Speckle-based deep learning approach for classification of orbital angular momentum modes.

We present a speckle-based deep learning approach for orbital angular momentum (OAM) mode classification. In this method, we have simulated the speckle fields of the Laguerre-Gauss (LG), Hermite-Gauss (HG), and superposition modes by multiplying these modes with a random phase function and then taking the Fourier transform. The intensity images of these speckle fields are fed to a convolutional neural network (CNN) for training a classification model that classifies modes with an accuracy >99%. We have trained and tested our method against the influence of atmospheric turbulence by training the models with perturbed LG, HG, and superposition modes and found that models are still able to classify modes with an accuracy >98%. We have also trained and tested our model with experimental speckle images of LG modes generated by three different ground glasses. We have achieved a maximum accuracy of 96% for the most robust case, where the model is trained with all simulated and experimental data. The novelty of the technique is that one can do the mode classification just by using a small portion of the speckle fields because speckle grains contain the information about the original mode, thus eliminating the need for capturing the whole modal field, which is modal dependent.

Bradyrhizobium arachidis mediated enhancement of (oxy)matrine content in the medicinal legume Sophora flavescens.

Effect of rhizobial inoculation and nitrate application on the content of bioactive compounds in legume plants is an interesting aspect for interactions among microbes, plants and chemical fertilizers, as well as for cultivated practice of legumes. In this study, nitrate (0, 5 and 20 mmol l-1 ) and Bradyrhizobium arachidis strain CCBAU 051107T were applied, individually or in combination, to the root rhizosphere of the medicinal legume Sophora flavescens Aiton (SFA). Then the plant growth, nodulation and active ingredients including (oxy)matrine of SFA were determined and compared. Rhizobial inoculation alone significantly increased the numbers and fresh weight of root nodules. Nodulation was significantly inhibited due to nitrate (5 and 20 mmol l-1 ). Only oxymatrine was detected in the control plants without rhizobial inoculation and nitrate supplement, while both oxymatrine and matrine were synthesized in plants treated with inoculation of B. arachidis or supplied with nitrate. The content of oxymatrine was the highest in plants inoculated solely with rhizobia and was not significantly altered by additional application of nitrate. Combinations of B. arachidis inoculation and different concentrations of nitrate did not significantly change the concentrations of (oxy)matrine in the plant. In conclusion, sole rhizobial inoculation was the best approach to increase the contents of key active ingredients oxymatrine and matrine in the medicinal legume SFA.

Optical-vortex diagnostics via Fraunhofer slit diffraction with controllable wavefront curvature.

Far-field slit diffraction of circular optical-vortex (OV) beams is efficient for measurement of the topological charge (TC) magnitude but does not reveal its sign. We show that this is because in the common diffraction schemes the diffraction plane coincides with the incident OV waist plane. Based on the examples of Laguerre-Gaussian incident beams containing a spherical wavefront component, we demonstrate that the far-field diffracted beam profile possesses an asymmetry depending on the incident wavefront curvature and the TC sign. This finding enables simple and efficient ways for the simultaneous diagnostics of the TC magnitude and sign, which can be useful in many OV applications, including OV-assisted metrology and information processing.

Rheological, physico-sensory and antioxidant properties of punicic acid rich wheat bread.

Punicic acid (PA), a predominant fatty acid (85%) in pomegranate seeds, also called as an ω-5 fatty acid, is known to render various health beneficial effects to humans. The objective of this study was to prepare and observe the effect of replacement of wheat flour with 5-12.5% punicic acid rich pomegranate seed powder (PSP, 9XXX fraction) on rheological, physico-sensory and antioxidant properties of bread. The increasing amount of PSP caused decrease in farinograph water absorption capacity, dough stability; amylograph peak viscosity; bread volume and overall quality score, whereas crumb hardness was increased. The combination of additives (CA) showed significant improvement in dough strength, texture and quality of bread with 10% PSP. The total polyphenol content (TPP) and radical scavenging activity (RSA) increased by 10- to 30-fold while PA was increased to 60-fold when compared to control. The recovery of PA from bread samples was in range of 45-60% and further increased by the addition of CA (65%). Hence, 10% PSP bread having 60% recovery of PA can be successfully considered for formulations without altering the rheological and sensory quality of bread. These results reveal that PA rich PSP prepared from a fruit industry by-product can be utilized for preparing antioxidant rich functional bread which also helps in overall improvement of bone health.

Tunable ultraviolet vortex source based on a continuous-wave optical parametric oscillator.

