fragments from infecting phage and subsequently exploiting them for phage restriction via an RNAi-like mechanism. Here, we develop and analyze a dynamical model of CRISPR-mediated prokaryote-phage coevolution that incorporates classical CRISPR kinetics along with the recently discovered infection-induced activation and autoimmunity side effects. Our analyses reveal two striking characteristics of the CRISPR defense strategy: that both restriction and abortive infections operate during coevolution with phages, driving phages to much lower densities than possible with restriction alone, and that CRISPR maintenance is determined by a key dimensionless combination of parameters, which upper bounds the activation level of CRISPRs in uninfected populations. We contrast these qualitative observations with experimental data on CRISPR kinetics, which offer insight into the spacer deletion mechanism and the observed low CRISPR prevalence in clinical isolates. More generally, we exploit numerical simulations to delineate four regimes of CRISPR dynamics in terms of its host, kinetic, and regulatory parameters.

To counteract viral infections, bacteria and archaea have evolved a variety of defense systems. These can broadly be classified into either restriction or suicide mechanisms. The former enforces nicks in the invading DNA making it unusable for production of further infectious particles; the latter, by contrast, induces cell death whereby an infected cell activates specific host suicidal pathways that are otherwise strongly repressed, thus inhibiting further infection. Examples of the former class include restriction-modification (R-M) and the recently discovered CRISPR systems, while the latter class includes a variety of toxin/anti-toxin systems. CRISPRs, in contrast to R-Ms, adapt to target viral genomes by updating the database of target sites they recognize. The adverse side effect of such a mechanism, however, is that CRISPRs can target the host genome itself resulting in undesirable cell death (autoimmunity). The recent discovery of infection-induced activation of CRISPR systems suggests that these negative side effects may be limited to periods of infection. This led us to hypothesize that such regulatory control—similar to abortive infection mechanisms—can be advantageous by limiting viral spread through suicide of infected cells. To test this hypothesis, we mathematically model CRISPR induced prokaryote-phage coevolutionary dynamics in the presence of infection-regulated CRISPR activity. Our results indicate that, except in limited growth rates, regulated CRISPRs exploit both autoimmunity and target restriction and can therefore be considered a hybrid class that leverages both restriction and suicide mechanisms to limit phage infection.

Structural, optical and electronic properties of homoepitaxial GaN nanowalls grown on GaN template by laser molecular beam epitaxy

We have grown homoepitaxial GaN nanowall networks on GaN template using an ultra-high vacuum laser assisted molecular beam epitaxy system by ablating solid GaN target under a constant r.f. nitrogen plasma ambient.

Sesamol induces apoptosis in human platelets via reactive oxygen species-mediated mitochondrial damage

Platelets play an indispensable role in human health and disease. Platelets are very sensitive to oxidative stress, as it leads to the damage of mitochondrial DNA, which is the initial step of a sequence of events culminating in the cell death through the intrinsic pathway of apoptosis. Owing to a lot of reports on secondary complications arising from oxidative stress caused by therapeutic drug overdose, the present study concentrated on the influence of sesamol on oxidative stress-induced platelet apoptosis. Sesamol, a phenolic derivative present in sesame seeds is an exceptionally promising drug with lots of reports on its protective functions, including its inhibitory effects on platelet aggregation at concentrations below 100 μM, and its anti-cancer effect at 1 mM. However, the present study explored the toxic effects of sesamol on human platelets. Sesamol at the concentration of 0.25 mM and above induced platelet apoptosis through endogenous generation of ROS, depletion of thiol pool, and Ca(2+) mobilization. It also induced mitochondrial membrane potential depolarization, caspase activation, cytochrome c translocation and phosphatidylserine exposure, thus illustrating the pro-apoptotic effect of sesamol at higher concentration. However, even at high concentration of 2 mM sesamol effectively inhibited collagen/ADP/epinephrine-induced platelet aggregation. The study demonstrates that even though sesamol inhibits platelet aggregation, it has the tendency to elicit platelet apoptosis at higher concentrations. Sesamol has a potential as thrombolytic agent, nevertheless the current work highlights the significance of an appropriate dosage of sesamol when it is used as a therapeutic drug.

Iterative method of baffle design for modified Ritchey-Chretien telescope

We developed a baffle design method based on a combination of the results of optical design software and analytical relations formulated herein. The method finds the exact solution for baffle parameters of a modified Ritchey-Chretien telescope by iteratively solving the analytical relations using the actual ray coordinates of the telescope computed with the aid of optical design software. The baffle system so designed not only blocks the direct rays of stray light reaching the image plane but also provides minimum obscuration to imaging light. Based on the iterative method, we proposed a baffle design approach for a rectangular-image-format telescope.

Hemostatic interference of Indian king cobra (Ophiophagus hannah) Venom. Comparison with three other snake venoms of the subcontinent

Unlike Naja naja, Bungarus caeruleus, Echis carinatus, and Daboia/Vipera russellii venoms, Ophiophagus hannah venom is medically ignored in the Indian subcontinent. Being the biggest poisonous snake, O. hannah has been presumed to inject several lethal doses of venom in a single bite. Lack of therapeutic antivenom to O. hannah bite in India makes any attempt to save the victim a difficult exercise. This study was initiated to compare O. hannah venom with the above said venoms for possible interference in hemostasis. Ophiophagus hannah venom was found to actively interfere in hemostatic stages such as fibrin clot formation, platelet activation/aggregation, and fibrin clot dissolution. It decreased partial thromboplastin time (aPTT), prothrombin time (PT), and thrombin clotting time (TCT). These activities are similar to that shown by E. carinatus and D. russellii venoms, and thus O. hannah venom was found to exert procoagulant activity through the common pathway of blood coagulation, while N. naja venom increased aPTT and TCT but not PT, and hence it was found to exert anticoagulant activity through the intrinsic pathway. Venoms of O. hannah, E. carinatus, and D. russellii lack plasminogen activation property as they do not hydrolyze azocasein, while they all show plasmin-like activity by degrading the fibrin clot. Although N. naja venom did not degrade azocasein, unlike other venoms, it showed feeble plasmin-like activity on fibrin clot. Venom of E. carinatus induced clotting of human platelet rich plasma (PRP), while the other three venoms interfered in agonist-induced platelet aggregation in PRP. Venom of O. hannah least inhibited the ADP induced platelet aggregation as compared to D. russellii and N. naja venoms. All these three venoms showed complete inhibition of epinephrine-induced aggregation at varied doses. However, O. hannah venom was unique in inhibiting thrombin induced aggregation.