CDH1 gene as biomarker towards breast cancer prediction.

Breast cancer is considered to be happened due to genetic aberration. Out of several genes expressed, it is found that cadherin 1, type 1 (CDH1) is responsible in several ways to control the metabolic order in human. Deregulation of the function of protein E-cadherin, expressed from CDH1 plays an important role in lobular breast cancer. In order to understand the root cause of this recent claim, we focus on CDH1 gene: whether the genetic information translated due to any deviation/alteration/modification in its sequence is related to the occurrence of the different types breast cancer. Towards this end, quantitative analysis of different biophysical and bio-chemical properties of CDH1 gene in genomic and proteomic levels from the available genomic (cDNA) sequences of CDH1 gene (obtained from the COSMIC Database for 78 patients, suffering from various types of breast cancer) clearly emphasizes that alternation/modification in the sequence of the CDH1 gene can be detrimental. Furthermore, Random forest, K-nearest neighbour and stochastic gradient descent (SGD) algorithms are applied on the derived dataset to classify the types of breast cancer, and to validate our hypothesis regarding the acute role of CDH1 as potential bio marker for breast cancer. Analysis of the mutated CDH1 gene sequences, and their related parameters using aforesaid machine learning techniques clearly establish that CDH1 gene can take the deterministic role in predicting the chances of occurrences of different types of breast cancer with an accuracy of >90%. Such an observation opens a new paradigm in diagnostic approach of breast cancer.Communicated by Ramaswamy H. Sarma.

Polarization independent grating in a GaN-on-sapphire photonic integrated circuit.

In this work, we report the realization of a polarization-insensitive grating coupler, single-mode waveguide, and ring resonator in the GaN-on-sapphire platform. We provide a detailed demonstration of the material characterization, device simulation, and experimental results. We achieve a grating coupler efficiency of -5.2 dB/coupler with a 1 dB and 3 dB bandwidth of 40 nm and 80 nm, respectively. We measure a single-mode waveguide loss of -6 dB/cm. The losses measured here are the lowest in a GaN-on-sapphire photonic circuit. This demonstration provides opportunities for the development of on-chip linear and non-linear optical processes using the GaN-on-sapphire platform. To the best of our knowledge, this is the first demonstration of an integrated photonic device using a GaN HEMT stack with 2D electron gas.

Analysing the genetic code degeneracy: a consequence towards bacterial staining.

As 20 naturally occurring amino acids are coded by 61 mRNA codons out of 64, it is obvious that 61→20 cannot have one-to-one mapping which generates the problem of codon degeneracy. Despite several efforts there is no specific outcome which can describe this well-known enigmatic degeneracy of the codon table. Since, every biological behaviour is regulated by protein which in turn consists of amino acids bearing the inherent characteristics of degeneracy among mRNA codons (Crick F.H.C. The Origin of the Genetic Code. J. Mol. Biol.1968; 38: 367-379), it is worthy to analyse the impact of such degeneracy on biological behaviours. Here, based on mathematical models using the concept of b-type of the nucleotide bases and hamming distances, an effort has been initiated to understand the impact of biasness of genetic code degeneracy on biological behaviours. The proposed models have been utilized to understand the characteristic features of bacterial genes of gram-positive and gram-negative bacteria. To the best of our knowledge, this is the first mathematical model to capture the effect of genetic code degeneracy, showing a paradigm towards understanding the behavioural difference between gram-positive and gram-negative bacteria, and thereby opening a new avenue for revealing differential biological properties.Communicated by Ramaswamy H. Sarma.

Thin-film wafer-scale mid-IR Fabry Perot cavity gas sensor.

We demonstrate a miniaturized wafer-scale optical gas sensor that combines the gas cell, an optical filter, and integrated flow channels. We present the design, fabrication and characterization of an integrated cavity-enhanced sensor. Using the module, we demonstrate absorption sensing of ethylene down to 100 ppm level.

An Explainable AI driven Decision Support System for COVID-19 Diagnosis using Fused Classification and Segmentation.

The coronavirus has caused havoc on billions of people worldwide. The Reverse Transcription Polymerase Chain Reaction(RT-PCR) test is widely accepted as a standard diagnostic tool for detecting infection, however, the severity of infection can't be measured accurately with RT-PCR results. Chest CT Scans of infected patients can manifest the presence of lesions with high sensitivity. During the pandemic, there is a dearth of competent doctors to examine chest CT images. Therefore, a Guided Gradcam based Explainable Classification and Segmentation system (GGECS) which is a real-time explainable classification and lesion identification decision support system is proposed in this work. The classification model used in the proposed GGECS system is inspired by Res2Net. Explainable AI techniques like GradCam and Guided GradCam are used to demystify Convolutional Neural Networks (CNNs). These explainable systems can assist in localizing the regions in the CT scan that contribute significantly to the system's prediction. The segmentation model can further reliably localize infected regions. The segmentation model is a fusion between the VGG-16 and the classification network. The proposed classification model in GGECS obtains an overall accuracy of 98.51 % and the segmentation model achieves an IoU score of 0.595.