We report a continuous-wave (cw) optical parametric oscillator (OPO) generating optical vortices tunable in the ultraviolet (UV). Based on MgO:sPPLT as the nonlinear crystal, the singly resonant OPO is pumped by a cw vortex beam in the green, and deploying intracavity sum-frequency generation (SFG) between the undepleted pump and the Gaussian resonant signal in the crystal of BiB3O6, it can generate optical vortices of order, luv=1 and 2, tunable across 332-344 nm in the UV with a maximum power of 12 mW. Due to conservation of orbital angular momentum in the parametric process, the OPO also produces a non-resonant idler output beam in a vortex spatial profile of order li=1 and 2, identical to the pump vortex, with the signal beam in Gaussian distribution. The idler vortex is tunable across 1172-1338 nm with maximum output power of 1.3 W.

Grape berry surface bacterial microbiome: impact from the varieties and clones in the same vineyard from central China.

AIMS: Bacterial microbiome on grape berry surface may play an important role in grape quality and health. This study aims to investigate the impact of grape varieties and clones on grape berry surface bacterial microbiome from the same vineyard. METHODS AND RESULTS: High-throughput sequencing strategy was used to investigate the bacterial diversity and abundance on the grape surfaces of 12 clones belonging to six varieties grown in the same vineyard of Zhengzhou Fruit Research Institute in Henan Province. In total, 45 bacterial phyla and 933 genera were detected from all samples. Cyanobacteria, Proteobacteria and Firmicutes were the most abundant and prevalent phyla, while Bacteroidetes, Chloroflexi, Acidobacteria and Planctomycetes were grape clone specific phyla. The nonrank genus from phylum Cyanobacteria occupied 30-81% of grape clones from Italian Riesling (GRX), Cabernet Franc (PLZ), Pinot Blanc (BBN) and Riesling (LSL). Interestingly, Bacillus, Pseudomonas and Lactococcus were the only three prevalent genera found on all the clones. Furthermore, the predicted functional activities of grape surface bacterial communities varied according to the clones. CONCLUSIONS: The present study revealed that in addition to the grape varieties, the variations in grape clone background may also affect the bacterial microbiome on grape surfaces which may ultimately determine their functional activities. SIGNIFICANCE AND IMPACT OF THE STUDY: This research provides an important information for grape planting and wine fermentation that not only the grape varieties need to be paid attention but also grape clones from the specific variety need to be concerned.

Direct transfer of pump amplitude to parametric down-converted photons.

In general, the spatial distribution of individual photons (signal or idler) generated by spontaneous parametric down-conversion (SPDC) does not evidently show any particular spatial mode structure because of their randomness in generation and the incoherent nature. Here, we numerically showed that all individual photons generated by the SPDC process carry the transverse amplitude as that of the pump and then confirmed it experimentally. The pump amplitude is revealed in SPDC when individual photons are spatially filtered from the total SPDC distribution. This is observed simply by imaging the photons that are filtered using a minimum-sized aperture. The phase measurements showed that the observed mode distribution does not possess the transverse phase distribution as that of the pump.

Investigation of propagation dynamics of truncated vector vortex beams.

In this Letter, we experimentally investigate the propagation dynamics of truncated vector vortex beams generated using a Sagnac interferometer. Upon focusing, the truncated vector vortex beam is found to regain its original intensity structure within the Rayleigh range. In order to explain such behavior, the propagation dynamics of a truncated vector vortex beam is simulated by decomposing it into the sum of integral charge beams with associated complex weights. We also show that the polarization of the truncated composite vector vortex beam is preserved all along the propagation axis. The experimental observations are consistent with theoretical predictions based on previous literature and are in good agreement with our simulation results. The results hold importance as vector vortex modes are eigenmodes of the optical fiber.

Time-Reversal Symmetry Breaking in Re-Based Superconductors.

To trace the origin of time-reversal symmetry breaking (TRSB) in Re-based superconductors, we performed comparative muon-spin rotation and relaxation (µSR) studies of superconducting noncentrosymmetric Re_{0.82}Nb_{0.18} (T_{c}=8.8 K) and centrosymmetric Re (T_{c}=2.7 K). In Re_{0.82}Nb_{0.18}, the low-temperature superfluid density and the electronic specific heat evidence a fully gapped superconducting state, whose enhanced gap magnitude and specific-heat discontinuity suggest a moderately strong electron-phonon coupling. In both Re_{0.82}Nb_{0.18} and pure Re, the spontaneous magnetic fields revealed by zero-field µSR below T_{c} indicate time-reversal symmetry breaking and thus unconventional superconductivity. The concomitant occurrence of TRSB in centrosymmetric Re and noncentrosymmetric ReT (T=transition metal), yet its preservation in the isostructural noncentrosymmetric superconductors Mg_{10}Ir_{19}B_{16} and Nb_{0.5}Os_{0.5}, strongly suggests that the local electronic structure of Re is crucial for understanding the TRSB superconducting state in Re and ReT. We discuss the superconducting order parameter symmetries that are compatible with the experimental observations.

