Modern PID/FOPID controllers for frequency regulation of interconnected power system by considering different cost functions

This article presents frequency regulation of an interconnected three-area power system (Thermal + Wind + Hydro). Fractional Order PID (FOPID) and Proportional-Integral-Derivative (PID) controllers are applied as subsidiary regulators to control the electrical power interconnected system at the time of sudden load variation. To accomplish this study, Genetic Algorithm (GA), Grey Wolf Optimizer (GWO), Sine Cosine Inspired Algorithm (SCIA) and Atom Search Inspired Algorithm (ASIA) are implemented to optimize the secondary regulators' gains (PID and FOPID) by considering various cost functions such as Integral Absolute Error (IAE), Integral Time Absolute Error (ITAE), Integral Square Error (ISE), and Integral Time Square Error (ITSE). Performance analysis in this work is conducted using various cost functions based on GA, GWO, SCIA and ASIA. The comparative analysis of the attained results reveals that GWO-PID and ASIA-PID settle at (83.83 s) and (30.31 s), respectively and ASIA-FOPID at (25.12 s). The controllers based on ITSE as a cost function outperform the comptrollers with other cost functions (ISE, IAE and ITAE). In addition, the ISE-based GA-PID and SCIA-PID settle at (113.92 s) and (35.1 s), respectively and SCIA-FOPID at (24.78 s). The ISE-based regulators yield improved response equated to other cost functions (ITSE, IAE and ITAE) optimized controllers. The robustness test also is carried out to validate the effectiveness of the proposed optimization techniques by changing the system parameters within ± 25% and ± 50% from their nominal values as well as changing the load pattern.

Promoting artificial recharge to enhance groundwater potential in the lower Bhavani River basin of South India using geospatial techniques

The artificial recharge is an alternative technique to augment surface water and groundwater and for providing continuous supply of water to the demand regions. The scope of contemporary study helps in evaluation of groundwater potential zones and to find proper zones and sites for groundwater recharge using geospatial and multi-criteria decision analysis (MCDA) techniques. In this study, the pragmatic methodology was proposed for the implementation of water harvesting structures. The satellite and conventional datasets with field inferences were systematically processed to obtain various thematic information of the study area. The analytical hierarchical process (AHP) in geographical information system (GIS) was utilized to assign the geometric mean and the normalized weight for the individual features. Further, groundwater potential zones were identified, and they were categorized into four types viz. very high (523.58 km²), high (798.22 km²), moderate (646.04 km²) and low (456.66 km²). Nearly, 54.52% of the study area falls in the 'very high' to 'high' potential categories. The GIS-based Boolean logical method was also executed to identify suitable areas for creating recharge structures such as check dams (127.47 km²), percolation ponds (115.23 km²), flood and furrows (63.01 km²) and ditch and furrows (1046.31 km²). Based on the above results, 36 water harvesting structures were promoted to augment the groundwater resources of the basin. The highest priority was given to check dams (19 Nos), followed by percolation ponds (7 Nos), flood and furrows (5 Nos) and ditch and furrows (5 Nos). The suggested structures would improve the groundwater availability for agriculture and domestic purposes in the study area. Further, the outcomes could deliver a scientific procedure to the decision makers and water scientists for effective water resources development and management planning. Overall, the integrated remote sensing, GIS and MCDA methods are an efficient and useful tool for planning and improving groundwater recharge in the basin scale.

Geochemical evaluation of fluoride contamination in groundwater from Shanmuganadhi River basin, South India: implication on human health

