Multivariate empirical mode decomposition

Despite empirical mode decomposition (EMD) becoming a de facto standard for time-frequency analysis of nonlinear and non-stationary signals, its multivariate extensions are only emerging; yet, they are a prerequisite for direct multichannel data analysis. An important step in this direction is the computation of the local mean, as the concept of local extrema is not well defined for multivariate signals. To this end, we propose to use real-valued projections along multiple directions on hyperspheres ( n -spheres) in order to calculate the envelopes and the local mean of multivariate signals, leading to multivariate extension of EMD. To generate a suitable set of direction vectors, unit hyperspheres ( n -spheres) are sampled based on both uniform angular sampling methods and quasi-Monte Carlo-based low-discrepancy sequences. The potential of the proposed algorithm to find common oscillatory modes within multivariate data is demonstrated by simulations performed on both hexavariate synthetic and real-world human motion signals.

Distribution of peroxisome proliferator-activated receptors (PPARs) in human skeletal muscle and adipose tissue: relation to insulin action

AIMS/HYPOTHESIS

To evaluate the tissue distribution and possible role of the peroxisome proliferator-activated receptors (PPARs) in insulin action in fat and muscle biopsy specimens from lean, obese and subjects with Type II (non-insulin-dependent) diabetes mellitus.

METHODS

We measured PPAR alpha, PPAR beta (delta) and PPAR gamma protein expression by western blot analysis. The PPAR gamma protein was also measured in muscle before and after 3-h hyperinsulinaemic (300 mU.m-2.min-1) euglycaemic clamps.

RESULTS

The PPAR alpha protein was expressed preferentially in muscle relative to fat (more than sevenfold). The PPAR beta protein was similar in fat and muscle. The amount of PPAR gamma protein found in muscle was, on average, two-thirds of that present in fat. There was no statistically significant difference between non-diabetic and diabetic subjects in baseline (preclamp) muscle PPAR (alpha, beta or gamma) protein expression. Subgroup analysis showed, however, significantly higher PPAR gamma protein in the most insulin resistant diabetic subjects with glucose disposal rates of 3-6 mg.kg-1.min-1 compared with their age and weight matched counterparts with glucose disposal rates of 6-9 (147 +/- 23 vs 88 +/- 10 AU/microgram protein, p < or = 0.01 in diabetic and vs 94 +/- 15, p < or = 0.04 in non-diabetic subjects). Muscle PPAR gamma protein and glucose disposal rates were inversely correlated in diabetic subjects (r = -0.47, p < or = 0.05).

CONCLUSION/INTERPRETATION

All PPARs (alpha, beta or gamma) are present in skeletal muscle and adipose tissue with different relative distributions. The PPAR gamma protein is abundant in skeletal muscle as well as adipose tissue. The altered expression of skeletal muscle PPAR gamma is consistent with a role for this nuclear protein in the impaired insulin action of Type II diabetes.

Anaerobic Biodegradation of Surfactants – Scientific Review

The anaerobic biodegradation of surfactants is used as an acceptability criterion in some environmental pieces of legislation (eco-label, risk assessment, etc.), without a proper evaluation of the relevance of such a characteristic. Available screening test methods to assess the anaerobic biodegradation do not simulate the real conditions prevailing in these anaerobic compartments but rather reflect more stringent conditions, due to the high test substance/biomass ratio, possibility of inhibitory effects and limited possibility for adaptation. Therefore positive results are indicative of a similar behaviour under environmental conditions, while a negative result cannot be necessarily interpreted as inherent anaerobic recalcitrance. The majority of surfactants entering the environment will be exposed to and degraded under aerobic conditions, and only less than 20 % will potentially reach temporarily anaerobic environmental compartments. In contrast to the well documented adverse effects observed in the absence of aerobic biodegradation, the lack of anaerobic biodegradation does not seem to be correlated with any apparent environmental problem for most compartments after more than 40 years of widely use of such products. The scientific review concluded that anaerobic biodegradability does not have the same environmental relevance as the aerobic one. Anaerobic biodegradability should not, therefore, be used as a pass/fail property for the environmental acceptability of surfactants which are readily biodegradable under aerobic conditions.