Valorization of rice biomass by a green approach to release phenolic compounds and their antioxidant activities.

In the present context, we have assessed the green approach for the extraction of phenolics from agro-residues of rice viz., rice bran, and rice straw using water as an extracting solvent. The extraction was optimized with respect to time, temperature, pH, and solid (agro-residues) to liquid (water) ratio. The hydrolysates obtained were determined for phenolics and their antioxidant activities. The maximum total phenolic content (61.32 mg/100 g GAE), flavonoid content (13.19 mg/100 g QE), and tannin content (58.33 mg/100 g TAE) were obtained for rice bran followed by rice straw at pH 5, 1:20 (solid: liquid) for 10 min of extraction. Also, higher antioxidant properties (78.03% for DPPH, 86.45% for ABTS, and 0.85 absorbance at 700 nm for FRAP) were observed for the extracts of rice bran. Caffeic acid, gallic acid, p-coumaric acid, syringic acid, ferulic acid, 2,5-dihydroxy benzoic acid, kaemferol, quercetin, and epicatechin were analyzed by HPLC in both the rice biomass used. This study significantly converts rice biomass to antioxidative phenolic compounds under simple extraction conditions favoring the waste management process and also adding value to the waste biomass.

Guided mode resonance aided polarization insensitive in-plane spectral filters for an on-chip spectrometer.

We demonstrate an on-chip in-plane polarization independent multi-spectral color filter in the visible to near-infrared wavelength band. We experimentally show a four-channel transmission and in-plane spectral filter characteristics spanning a 400-nm spectral range. Engineered 2D guided mode resonance structures in a silicon nitride-on-sapphire substrate are used to realize the filters. The in-plane color filters could provide the necessary impetus for developing robust integrated photonic platforms for on-chip devices and applications.

Polar Semiconducting Scandium Nitride as an Infrared Plasmon and Phonon-Polaritonic Material.

The interaction of light with collective charge oscillations, called plasmon-polariton, and with polar lattice vibrations, called phonon-polariton, are essential for confining light at deep subwavelength dimensions and achieving strong resonances. Traditionally, doped-semiconductors and conducting metal oxides (CMO) are used to achieve plasmon-polaritons in the near-to-mid infrared (IR), while polar dielectrics are utilized for realizing phonon-polaritons in the long-wavelength IR (LWIR) spectral regions. However, demonstrating low-loss plasmon- and phonon-polaritons in one host material will make it attractive for practical applications. Here, we demonstrate high-quality tunable short-wavelength IR (SWIR) plasmon-polariton and LWIR phonon-polariton in complementary metal-oxide-semiconductor compatible group III-V polar semiconducting scandium nitride (ScN) thin films. We achieve both resonances by utilizing n-type (oxygen) and p-type (magnesium) doping in ScN that allows modulation of carrier concentration from 5 × 1018 to 1.6 × 1021 cm-3. Our work enables infrared nanophotonics with an epitaxial group III semiconducting nitride, opening the possibility for practical applications.

On-chip silicon nano-slab photodetector integrated wavelength division de-multiplexer in the 850 nm band.

We present an on-chip photodetector integrated wavelength filter on a SiN-on-silicon-on-insulator (SOI) platform in the 850 nm wavelength window. The wavelength filter is designed using an echelle grating with a distributed Bragg reflector as the grating reflectors. We present the design and experimental realization of a six-channel wavelength filter with a channel spacing of 10 nm. Experimentally, we achieve an insertion loss of 4.3 dB and an adjacent channel cross talk of 22 dB. We demonstrate a silicon nano-slab waveguide integrated metal-semiconductor-metal photodetector with a maximum responsivity of 0.56 A/W and dark current of 217 nA. Furthermore, we demonstrate the integration of the echelle grating with the detector and show the feasibility of a CMOS compatible SiN-on-SOI platform for various applications, including short-reach communication and sensing applications.

Comprehensive grating enabled silicon nitride fiber-chip couplers in the SNIR wavelength band.

We present silicon nitride grating enabled fiber-chip coupling in the sub-near-infrared band. We present a comprehensive design and simulation and experimental demonstration of uniform and apodized grating couplers, with and without bottom reflectors. The mode engineering yields a best efficiency of -1.6 dB for apodized grating design, which is further improved to -0.66 dB with a bottom reflector. Experimentally, we demonstrate a coupling efficiency of -2.2 dB for the optimized design. Furthermore, we present a detailed simulation and measurement comparison of various grating parameters and the effect of fabrication tolerances on the grating performance.

