Punzi-loss:: a non-differentiable metric approximation for sensitivity optimisation in the search for new particles.

We present the novel implementation of a non-differentiable metric approximation and a corresponding loss-scheduling aimed at the search for new particles of unknown mass in high energy physics experiments. We call the loss-scheduling, based on the minimisation of a figure-of-merit related function typical of particle physics, a Punzi-loss function, and the neural network that utilises this loss function a Punzi-net. We show that the Punzi-net outperforms standard multivariate analysis techniques and generalises well to mass hypotheses for which it was not trained. This is achieved by training a single classifier that provides a coherent and optimal classification of all signal hypotheses over the whole search space. Our result constitutes a complementary approach to fully differentiable analyses in particle physics. We implemented this work using PyTorch and provide users full access to a public repository containing all the codes and a training example.

Transfer of CVD-grown graphene for room temperature gas sensors.

An easy transfer procedure to obtain graphene-based gas sensing devices operating at room temperature (RT) is presented. Starting from chemical vapor deposition-grown graphene on copper foil, we obtained single layer graphene which could be transferred onto arbitrary substrates. In particular, we placed single layer graphene on top of a SiO2/Si substrate with pre-patterned Pt electrodes to realize a chemiresistor gas sensor able to operate at RT. The responses to ammonia (10, 20, 30 ppm) and nitrogen dioxide (1, 2, 3 ppm) are shown at different values of relative humidity, in dark and under 254 nm UV light. In order to check the sensor selectivity, gas response has also been tested towards hydrogen, ethanol, acetone and carbon oxide. Finally, a model based on linear dispersion relation characteristic of graphene, which take into account humidity and UV light effects, has been proposed.

Hybrid opto-chemical doping in Ag nanoparticle-decorated monolayer graphene grown by chemical vapor deposition probed by Raman spectroscopy.

The novel opto-chemical doping effect in Ag nanoparticle-decorated monolayer graphene grown by chemical vapor deposition has been investigated using Raman spectroscopy for the first time. We used both noble metal nanoparticles and optical excitation, in a hybrid opto-chemical route, to tune the doping level in graphene. Metal nanoparticle-induced chemical effects and laser power-induced substrate effects alter the doping nature of graphene from p- to n-type. Compared with earlier studies, the proposed method significantly lowers the laser intensity required for optical power-dependent doping, resulting in prevention of damage to the sample due to local heating. Some other interesting observations are the enhanced peak intensity in the Raman spectrum of graphene, enhancement of the D-band intensity and the introduction of G-band splitting. This novel, cheap and easily implemented hybrid optical-chemical doping strategy could be very useful for tuning graphene plasmons on the widely used Si/SiO2 substrates for various photonic device applications.

Photocatalytic and antibacterial activity of cadmium sulphide/zinc oxide nanocomposite with varied morphology.

Nanocomposites with multifunctional application prospects have already dragged accelerating interests of materials scientists. Here we present CdS/ZnO nanocomposites with different morphology engineering the precursor molar ratio in a facile wet chemical synthesis route. The materials were structurally and morphologically characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), energy dispersive X-ray analysis (EDX) and high-resolution transmission electron microscopy (HRTEM). The growth mechanism of the composite structure with varying molar ratio is delineated with oriented attachment self assemble techniques. Photocatalytic activity of CdS/ZnO nanocomposites with varying morphology were explored for the degradation of rhodamine B (RhB) dye in presence of visible light irradiation and the results reveal that the best catalytic performance arises in CdS/ZnO composite with 1: 1 ratio. The antibacterial efficiency of all nanocomposites were investigated on Escherichia coli, Staphylococcus aureus and Klebsiella pneumonia without light irradiation. Antibacterial activity of CdS/ZnO nanocomposites were studied using the bacteriological test-well diffusion agar method and results showed significant antibacterial activity in CdS/ZnO composite with 1:3 ratio. Overall, CdS/ZnO nanocomposites excel in different potential applications, such as visible light photocatalysis and antimicrobial activity with their tuneable structure.

Research advances in major cereal crops for adaptation to abiotic stresses.

With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers' fields.