Effect of sperm exposure time on in vitro fertilization and embryo development of bovine oocytes matured in vitro

This study was designed to investigate the effect of sperm exposure time on the fertilization rate and subsequent developmental capacity of bovine oocytes matured in vitro. Cumulus oocyte complexes (COCs) obtained from 2 to 6 mm follicles were matured for 24 h in TCM-199 supplemented with fetal bovine serum (FBS) and hormones (FSH, LH and estradiol 17-beta). In vitro fertilization (IVF) was performed by incubating 15 to 20 matured oocytes with 1 x 10(6) percoll separated frozen-thawed spermatozoa in 1 ml of IVF-TL medium for either 4, 8, 12, 16, 20, 24 or 28 h. Following sperm exposure for different periods of times, the presumptive zygotes were co-cultured with Buffalo Rat Liver cells (BRLC) monolayers in CZB medium without glucose, a simple semi-defined medium developed for mouse embryo culture, for 3 d post-insemination and then in M199/FBS (TCM-199-HEPES supplemented with 20% heat-treated FBS and 1 mM sodium pyruvate) for 5 d. The fertilization rates differed significantly among the 7 treatment groups, with higher frequencies obtained by co-incubation of gametes for 20, 24 or 28 h (67 to 76%) than for 4, 8 and 12 h (26 to 54.5%), with 16 h (57%) being intermediate. However, the length of sperm exposure time did not significantly affect subsequent embryo development, although an increasing trend was noted from 4 h to 20 h. The number of fertilized oocytes at 3 d post-insemination cleaving to 2- to 4-cell vs 8-cell stage was not different among treatment groups. Development of 8-cell embryos to morulae and blastocysts did not differ among the treatment groups. These data suggest that the optimum duration of sperm-oocyte incubation is 24 h, and periods shorter than 16 h may result in a reduced fertilization rate.

Development of in vitro matured and fertilized bovine oocytes co-cultured with Buffalo Rat Liver cells

This study was designed to evaluate the efficacy of Buffalo Rat Liver cells (BRLC) monolayers in supporting the development of in vitro matured and fertilized (IVM/IVF) bovine oocytes through to the hatched blastocyst stage compared to the commonly used co-culture system of bovine oviduct epithelial cells (BOEC). Cumulus oocyte complexes (COCs) obtained from 2- to 6-mm ovarian follicles at slaughter were matured for 24 h in TCM-199 supplemented with FBS and hormones (FSH, LH and estradiol 17-beta). In vitro fertilization (IVF) was performed using 1 x 10(6) percoll separated frozen-thawed spermatozoa in 1 ml of IVF-TL medium containing 18 to 20 matured oocytes. After 20 to 22 h of sperm exposure, 584 presumptive zygotes in 2 separate trials were randomly assigned to 3 treatment groups (BRLC co-culture, BOEC co-culture and control, consisting of medium alone). Zygotes were cultured in CZB media, a simple semi-defined medium, without glucose for the first 2 d, transferred to M199/FBS (TCM-199-HEPES supplemented with 20% HTFBS, 1 mM Sodium pyruvate), and cultured for an additional 8 days. Cleavage and development to morula and various blastocyst stages were recorded between d 3 and 11 after the start of IVF. Overall average cleavage rate was 75% (440 584 ) and did not vary across the treatments or trials. The proportion of embryos that reached the morula stage in both co-culture systems did not differ (P > 0.05) and was significantly higher (P > 0.05) compared to the control group. However, the percentage of the number of blastocysts, expanded blastocysts and hatched blastocysts varied across the treatment groups (P < 0.05), with the highest results obtained in the BRLC co-culture system. The production of blastocysts in BOEC co-culture was inconsistent between the 2 trials where a significant difference (40.6 vs 53.0%; P > 0.05) was observed. Rate of development to the blastocyst stage was similar between the 2 co-culture systems, with most of the embryos reaching the blastocyst stage by d 8 post insemination. The results of this study show that BRLC from a commercially available established cell line offer a more reliable alternative to a BOEC co-culture system for in vitro maturation, fertilization and culture of bovine embryos.