High-efficiency vertical fibre-to-polymer waveguide coupling scheme for scalable polymer photonic circuits.

Polymer photonic circuits offer a versatile platform for various applications, including communication, sensing and optical signal processing. Though polymers offer broadband, linear and nonlinear optical properties, the coupling between an optical fibre and a polymer waveguide has been a challenge. In this work, we propose and demonstrate a wafer-scale vertical coupling scheme for polymer waveguides. The scheme uses a silicon nitride grating coupler with an inverse taper to couple between an optical fibre and a SU8 polymer waveguide. We demonstrate a maximum coupling efficiency of -3.55 dB in the C-band and -2.92 dB in the L-band with a 3-dB bandwidth of 74 and 80 nm, respectively. A detailed design and simulation, fabrication, and characterisation results are presented. The scheme demonstrates a scalable and efficient surface grating approach for polymer photonic integrated circuits.

Livelihood Vulnerability to Flood Hazard: Understanding from the Flood-prone Haor Ecosystem of Bangladesh.

Bangladesh is a country of natural disasters and climatic hazards, which frequently affect its inhabitants' lives and livelihoods. Among the various risks and disasters, floods are the most frequent hazard that makes haor households vulnerable. Therefore, this study was undertaken to estimate livelihood vulnerability to flooding within the flood-prone haor ecosystem in Bangladesh. Primary data were collected from 100 haor households each from Kishoreganj, Netrokona, and Sunamganj districts (N = 300) by applying a multistage random sampling technique. Data were collected through face-to-face interviews using a pretested structured questionnaire. The Livelihood Vulnerability Index (LVI) and the Intergovernmental Panel on Climate Change (IPCC) framework of vulnerability were applied to compare vulnerabilities among the selected haor-based communities. The empirical results revealed that haor households in Sunamganj district were more vulnerable to flood hazard and natural disaster in terms of food, water, and health than households in the other two districts. Taking into account the major components of the LVI, the IPCC framework of vulnerability indicated that households in Sunamganj district were the most vulnerable due to their lowest adaptive capacity and highest sensitivity and exposure. These findings enable policymakers to formulate and implement effective strategies and programs to minimize vulnerability and enhance resilience by improving the livelihoods of the vulnerable haor households of Bangladesh, especially those in Sunamganj district.

Plastome of Saraca asoca (Detarioideae, Fabaceae): Annotation, comparison among subfamily and molecular typing.

Saraca asoca (Roxb.) Willd. (subfamily Detarioideae, family Fabaceae) is a perennial evergreen sacred medicinal tree classified under 'vulnerable' by the IUCN. The chloroplast (cp) genome/plastome which follows uniparental inheritance contains many useful genetic information because of its conservative rate of evolution. The assembled cp genome of S. asoca which maps as a conserved circular structure revealed extensive rearrangement in gene organization, comprising total length 160,003 bp including LSC, SSC, IRa, and IRb, and GC content was 35.26%. Herein a set of rbcL and matK gene were established using molecular phylogenetic analyses for molecular typing of S. asoca.

On-chip silicon photonics based grating assisted vibration sensor.

We present a compact, highly sensitive and scalable on-chip photonic vibration measurement scheme for vibration sensing. The scheme uses a silicon photonic diffraction-grating based sensor integrated underneath a silicon cantilever. We demonstrate a static and dynamic measurement sensitivity (ΔT/Δgap) of 0.6 % change in intensity per nm displacement. The electrostatically driven dynamic response measurement of the grating based sensor shows an excellent agreement with commercial Laser Doppler Vibrometer (LDV) measurement. We demonstrate the thermo-mechanical noise measurement on the cantilever in ambience, which is verified using LDV. A minimum displacement of 1.9 pm is measured with a displacement sensitivity of 10 µW/nm for a measurement bandwidth of 16 Hz. The demonstrated sensitivity is 2 orders of magnitude better than that obtained from measurements of static displacement. We also present a detailed 2D-FDTD simulation and optimization of the grating-based sensor to achieve maximum displacement sensitivity.

Purification, Biochemical Characterization, and Facile Immobilization of Laccase from Sphingobacterium ksn-11 and its Application in Transformation of Diclofenac.