Rapid visual isothermal nucleic acid-based detection assay of Brucella species by polymerase spiral reaction.

AIM: The aim of this study was to develop polymerase spiral reaction (PSR) for rapid, sensitive and specific detection of Brucella sp. METHODS AND RESULTS: Polymerase spiral reaction assay was developed using specifically designed primers targeting the conserved multicopy IS711 gene of Brucella sp. The assay could be performed within 60 min at an isothermal temperature of 64°C. The lower limit of detection of PSR was 11·8 fg and conventional PCR was 1·18 pg of Brucella abortus genomic DNA. Thus, PSR was found to be 100-fold more sensitive than conventional PCR and was comparable to real-time PCR. The specificity of PSR was tested with other non-Brucella bacteria and also with some bacterial and viral pathogens causing abortions. The assay was found to be specific as it did not detect any putative pathogens other than Brucella sp. Fifty-six clinical samples suspected for brucellosis (aborted fetal stomach content) were screened with PSR to validate the applicability of the test to detect Brucella DNA. The same samples were also screened with conventional PCR and real-time PCR. Of 56 samples, 25 samples were found to be positive with both PSR as well as real-time PCR, whereas only 20 samples were found positive with conventional PCR. CONCLUSIONS: The results of this study indicated that the PSR assay is a simple, rapid, sensitive and specific method for the detection of Brucella sp. that may improve diagnostic potential in clinical laboratories or can be used at diagnostic laboratories with minimal infrastructure. SIGNIFICANCE AND IMPACT OF THE STUDY: The PSR assay, because of its simplicity and low cost, can be preferred to other molecular methods in the diagnosis of infectious diseases.

Rhizobial biogeography and inoculation application to soybean in four regions across China.

AIMS: The aim of the study was to survey rhizobial biogeography and to inoculate soybean with selected rhizobia in China to enhance symbiotic nitrogen fixation (SNF). METHODS AND RESULTS: Biogeography, genetic diversity and phylogeny of soybean rhizobia were surveyed. Inocula were prepared and applied to soybean. Results showed that Bradyrhizobium elkanii and Ensifer fredii were widely distributed in acid and alkaline soils respectively. Available iron was detected as the first determinant for distribution of the two rhizobia and the soybean varieties did not greatly affect the rhizobial compatibility. Geographical latitude and precipitation in June were the main geographical and climatic factors affecting the rhizobial distribution. Inoculation with selected rhizobia increased the nodule number, fresh weight, occupation ratio, seed protein content and soybean yields. CONCLUSIONS: Selection and application of effective soybean rhizobia across China according to biogeography were clarified to promote the SNF, thereby improving soybean yield. SIGNIFICANCE AND IMPACT OF THE STUDY: Rhizobial diversity and biogeography were evaluated systematically in six sites across China. Available iron and soil pH are found to be the most important determinants for the distribution of soybean rhizobia. Inoculation to soybean enhances SNF, positively correlating to the increase in soybean yield and seed protein content.

Baculovirus expression and purification of peste-des-petits-ruminants virus nucleocapsid protein and its application in diagnostic assay.

Peste-des-petits-ruminants (PPR) is a contagious and highly devastating disease of small ruminants. For control of endemic PPR, adequate supply of affordable and reliable diagnostics is critical for effective surveillance, along with the use of highly efficacious live vaccines that are currently available. The nucleocapsid (N) protein of PPR virus (PPRV) is an important candidate antigen for developing specific diagnostic, as it is a major viral protein being highly immunogenic and conserved among the structural proteins. In the present study, we expressed the N protein of PPRV (Sungri/96 strain), in baculovirus expression system and purified using affinity column chromatography. The recombinant protein reacted well with PPRV anti-N monoclonal antibodies and PPRV-specific polyclonal antiserum, suggesting that the expressed protein was authentic and in native form. The recombinant protein was evaluated as antigen in the diagnostic ELISA as reference positive control in place of whole virus antigen. The utility of recombinant PPRV N protein circumvents the need to use live PPRV antigen in the routinely used diagnostics targeting 'N' protein of PPRV, thus allowing large-scale field application of the test.