Development of IVM-IVF produced 8-cell bovine embryos in simple, serum-free media after conditioning or co-culture with buffalo rat liver cells

Development of 8-cell bovine embryos derived from in vitro matured/in vitro fertilized (IVM/IVF) oocytes was evaluated in two simple, serum-free media (CZB and SOM) with buffalo rat liver cells co-culture (BRLC) or after conditioning compared to a commonly used, serum-supplemented complex medium TCM-199. In a 3 x 4 factorial design, 578 eight-cell embryos were randomly assigned to 12 treatment groups. The factors were: first, type of culture medium (M199/FBS, CZBg and SOM), and second, the use of BRLC (as co-culture or to condition media for 24 hr and 48 hr) and unconditioned media. Development to morula was not affected by the type of medium, but co-culture and 48 hr conditioning within media type resulted in better development when compared to the 24-hr conditioned or unconditioned groups. Blastocyst development in SOM (38.9%) was different (P < 0.05) than in CZBg (46.6%) and M199/FBS (48.7%) and was lowest in the unconditioned group (27.8%) followed by 24 hr conditioned (33.3%), 48 hr (56.3%), and co-culture (59.6%). No blastocyst expansion was observed with unconditioned media and 24 hr conditioned SOM. Significant differences (P < 0.05) were found among all treatment groups except the co-culture and 48-hr conditioned groups. Hatching occurred only with co-culture and 48-hr conditioned groups of M199/FBS and CZBg media. These data show that CZB with glucose conditioned by BRLC monolayers for 48 hr can support the development of IVM/IVF produced bovine embryos to blastocyst compared to culture in TCM-199 with serum.

Retinoid X receptor expression in skeletal muscle of nondiabetic, obese and type 2 diabetic individuals

Retinoid X receptor (RXR) is a nuclear receptor that functions as an obligate heterodimeric partner of peroxisome proliferator-activator receptor (PPAR). Studies have shown that the alpha isoform of RXR and PPARgamma act synergistically to regulate gene expression and insulin action. The aim of the current study was to compare the expression and regulation of RXR in the primary insulin-sensitive tissue, skeletal muscle, of various degrees of insulin-resistant states including obese type 2 diabetic (T2D), obese nondiabetic (OND), and lean nondiabetic (LND) subjects. Insulin action/resistance was determined by a 3-hour hyperinsulinemic, euglycemic (5.0 to 5.5 mmol/L) clamp. Percutaneous biopsy of the vastus lateralis muscle was performed before and after the clamp. RXRalpha mRNA was measured using a quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) assay, while protein was determined by Western blotting. All 3 isoforms of RXR, alpha, beta, and gamma, were present in skeletal muscle. Protein expression of RXR isoforms did not differ between groups; RXR alpha mRNA was also similar between groups. Neither RXR alpha mRNA, RXR -beta nor -gamma protein displayed significant relationships with any of the clinical or laboratory parameters measured, including insulin sensitivity. RXR alpha exhibited a negative correlation with free fatty acids levels (r, -.42, P <.05). There was also no relationship between RXR alpha and PPARgamma protein levels. RXR alpha mRNA was unaltered following insulin infusion. We conclude that RXR isoform (alpha, beta, gamma) expression is not tightly controlled by insulin, insulin resistance or type 2 diabetes. Instead, RXR isoforms are likely constitutive proteins or controlled by other factors.