An extracellular laccase enzyme secreted from Sphingobacterium ksn-11 was purified to electrophoretic homogeneity, showing a molecular weight of 90 kDa. The purified enzyme was monomeric in nature confirmed by sodium dodecyl gel electrophoresis. The optimum temperature and pH were found to be 40 °C and 4.5 respectively. The enzyme showed highest substrate specificity for 2,2 azino-bis (ethylthiozoline-6-sulfonate) (ABTS), followed by syringaldazine. The Km value for ABTS was 2.12 mM with a Vmax value of 33.33 U/mg which was higher when compared with syringaldazine and guaiacol substrates. Sodium azide and EDTA inhibited the activity by 30%, whereas presence of Ca2+ and iron increased activity by 50%. The purified enzyme was immobilized in sodium alginate-silicon dioxide-polyvinyl alcohol beads and evaluated for diclofenac transformation studies. LC-MS analysis confirmed that immobilized laccase transformed diclofenac to 4-OH diclofenac after 4 h of incubation. 45 % of diclofenac was able to transform even at 3rd cycle of immobilized laccase use. Therefore, immobilized laccase can be used to transform or degrade several recalcitrant compounds from industrial effluents.

Publisher Correction: Purification, Biochemical Characterization, and Facile Immobilization of Laccase from Sphingobacterium ksn-11 and its Application in Transformation of Diclofenac.

The original version of this article unfortunately contained a mistake in the equation under "Immobilized Laccase Activity and its Storage Stability" section.

Enhanced nonlinear spectral broadening and sub-picosecond pulse generation by adaptive spectral phase optimization of electro-optic frequency combs.

We utilize adaptive optimization to enhance the spectral broadening of an amplified electro-optic frequency comb with a 25 GHz repetition rate in a highly nonlinear fiber and subsequently generate sub-picosecond pulses. The spectral phase of the comb is adaptively optimized by a Fourier pulse shaper in a closed control loop with the HNLF output spectrum as the process variable to be optimized. Enhanced spectral broadening also increases the stimulated Brillouin scattering threshold allowing increased power scaling and thereby boosting the bandwidth by a factor of more than 13 times over the initial comb. System versatility to varying conditions is demonstrated by achieving consistent bandwidth enhancement (nearly or more than 100 lines) in varying operating conditions that distort the temporal profile of the comb. In all cases, the optimization yields a near transform limited pulse that enters the nonlinear fiber. Sub-picosecond pulse generation is achieved with a short length of single mode fiber post the nonlinear fiber.

Microwave power induced resonance shifting of silicon ring modulators for continuously tunable, bandwidth scaled frequency combs.

We demonstrate a technique to continuously tune center frequency and repetition rate of optical frequency combs generated in silicon microring modulators and bandwidth scale them. We utilize a drive frequency dependent, microwave power induced shifting of the microring modulator resonance. In this work, we demonstrate center frequency tunability of frequency combs generated in silicon microring modulators over a wide range (∼8nm) with fixed number of lines. We also demonstrate continuously tunable repetition rates from 7.5GHz to 15GHz. Further, we use this effect to demonstrate a proof-of-principle experiment to bandwidth scale an 8-line (20dB band) comb generated from a single ring modulator driven at 10GHz to a comb with 12 and 15 lines by cascading two and three ring modulators, respectively. This is accomplished by merging widely spaced ring modulator resonances to a common location, thus coupling light simultaneously into multiple cascaded ring modulators.

Broadly tunable and low power penalty radio frequency phase shifter using a coupled silicon microcavity.

We present a continuously tunable silicon photonics assisted radio frequency (RF) phase shifter using a coupled microring resonator. Using the coupled cavity, we demonstrate a sub-1 dB power penalty for a RF bandwidth of 34.5 GHz (9-43.5 GHz) and a phase shift of π over the reported frequency range. Rigorous optimization of the cavity design using the coupled-mode theory is carried out to realize ultranarrow resonance peaks with a low-extinction ratio and large phase shift. Thermal tuning of the cavity is used to tune the phase while all-optical tuning is exploited to achieve broadband operation. We present a detailed simulation and experimental study of the proposed configuration. The proposed device configuration exhibits a configurable resonance linewidth and extinction ratio that allows for a broad bandwidth and an extremely low power penalty microwave phase shifter. We believe the demonstration would allow better integration of the on-chip functional elements of integrated microwave photonics.

Optical frequency comb based on nonlinear spectral broadening of a phase modulated comb source driven by dual offset locked carriers.

We demonstrate a versatile technique to generate a broadband optical frequency comb source in the C-band. This is accomplished by nonlinear spectral broadening of a phase modulated comb source driven by dual frequency offset locked carriers. The locking is achieved by setting up a heterodyne optical frequency locked loop to lock two phase modulated electro-optic 25 GHz frequency combs sourced from individual seed carriers offset by 100 GHz, to within 6.7 MHz of each other. We realize spectral broadening in highly nonlinear fiber after suitable amplification to obtain an equalized, nonlinearly broadened frequency comb. We obtain $\sim 86 $∼86 lines in a 20 dB band spanning over 2 THz.