Tunable optical properties of graphene oxide by tailoring the oxygen functionalities using infrared irradiation.

The modification of individual oxygen functional groups and the resultant optical properties of a graphene oxide suspension were investigated using a controlled photothermal reduction by infrared irradiation. The evolution of the structural and optical characteristics of GO suspensions was obtained from Raman spectra, x-ray photoelectron spectroscopy, optical absorption, and steady state and time-resolved photoluminescence spectroscopy. The results suggest the gradual restoration of sp(2) clusters within the sp(3) matrix with an increase of the reduction time and power density. The yellow-red emission (∼610 nm) originated from the defect-assisted localized states in GO due to epoxy/hydroxyl (C-O/-OH) functional groups and that of the blue emission (∼500 nm) was ascribed to the carbonyl (C=O)-assisted localized electronic states. With an increase in the reduction time and IR power density, the intensity of the yellow-red emission was found to decrease, with the blue emission being prominent. These experimental findings open up a new dimension for controlling the optical absorption and emission properties of graphene oxide by tailoring the oxygen functional groups, which may lead to the potential application of graphene-based optoelectronic devices.

Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes.

Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated sequence content in a genome, we suggest that the amount and activity of repeated sequences are important factors determining the number of genes in a genome.

Mechanism of ultrasonic energy-assisted formation of V-, Y-shaped nano-structures in conjugated polymers.

Recently, hydrocarbon-nanostructures from organic solvent using ultrasonic energy were reported. However, their formation-dynamics remained unexplored. Here, we describe a new technique to synthesize controlled nanostructures (V-, Y-shape) from nanorods of conducting polyaniline applying ultrasonic energy. To characterize the conducting state (emaraldine) of these polyaniline nanorods, electrical measurements have been carried out from which it is seen that there is a crossover from metallic to semiconductor as temperature increases. The observed crossover has been explained by the core-shell structure of the nanorods with core resistivity much higher than the shell resistivity. The nonlinear current-voltage behavior is attributed to the formation of alternate ordered/disordered chain segments along the length of the nanorods. We also propose a model to explore the mechanism of formation of these V-, Y-shaped nanostructures. It is believed that bubble-formation occurs in liquid due to ultrasonic vibration; and asymmetry in the bubble is created when formed near the solid surface leading to jet formation. Liquid jets of collapsing bubble move with incredible velocity (400 km/h); collide with the nanorod to cause fragmentations followed by V-, Y-shaped structure formation when the imparted kinetic energy of jets is comparable with elastic energy of fragments.

What can comparative genomics tell us about species concepts in the genus Aspergillus?

Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.

Management of fluoride induced testicular disorders by calcium and vitamin-E co-administration in the albino rat.

Fluoride contamination of drinking water can disrupt male gametogenesis and steroidogenesis and induce testicular oxidative stress. Treatment of rats with sodium fluoride at the dose of 20 mg/kg/day for 28 days resulted in significant diminution of testicular Delta5,3beta-hydroxysteroid dehydrogenase (HSD) and 17beta-hydroxysteroid dehydrogenase (HSD) activities and low plasma levels of testosterone, follicular stimulating hormone (FSH) and leutinizing hormone (LH). Spermatogenesis inhibited after sodium fluoride treatment has been assessed here by the quantification of different generation of germ cells like spermatogonia A (ASg), preleptotene spermatocyte (PLSc), midpachytene spermatocyte (MPSc) and step 7 spermatid (7Sd) at stage VII of seminiferous epithelial cycle. Furthermore, fluoride treatment was associated with low activities of testicular, prostatic and epididymal catalase (CAT), superoxide dismutase (SOD) and peroxidase along with elevation of malondialdehyde (MDA) and conjugated dienes (CD) in those tissues. Co-administration of calcium and Vitamin-E with fluoride resulted in a significant recovery from testicular disorders and oxidative stress in the testis and male accessory sex organs. The results of this study demonstrate that fluoride exposure, at the dose available in drinking water in contaminated areas, led to inhibition of testicular gametogenesis and steroidogenesis in association with oxidative stress in the testis and male accessory sex organs, which are protected significantly by dietary agents like Vitamin-E and calcium.