In order to assess the geochemical mechanism liable for fluoride contamination in groundwater and its health effects on the people of the Shanmuganadhi River basin, Tamil Nadu, India, 61 groundwater samples were collected during post- and pre-monsoon seasons from the wells used for drinking purposes. Collected samples were analysed for various physico-chemical parameters. The parameters estimated in the present study are hydrogen ion concentration (pH), total dissolved solids, electrical conductivity, calcium (Ca²⁺), magnesium (Mg²⁺), sodium (Na⁺), potassium (K⁺), bicarbonate (HCO₃^-), chloride (Cl^-), sulphate (SO₄^2-), nitrate (NO₃^-), phosphate (PO₄^3-) and fluoride (F^-). The fluoride ion concentration in the groundwater samples of this region varied from 0.01 to 2.50 mg/l and 0.01 to 3.30 mg/l during post- and pre-monsoon seasons, respectively. Out of 61 groundwater samples, 14 samples of post-monsoon season and 16 samples of pre-monsoon season represented high, very high and extremely high classes of fluoride, which cause dental fluorosis in this region. The fluoride-bearing minerals in the granitic and gneissic rocks such as apatite, hornblende, muscovite, biotite and amphiboles are the major sources for fluoride contamination in this area. In addition to the geogenic sources, applications of synthetic fertilizers in the agricultural fields also contribute significant amount of fluoride ions to groundwater. The spatial distribution of fluoride in different geological formations clearly indicate that the wells located in charnockite terrain were possessing very low fluoride concentration when compare with the wells located in the hornblende-biotite gneiss formation. Therefore, dental fluorosis risks are mostly associated with rock types in this region. People living over the basement rock comprising of hornblende-biotite gneiss are prone for fluorosis. Fluoride exhibited good positive correlation with bicarbonate in groundwater. As fluoridated endemic regions normally acquire lot of bicarbonate in groundwater samples, Shanmuganadhi basin falls under fluoride endemic category. The present study identified 26 villages in Shanmuganadhi basin as probable fluorosis risk areas where attention should be given to treat the fluoride-rich groundwater before drinking water supply. The groundwater level fluctuation study also designates that rise in water level reduces the concentration of fluoride due to dilution mechanism. Therefore, recharge of groundwater by artificial methods will definitely improve the present scenario.

Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal

In bacteria, the assembly factors tightly orchestrate the maturation of ribosomes whose competency for protein synthesis is validated by translation machinery at various stages of translation cycle. However, what transpires to the quality control measures when the ribosomes are produced with assembly defects remains enigmatic. In Escherichia coli, we show that 30S ribosomes that harbour assembly defects due to the lack of assembly factors such as RbfA and KsgA display suboptimal initiation codon recognition and bypass the critical codon–anticodon proofreading steps during translation initiation. These premature ribosomes on entering the translation cycle compromise the fidelity of decoding that gives rise to errors during initiation and elongation. We show that the assembly defects compromise the binding of initiation factor 3 (IF3), which in turn appears to license the rapid transition of 30S (pre) initiation complex to 70S initiation complex by tempering the validation of codon–anticodon interaction during translation initiation. This suggests that the premature ribosomes harbouring the assembly defects subvert the IF3 mediated proofreading of cognate initiation codon to enter the translation cycle.

Cas3/I-C mediated target DNA recognition and cleavage during CRISPR interference are independent of the composition and architecture of Cascade surveillance complex

In type I CRISPR-Cas system, Cas3—a nuclease cum helicase—in cooperation with Cascade surveillance complex cleaves the target DNA. Unlike the Cascade/I-E, which is composed of five subunits, the Cascade/I-C is made of only three subunits lacking the CRISPR RNA processing enzyme Cas6, whose role is assumed by Cas5. How these differences in the composition and organization of Cascade subunits in type I-C influence the Cas3/I-C binding and its target cleavage mechanism is poorly understood. Here, we show that Cas3/I-C is intrinsically a single-strand specific promiscuous nuclease. Apart from the helicase domain, a constellation of highly conserved residues—which are unique to type I-C—located in the uncharacterized C-terminal domain appears to influence the nuclease activity. Recruited by Cascade/I-C, the HD nuclease of Cas3/I-C nicks the single-stranded region of the non-target strand and positions the helicase motor. Powered by ATP, the helicase motor reels in the target DNA, until it encounters the roadblock en route, which stimulates the HD nuclease. Remarkably, we show that Cas3/I-C supplants Cas3/I-E for CRISPR interference in type I-E in vivo, suggesting that the target cleavage mechanism is evolutionarily conserved between type I-C and type I-E despite the architectural difference exhibited by Cascade/I-C and Cascade/I-E.