Surface-Enhanced Raman Spectroscopy for Monitoring the Biochemical Changes Due to DNA Mutations Induced by CRISPR-Cas9 Genome Editing in the Aspergillus niger Fungus

In this study, surface-enhanced Raman spectroscopy (SERS) technique, along with principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA), is used as a simple, quick, and cost-effective analysis method for identifying biochemical changes occurring due to induced mutations in the Aspergillus niger fungus strain. The goal of this study is to identify the biochemical changes in the mutated fungal cells (cell mass) as compared to the control/nonmutated cells. Furthermore, multivariate data analysis tools, including PCA and PLS-DA, are used to further confirm the differentiating SERS spectral features among fungal samples. The mutations are caused in A. niger by the clustered regularly interspaced palindromic repeat CRISPR-Cas9 genomic editing method to improve their biotechnological potential for the production of cellulase enzyme. SERS was employed to detect the changes in the cells of mutated A. niger fungal strains, including one mutant producing low levels of an enzyme and another mutant producing high levels of the enzyme as a result of mutation as compared with an unmutated fungal strain as a control sample. The distinctive features of SERS corresponding to nucleic acids and proteins appear at 546, 622, 655, 738, 802, 835, 959, 1025, 1157, 1245, 1331, 1398, and 1469 cm-1. Furthermore, PLS-DA is used to confirm the 89% accuracy, 87.7% precision, 87% sensitivity, and 88.9% specificity of this method, and the value of the area under the curve (AUROC) is 0.67. It has been shown that surface-enhanced Raman spectroscopy is an effective method for identifying and differentiating biochemical changes in genome-modified fungal samples.

Emergence of multi-drug resistance among beta-lactamase producing Salmonella

Multi-drug resistant strains of Salmonella isolated from blood and bone marrow cultures of pyrexial patients received from physicians, hospitals and different clinics were studied from May to November, 1993. Of 2143 samples collected, 424(20%) cases yielded the growth of different organisms. Out of these 266(63%) were positive for Salmonella strains. The strains isolated were Salmonella typhi 239(90%) and Salmonella paratyphi A 27(10%). Two hundred twenty (82%) strains of Salmonella showed increased beta-lactamase activity and an alarming increase in resistance against commonly used antibiotics for enteric fever.

Differentiation of different dibenzothiophene (DBT) desulfurizing bacteria via surface-enhanced Raman spectroscopy (SERS)

Fossil fuels are considered vital natural energy resources on the Earth, and sulfur is a natural component present in them. The combustion of fossil fuels releases a large amount of sulfur in the form of SO x in the atmosphere. SO x is the major cause of environmental problems, mainly air pollution. The demand for fuels with ultra-low sulfur is growing rapidly. In this aspect, microorganisms are proven extremely effective in removing sulfur through a process known as biodesulfurization. A major part of sulfur in fossil fuels (coal and oil) is present in thiophenic structures such as dibenzothiophene (DBT) and substituted DBTs. In this study, the identification and characterization of DBT desulfurizing bacteria (Chryseobacterium sp. IS, Gordonia sp. 4N, Mycolicibacterium sp. J2, and Rhodococcus sp. J16) based on their specific biochemical constituents were conducted using surface-enhanced Raman spectroscopy (SERS). By differentiating DBT desulfurizing bacteria, researchers can gain insights into their unique characteristics, thus leading to improved biodesulfurization strategies. SERS was used to differentiate all these species based on their biochemical differences and different SERS vibrational bands, thus emerging as a potential technique. Moreover, multivariate data analysis techniques such as principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were employed to differentiate these DBT desulfurizing bacteria on the basis of their characteristic SERS spectral signals. For all these isolates, the accuracy, sensitivity, and specificity are above 90%, and an AUC (area under the curve) value of close to 1 was achieved for all PLS-DA models.