Characterization of Leaf Rust and Stripe Rust Resistance in Spring Wheat 'Chilero'.

Since 1984, the 'Chilero' spring wheat line developed by CIMMYT has proven to be highly resistant to leaf rust and stripe rust. Amid efforts to understand the basis of resistance of this line, a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero was studied. The parents and RILs were characterized in field trials for leaf rust and stripe rust in three locations in Mexico between 2012 and 2015 and genotyped with DArT-array, DArT-GBS, and SSR markers. A total of 6,168 polymorphic markers were used to construct genetic linkage maps. Inclusive composite interval mapping detected four colocated resistance loci to both rust diseases and two stripe rust resistant loci in the Avocet × Chilero population. Among these, the quantitative trait locus (QTL) on chromosome 1BL was identified as a pleotropic adult plant resistance gene Lr46/Yr29, whereas QLr.cim-5DS/QYr.cim-5DS was a newly discovered colocated resistance locus to both rust diseases in Chilero. Additionally, one new stripe rust resistance locus on chromosome 7BL was mapped in the current population. Avocet also contributed two minor colocated resistance QTLs situated on chromosomes 1DL and 4BS. The flanking SNP markers can be converted to breeder friendly Kompetitive Allele Specific PCR (KASP) markers for wheat breeding programs.

Scattering of Poincaré beams: polarization speckles.

Polarization speckle is a fine granular light pattern having spatially varying random polarization profile. We generate these speckle patterns by using the scattering of Poincaré beams, a special class of vector vortex beams, through a ground glass plate. Here, the Poincaré beams are generated using a polarization sensitive spatial light modulator displaying an on-axis hologram corresponding to an optical vortex phase profile. The different inhomogeneities of the rough surface experience different polarizations, which control the ability for scattered waves to interfere at the detection plane and causes a spatially varying polarization profile. We experimentally determined the spatial variation of local degree of polarization and orientation of the polarization ellipse for these speckle patterns from the Stokes analysis. We also determined the size of scalar speckles using the auto-correlation function of Stokes parameter S0 and the size of polarization speckles using the sum of auto-correlation functions of remaining three Stokes parameters. We found that the change in scalar speckle size with the index of the vector beam is very small and of the order of 1 pixel size of the camera but the size of polarization speckles decreases with the increase in index of the vector beam.

Continuous-wave, singly resonant parametric oscillator-based mid-infrared optical vortex source.

We report on a high-power, continuous-wave source of optical vortices tunable in the mid-infrared (mid-IR) wavelength range. Using the orbital angular momentum (OAM) conservation of the parametric processes and the threshold conditions of the cavity modes of the singly resonant optical parametric oscillator (SRO), we have transferred the OAM of the pump beam at the near-infrared wavelength to the idler beam tunable in the mid-IR. Pumped with a vortex beam of order lp=1 at 1064 nm, the SRO, configured in a four curved mirror-based ring cavity with a 50 mm long MgO-doped periodically poled LiNbO3 crystal, produces an idler beam with an output power in excess of 2 W in a vortex spatial profile with the order li=1, tunable across 2217-3574 nm and corresponding signal beam in Gaussian intensity distribution across 1515-2046 nm. For pump vortices of the order lp=1 and 2, and a power of 22 W, the SRO produces idler vortices of the same order as that of the pump beam with a maximum power of 5.23 and 2.3 W, corresponding to near-IR to mid-IR vortex conversion efficiency of 23.8% and 10.4%, respectively. The idler vortex beam has a spectral width, and a passive rms power stability of 101 MHz and 4.9% over 2 h, respectively.

Topological structures in vector speckle fields.

We here demonstrate on both theoretical and experimental bases a method to recover the topological structure of a monochromatic optical field that has suffered diffuse transmission. This method consists of two steps: first, a linearly polarized sample beam is mixed with a coaxial Gaussian beam in orthogonal polarization states resulting in a Poincaré beam; second, a polarization-related spatial correlation function is considered and measured for the overall speckle field arising by optical diffusion. The singularities of the sample beam turn out to be imaged into the correlation function of the vector speckle field.

Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography.