High level extracellular production of recombinant human interferon alpha 2b in glycoengineered Pichia pastoris: culture medium optimization, high cell density cultivation and biological characterization

AIMS

The present study was aimed at design of experiments (DoE)- and artificial intelligence-based culture medium optimization for high level extracellular production of a novel recombinant human interferon alpha 2b (huIFNα2b) in glycoengineered Pichia pastoris and its characterization.

METHODS AND RESULTS

The artificial neural network-genetic algorithm model exhibited improved huIFNα2b production and better predictability compared to response surface methodology. The optimized medium exhibited a fivefold increase in huIFNα2b titre compared to the complex medium. A maximum titre of huIFNα2b (436 mg l^-1 ) was achieved using the optimized medium in the bioreactor. Real-time capacitance data from dielectric spectroscopy were utilized to model the growth kinetics with unstructured models. Biological characterization by antiproliferative assay proved that the purified recombinant huIFNα2b was biologically active, exhibiting growth inhibition on breast cancer cell line.

CONCLUSIONS

Culture medium optimization resulted in enhanced production of huIFNα2b in glycoengineered P. pastoris at both shake flask and bioreactor level. The purified huIFNα2b was found to be N-glycosylated and biologically active.

SIGNIFICANCE AND IMPACT OF THE STUDY

DoE-based medium optimization strategy significantly improved huIFNα2b production. The antiproliferative activity of huIFNα2b substantiates its potential scope for application in cancer therapy.

AGC of Multi-Area Hydro-Thermal Power Systems With GRC Non-Linearity and Classical Controller

In this article, the optimal gain value of classical controller gain values is obtained by using different performance indices in Automatic Generation Control. These are interconnected by the three areas of a hydro-thermal power system. The thermal and hydro areas are incorporated with a reheat turbine and a mechanical governor, respectively. The current article was created to select a suitable technique for the tuning of controller gain, when 1% of a step load is given to the thermal area (Area 1). The performance of several controllers, such as Integral (I), Proportional-Integral (PI), and Integral-Derivative (ID) were evaluated and were compared to the cases of with and without Generation Rate Constraint (GRC) non-linearity. The classical controller gain value optimization was performed using the Integral Time Square Error (ITSE), Integral Square Error (ISE) and Integral Time Absolute Error (ITAE) performance indices. The minimum optimal value of controller gain normally offers better dynamic response. The obtained results established that the optimization based on the ITAE-PI controller always guarantees superior dynamic performances compared to other indices and controllers.

Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

CRISPR-Cas system epitomizes prokaryote-specific quintessential adaptive defense machinery that limits the genome invasion of mobile genetic elements. It confers adaptive immunity to bacteria by capturing a protospacer fragment from invading foreign DNA, which is later inserted into the leader proximal end of CRIPSR array and serves as immunological memory to recognize recurrent invasions. The universally conserved Cas1 and Cas2 form an integration complex that is known to mediate the protospacer invasion into the CRISPR array. However, the mechanism by which this protospacer fragment gets integrated in a directional fashion into the leader proximal end is elusive. Here, we employ CRISPR/dCas9 mediated immunoprecipitation and genetic analysis to identify Integration Host Factor (IHF) as an indispensable accessory factor for spacer acquisition in Escherichia coli Further, we show that the leader region abutting the first CRISPR repeat localizes IHF and Cas1-2 complex. IHF binding to the leader region induces bending by about 120° that in turn engenders the regeneration of the cognate binding site for protospacer bound Cas1-2 complex and brings it in proximity with the first CRISPR repeat. This appears to guide Cas1-2 complex to orient the protospacer invasion towards the leader-repeat junction thus driving the integration in a polarized fashion.