Fluoride-induced immunotoxicity in adult male albino rat: a correlative approach to oxidative stress.

Fluoride pollution in drinking water is an international problem as the fluoride present is often at levels above acceptable limits. In the studies reported here, sodium fluoride (NaF) treatment of rats by gavage for 28 days resulted in the induction of oxidative stress and immunotoxicity. It was shown here that NaF treatment lowered cellular immunity in the rats as illustrated by a significant diminution in peripheral blood lymphocyte, monocyte and neutrophil counts in conjunction with a reduction in splenocyte counts. Effects of NaF treatment on humoral immunity were reflected here in a lowering of the levels of plasma IgG specific to a test antigen (i.e., bovine serum albumin). Disorganization in the histoarchitecture was also noted in the host spleen and thymus after NaF treatment. To determine if oxidative stress was among the potential possible causes for the observed induced immunotoxicities, catalase and peroxidase activities along with malondialdehyde (MDA, product of free radical damage to cells) levels in the spleen and peripheral blood packed cells were also measured. The results indicated that there was a significant diminution in the activities of both the enzymes along with an elevation in MDA levels in both the tissues in treated rats. This report highlights the proposition that chronic exposure to fluoride contaminated drinking water is likely to result in immunotoxicity and, furthermore, that the damage to primary immune organs is due to an induction of oxidative stress.

Whole genome comparison of the A. fumigatus family.

The availability of the genome sequences of multiple Aspergillus spp. presents the research community with an unprecedented opportunity for discovery. The genomes of Neosartorya fischeri and Aspergillus clavatus have been sequenced in order to extend our knowledge of Aspergillus fumigatus, the primary cause of invasive aspergillosis. Through comparative genomic analysis, we hope to elucidate both obvious and subtle differences between genomes, developing new hypotheses that can be tested in the laboratory. A preliminary examination of the genomes and their predicted proteomes reveals extensive conservation between protein sequences and significant synteny, or conserved gene order. Comparative genomic analysis at the level of these closely related aspergilli should provide important insight into the evolutionary forces at play and their effect on gene content, regulation and expression.

Induction of oxidative stress on reproductive and metabolic organs in sodium fluoride-treated male albino rats: protective effect of testosterone and vitamin e coadministration.

The present study was undertaken to search out the effect of sodium fluoride, a water pollutant noted throughout the world, including India, on oxidative stress induction in reproductive tissues, sperm pellet, and metabolic tissues like the liver and kidney. The protective effects of testosterone or vitamin-E coadministration were also observed on oxidative stress in the above mentioned samples. A significant diminution was noted in the activities of catalase and peroxidase, important antioxidant enzymes in testicular tissue, sperm pellet, prostate, and epididymis in sodium fluoride-treated rats at the dose of 20 mg/kg body weight/day (the level noted in drinking water in fluoride intoxicated areas) for 30 days by oral gavage. Coadministration of testosterone by intraperitoneal injection at the dose of 40 mug/100 g body weight/alternate day, 3 hours after fluoride treatment, resulted in a significant protection in the above mentioned parameters of all these samples. Moreover, fluoride treatment also resulted a significant elevation in the level of malondialdehyde and conjugated dienes, indicators of oxidative stress, in all the above mentioned samples, which were resettled toward the control level after testosterone coadministration. Testiculo-somatic, prostato-somatic, and epididymo-somatic indices were decreased significantly in the fluoride-treated group when compared to the vehicle-treated control group. Testosterone coadministration resulted in significant restoration of these indices to the control level. We also measured the above parameters for the evaluation of oxidative stress in the liver and kidney, important metabolic organs, and noted that there was also a significant elevation in malondialdehyde and conjugated dienes along with diminution in catalase and peroxidase activities in the fluoride treated-group, with respect to the vehicle treated control group. Testosterone coadministration resulted a significant protection in these parameters toward the vehicle-treated control level. There was no significant change in hepato-somatic and reno-somatic indices among fluoride-treated, testosterone coadministered, and vehicle-treated rats. Body weight of the animals among these three groups were not changed significantly. To find out the antioxidative property of testosterone compared to vitamin E, one group of fluoride-treated animals were subjected to coadministration of vitamin E at the dose of 20 mg/100 g body weight. It was noted that in reproductive organs and in metabolic organs, oxidative stress parameters were recovered toward the control level. The results of our experiment suggests that fluoride at the dose noted in drinking water in contaminated areas may induce oxidative stress in reproductive and metabolic organs that can be ameliorated significantly by testosterone or vitamin E coadministration. Moreover, as there was no significant variation in body weights among these groups, it may be predicted that this effect of fluoride on reproductive and metabolic organs is specific and is not due to general effect of fluoride.