Surface-enhanced Raman spectroscopy for the study of interaction of an antibacterial agent ([bis(1,3-dipentyl-1H-imidazol-2(3H)-ylidene)silver(i)]bromide) with Bacillus subtilis bacterial biofilms

Bacterial resistance towards antibiotics is a significant challenge for public health, and surface-enhanced Raman spectroscopy (SERS) has great potential to be a promising technique to provide detailed information about the effect of antibiotics against biofilms. SERS is employed to check the antibacterial potential of a lab synthesized drug ([bis(1,3-dipentyl-1H-imidazol-2(3H)-ylidene)silver(i)] bromide) against Bacillus subtilis and to analyze various SERS spectral features of unexposed and exposed Bacillus strains by observing biochemical changes in DNA, protein, lipid and carbohydrate contents induced by the lab synthesized imidazole derivative. Further, PCA and PLS-DA are employed to differentiate the SERS features. PCA was employed to differentiate the biochemical contents of unexposed and exposed Bacillus strains in the form of clusters of their representative SERS spectra and is also helpful in the pairwise comparison of two spectral data sets. PLS-DA provides authentic information to discriminate different unexposed and exposed Bacillus strains with 91% specificity, 93% sensitivity and 97% accuracy. SERS can be employed to characterize the complex and heterogeneous system of biofilms and to check the changes in spectral features of Bacillus strains by exposure to the lab synthesized imidazole derivative.

Topiramate: a new safe and effective antiepileptic

Twenty patients of either sex, with refractory partial epilepsy with or without secondary generalisation were entered in an open label study to evaluate the efficacy and safety of topiramate in them. Topiramate was used as an adjunctive therapy with an initial starting dose of 50 mg/day. The dose was then titrated upwards with increments of 50 mg per week, till a time the most effective and the best tolerated dose was reached. This most effective/tolerated dose was then continued for 6 months. Of the 17 patients entering the maintenance phase, 4 patients (24%) became seizure free, while a total of 14 patients (83%) out of 17 cases responded with a reduction in monthly seizures rate by 50% or more. Mean reduction of 68.9% was observed in monthly seizure rate during the maintenance phase. The median effective dose of topiramate was 600 mg per day. Five patients dropped out of the study due to adverse events such as anxiety, aggressiveness, rash, lethargy, etc. The central nervous system (CNS) related side effects such as dizziness, headache, and tremor were reported, which are commonly seen with other presently available antiepileptics like carbamazepine, phenytoin sodium, sodium valproate, etc, as well. Most adverse events, however, were mild and transient and did not interfere with the day to day activity of the patients. Topiramate was not associated with any abnormality in laboratory or neurological examination findings. The excellent response with topiramate therapy in Indian patients, uncontrolled with the available antiepileptics, as well as its good safety profile endorse the international efficacious and safe image of topiramate.

Antibiotic susceptibility of Streptococcus pneumoniae in Karachi

OBJECTIVE

To evaluate, record and analyse the comparative activity of a range of oral antibiotics against Streptococcus pneumoniae.

SETTING

Specimen collected at a private laboratory and some received from different hospitals and clinics.

MATERIALS

The specimen comprised of Sputum, Throat Swabs, C.S.F., Pus, Pleural fluid, Ear Swabs, Eye Swabs, Bronchial Wash, Prostatic discharge and Antral Secretions.

METHODS

The isolates were tested for their antibiotic susceptibility using the E-test by the methods described in the study protocol. The groups of antibiotics tested were Amoxicillin--Clavulanate, Clarithromycin, Cefaclor, Cefuroxime, Ceftriaxone and Penicillin.

RESULTS

A total of 116 strains of Streptococcus pneumoniae were isolated and susceptibility to Amoxicillin-Clavulanate was 100%, 99.1% strains were susceptible to Cefuroxime and 0.9% were intermediate. Susceptibility to Penicillin was 80.2% and 19.8% of the strains were in intermediate category, while susceptibility to Clarithromycin was 89.7%, 1.7% were in intermediate region and 8.6% of the strains were resistant to this antibiotic. The susceptibility pattern of Cefaclor was not calculated as there is no current NCCLS--97 Cefaclor breakpoints available.

CONCLUSION

The percentage of drug resistant Streptococcus pneumoniae was negligible in Karachi during the study period, however it is important to monitor the susceptibility pattern to keep a check on an increase in the number of DRSP as reported at different centres in Turkey, Saudi Arabia, Singapore, Thailand, Hong Kong and Indonesia.