Peste des petits ruminants is an important transboundary disease infecting small ruminants. Genome or gene sequence analysis enriches our knowledge about the evolution and transboundary nature of the causative agent of this disease, peste des petits ruminants virus (PPRV). Although analysis using whole genome sequences of pathogens leads to more precise phylogenetic relationships, when compared to individual genes or partial sequences, there is still a need to identify specific genes/genomic regions that can provide evolutionary assessments consistent with those predicted with full-length genome sequences. Here the virulent Izatnagar/94 PPRV isolate was assembled and compared to all available complete genome sequences (currently in the NCBI database) to estimate nucleotide diversity and to deduce evolutionary relationships between genes/genomic regions and the full length genomes. Our aim was to identify the preferred candidate gene for use as a phylogenetic marker, as well as to predict divergence time and explore PPRV phylogeography. Among all the PPRV genes, the H gene was identified to be the most diverse with the highest evolutionary relationship with the full genome sequences. Hence it is considered as the most preferred candidate gene for phylogenetic study with 93% identity set as a nucleotide cutoff. A whole genome nucleotide sequence cutoff value of 94% permitted specific differentiation of PPRV lineages. All the isolates examined in the study were found to have a most recent common ancestor in the late 19th or in the early 20th century with high posterior probability values. The Bayesian skyline plot revealed a decrease in genetic diversity among lineage IV isolates since the start of the vaccination program and the network analysis localized the ancestry of PPRV to Africa.

Synthesis, characterization of nano-sized anatase TiO2 and its adsorption behaviour for environmental contaminant.

TiO2 is one of the most studied material due to its unique properties like chemical stability, non toxicity and cost effectiveness.  Nano-sized TiO2   has been prepared by sol -gel method using titanium butoxide as precursor. X- ray diffraction analysis was used to characterize the phase and crystal size of the synthesized TiO2 particles. It was found that sizes of the particles ranged from 6 to 12 nanometre. FT-IR spectrum was also recorded for the TiO2  particles to detect the remaining organic residue .Heavy metals like Cr, Cu, Fe, Ni etc are considered major environmental contaminant in water due to their non biodegradable nature and adverse health effect in living beings. In this work the adsorption behavior of heavy metals towards nano-sized TiO2 was investigated.

Identification and Mapping of Adult Plant Resistance Loci to Leaf Rust and Stripe Rust in Common Wheat Cultivar Kundan.

Leaf rust (LR) and stripe rust (YR) are important diseases of wheat worldwide. We used 148 recombinant inbred lines (RIL) from the cross of Avocet × Kundan for determining and mapping the genetic basis of adult plant resistance (APR) loci. The population was phenotyped LR and YR for three seasons in field trials conducted in Mexico and genotyped with the diversity arrays technology sequencing (DArT-Seq) and simple sequence repeat markers. The final genetic map was constructed using 2,937 polymorphic markers with an average distance of 1.29 centimorgans between markers. Inclusive composite interval mapping identified two co-located APR quantitative trait loci (QTL) for LR and YR, two LR QTL, and three YR QTL. The co-located resistance QTL on chromosome 1BL corresponded to the pleiotropic APR gene Lr46/Yr29. QLr.cim-2BL, QYr.cim-2AL, and QYr.cim-5AS could be identified as new resistance loci in this population. Lr46/Yr29 contributed 49.5 to 65.1 and 49.2 to 66.1% of LR and YR variations, respectively. The additive interaction between detected QTL showed that LR severities for RIL combining four QTL ranged between 5.3 and 25.8%, whereas the lowest YR severities were for RIL carrying QTL on chromosomes 1BL + 2AL + 6AL. The high-density DArT-Seq markers across chromosomes can be used in fine mapping of the targeted loci and development SNP markers.

Aspergillus niger PA2: a novel strain for extracellular biotransformation of L-tyrosine into L-DOPA.

L-DOPA (3,4-dihydroxyphenyl-L-alanine), an amino acid derivative is the most widely used drug of choice for the treatment of Parkinson's disease and other neurologic injuries. The present study deals with the elevated biochemical transformation of L-tyrosine to L-DOPA by Aspergillus niger PA2, a potent tyrosinase producer, isolated from decomposed food wastes. This appears to be the first report on A. niger as a notable extracellular tyrosinase producer. The extracellular tyrosinase activity produced remarkably higher levels of L-DOPA, i.e. 2.44 mg mL(-1) when the media was supplemented with 5 mg mL(-1) L-tyrosine. The optimum pH for tyrosinase production was 6.0, with the maximal L-DOPA production at the same pH. The product thus produced was analyzed by thin-layer chromatography, UV spectroscopy, high-performance liquid chromatography and Fourier transform infrared spectroscopy, that had denoted this to be L-DOPA. Kinetic parameters viz. Y p/s, Q s and Q p had further indicated the notable levels of production. Thus, Aspergillus niger PA2 could be a promising resource and may be further exploited for large-scale production of L-DOPA.