Antidiabetic effect of aqueous extract of seed of Tamarindus indica in streptozotocin-induced diabetic rats.

In Indian traditional system of medicine, herbal remedies are prescribed for the treatment of diseases including diabetes mellitus. In recent years, plants are being effectively tried in a variety of pathophysiological states. Tamarindus indica Linn. is one of them. In the present study, aqueous extract of seed of Tamarindus indica Linn. was found to have potent antidiabetogenic activity that reduces blood sugar level in streptozotocin (STZ)-induced diabetic male rat. Supplementation of this aqueous extract by gavage at the dose of 80 mg/0.5 ml distilled water/100 g body weight per day in STZ-induced diabetic rat resulted a significant diminution of fasting blood sugar level after 7 days. Continuous supplementation of this extract for 14 days resulted no significant difference in this parameter from control level. Moreover, this supplementation produced a significant elevation in liver and skeletal muscle glycogen content, activity of liver glucose-6-phosphate dehydrogenase in respect to diabetic group. Activities of liver glucose-6-phosphatase, liver and kidney glutamate oxaloacetate transaminase (GOT) and glutamate pyruvate transaminase (GPT) activities were decreased significantly in the aqueous extract supplemented group in respect to diabetic group. All these parameters were not resettled to the controlled level after 7 days of this extract supplementation but after 14 days of this supplementation, all the above mentioned parameters were restored to the control level.

Effect of Stephania hernandifolia leaf extract on testicular activity in rats.

AIM: The testicular inhibitory effect of the aqueous fraction of methanol extract of Stephania hernandifolia leaf was studied in male Wistar rats. METHODS: The supernatent and the precipitate part of aqueous fractions of the methanol extract of the leaf were gavaged separately to rat at a similar dose of 200 mg/mL per 100 g body weight per day for 28 days. After cessation of treatment, various observations were conducted. RESULTS: In both treated groups, there were significant decreases in the relative weights of the sex organs, the testicular key androgenic enzymes activities, the plasma level of testosterone, the number of different germ cells at stage VII of seminiferous epithelial cell cycle and the seminiferous tubular diameter in comparison to the controls. Neither of the parts had somatic, renal and hepatic toxicity. This study suggested that the active molecules present in the aqueous fraction of methanol extract of Stephania hernandifolia leaves might be steroids as indicated by thin layer chromatography using specific staining substance for steroid molecules. CONCLUSION: In rats, the aqueous fraction of methanol extract of the S. hernandifolia leaves possesses certain testis-inhibitory substances, which may be steroid-like agents.

Testicular toxicity in sodium fluoride treated rats: association with oxidative stress.

This study examined the effect of sodium fluoride, a water pollutant important through the world, including India, on testicular steroidogenic and gametogenic activities in relation to testicular oxidative stress in rats. Sodium fluoride treatment at 20mg/kg/day for 29 days by oral gavage resulted in significant diminution in the relative wet weight of the testis, prostate, and seminal vesicle without alteration in the body weight gain. Testicular delta(5),3beta-hydroxysteroid dehydrogenase (HSD) and 17beta-HSD activities were decreased significantly along with significant diminution in plasma levels of testosterone in the fluoride-exposed group compared to the control. Epididymal sperm count was decreased significantly in the fluoride-treated group and qualitative examination of testicular sections revealed fewer mature luminal spermatozoa in comparison to the control. The seminiferous tubules were dilated in treated animals. Fluoride treatment was associated with oxidative stress as indicated by an increased level of conjugated dienes in the testis, epididymis, and epididymal sperm pellet with respect to control. Peroxidase and catalase activities in the sperm pellet were decreased significantly in comparison to the control. The results of this experiment indicate that fluoride at a dose encountered in drinking water in contaminated areas exerts an adverse effect on the male reproductive system and this effect is associated with indicators of oxidative stress.

Effect of human chorionic gonadotrophin coadministration on ovarian steroidogenic and folliculogenic activities in cyclophosphamide treated albino rats.

Quantitative evaluation of ovarian Delta5,3beta- hydroxysteroid dehydrogenese (HSD) and 17beta - HSD activities along with radioimmunoassay of plasma levels of gonadotrophins (FSH and LH), and estradiol (E2), and quantification of different types of developing follicles and regressive follicles were noted in mature rats of the Wistar strain following treatment with cyclophosphamide at a dose of 5 mg/kg body weight/day for 28 days. A significant reduction in plasma levels of LH and E2 along with significant diminution in the activities of ovarian Delta5,3beta -HSD and 17beta- HSD were observed following cyclophosphamide treatment for 28 days without any change in the plasma level of FSH. This treatment also produced a marked degree of degeneration in different types of follicles. Coadministration of hCG at 5 IU/kg body weight/day for 28 days in the cyclophosphamide-treated group provided significant protection except with respect to plasma LH. These results suggest the possibility of an indirect action of cyclophosphamide at the level of the ovary.

Effect of human chorionic gonadotrophin coadministration on the activities of ovarian Delta5-3beta-hydroxysteroid dehydrogenase, and 17beta-hydroxysteroid dehydrogenase, and ovarian and uterine histology in lithium chloride-treated albino rats.

Lithium chloride, a compound with clinical use in bipolar disorder, produces adverse effects on ovarian function in amphibian and rodent models. This study examined the effect of human chorionic gonadotrophin coadministration on ovarian steroidogenic and gametogenic activities in lithium chloride-treated rats. Relative ovarian and uterine weights, ovarian Delta(5)-3beta-hydroxysteroid dehydrogenase and 17beta-hydroxysteroid dehydrogenase activities, folliculogenesis, uterine diameter, endometrial and myometrial thickness, and uterine luminal epithelial height were decreased significantly after lithium chloride treatment for 28 days at 1.6 mg/kg/day, the human therapeutic dose. These parameters were unchanged from the control level when subcutaneous (s.c.) human chorionic gonadotrophin (hCG) at 25 microg/kg/day was coadministered with the lithium chloride. The duration of the oestrous cycle was increased in lithium chloride-treated rat with longer metestrous and diestrous phases. Administration of hCG with lithium chloride prevented these estrous cycle alterations. We conclude that hCG can protect ovarian steroidogenic and gametogenic function after lithium chloride treatment.

Mimicking oxide surfaces: different types of defects and ligand coordination at well defined positions of a molybdenum oxide based nanocluster.

The mixed valence cluster anion of the compound (NH4)32[MoVI110MoV28O416H6(H2O)58(CH3CO2)6].xH2O 1 (x approximately 250), synthesized under one-pot conditions, contains well-defined different types of defects--missing groups compared to the complete parent (Mo154) type cluster with full D7d symmetry--and acetate ligand coordination; this proves that the giant-wheel type anion can be considered as an object with a variety of nanoscale structural features ("nanostructured landscape") allowing reactions at a variety of well defined centers.

Effect of mild irritant on gastric mucosal offensive and defensive factors.

The effect of hypotonic medium (Distilled water: DW) and hypertonic saline (HS: 5% NaCl) compared to control normal saline (NS) was studied on gastric ulcer induced by aspirin, 6 h cold restraint stress, ethanol, and pylorus ligation in rats. DW did not afford any protection while HS showed significant ulcer protective effects in all gastric ulcer models studied. The cytoprotective effect of HS seemed to be not only due to its effect on gastric acid secretion but also its effect on mucosal defensive factors like enhanced mucin secretion and decreased cell shedding. As determined by radioimmunoassay, DW did not produce any change in the accumulation of PGE and PGI2, while HS increased them significantly in the human gastric mucosal incubates compared to NS. However, in the incubates of human colonic mucosa, both DW and HS showed a significant increase in PGE with a tendency to increase in PGI2 accumulation.