Virtual fracture clinic delivers British Orthopaedic Association compliance

INTRODUCTION The British Orthopaedic Association recommends that patients referred to fracture clinic are thereafter reviewed within 72 hours. With the aim of improving care by seeking to meet this target, waiting times for fracture clinic appointments in a district general hospital were audited prospectively against this national guideline, with the intervening implementation of a virtual fracture clinic. MATERIALS AND METHODS The study was conducted as a prospective closed-loop audit in which the second cycle took place several months after a change in the clinical pathway for all referrals from the emergency department to fracture clinic. Data were gathered in real-time via a pro forma during fracture clinic consultations. RESULTS The first cycle demonstrated a non-compliant mean waiting time of 10.7 days, with 6% of patients being seen within the 72-hour target. Following the implementation of the virtual fracture clinic, the second cycle found that all patients were reviewed within the 72-hour target (mean 1.3 days). DISCUSSION The improvement in performance was delivered with no increase in clinic capacity. The cost of implementation was negligible. CONCLUSION A simple virtual fracture clinic model delivered a significant reduction in waiting times and achieved compliance with the British Orthopaedic Association guideline. Similar results could be achieved in subsequent deployment elsewhere in the NHS.

Squamous cell carcinoma and dental implants: A systematic review of case reports

Cancer is one of the leading causes of death world-wide. Apart from the most common etiopathological factors related to cancer, at times very rare causes such as irritant or foreign body induced carcinogenesis is not to be overlooked. To systematically review case reports concerned with the association between dental implants and oral squamous cell carcinoma. A Medline (PubMed), Cochrane database, and Google Scholar search was conducted of dental article published in English related to case reports concerned with oral squamous cell carcinoma occurring around dental implants from 2000 to 2014. Twenty articles were retrieved, which included 20 rare case reports which were systematically reviewed and the results were obtained pertaining to age, clinical symptoms, habits, previous history of cancer, potentially malignant disorders, systemic illness, and local factors. It is imperative to identify promptly persisting inflammation associated with implants. Since malignancy may disguise as periimplantitis, especially in patients who are at risk with contributing prominent predisposing factors.

Robotics and medicine: A scientific rainbow in hospital

The journey of robotics is a real wonder and astonishingly can be considered as a scientific rainbow showering surprising priceless power in the era of future technologies. The astonishing seven technologies discussed in this paper are da Vinci Robotic surgical system and sperm sorters for infertility, Veebot for blood investigation, Hanako the robotic dental patient for simulating the dental patient and helping a trainee dentist, RP-7 robot who is around-the-clock physician connecting the physician and patient, Robot for Interactive Body Assistance (RIBA) who is a RIBA serving as a nurse, Bushbot serving as a brilliant surgeon, and Virtibot helping in virtual autopsy. Thus, robotics in medicine is a budding field contributing a great lot to human life from before birth to afterlife in seven forms thus gracefully portraying a scientific rainbow in hospital environment.

Theranostics: A treasured tailor for tomorrow

Emerging as a targeted, safe, and efficient pharmacotherapy is the approach of theranostics, which focuses on patient-centered care. It is a combination of diagnosis and therapeutics. It provides a transition from conventional medicine to personalized medicine. It deals with the custom made treatment plan based on uniqueness of every individual thus resulting in right drug for the right patient at the right time. Genetics plays a significant role in theranostics. Theranostics provides a cost-effective specific successful treatment protocol. Pharmacogenetics, proteomics and biomarker profiling forms the backbone of theranostics. The role of theranostics is interestingly appreciated at multi levels with special consideration in oncology wherein nano formulations in the form of liposomes, dendrimers, polymeric nanoparticles, metallic nanoparticles, quantum dots and carbon nanotubes play a very important role. Thus, theranostics is a holistic transition from trial and error medicine to predictive, preventive and personalized medicine leading to improved quality care of pharmacotherapy.

Analysis of association of TaqI VDR gene polymorphism with the chronic periodontitis in Dravidian ethnicity

AIM

The aim of this study is to analyze the association of TaqI vitamin D receptor (VDR) gene polymorphism with the chronic periodontitis (CP) in Dravidian ethnicity.

MATERIALS AND METHODS

A total of 120 subjects were recruited for this study, which included 60 CP and 60 healthy controls. TaqI VDR gene polymorphism was analyzed using specific primers and amplified by polymerase chain reaction (PCR) and visualized under 2% agarose gel.

RESULTS

Our study results showed that Tt and tt genotype had a higher frequency of occurrence in CP compared with controls. Similarly, t allele was found to be associated with CP.

CONCLUSION

Our study concludes that TaqI VDR gene polymorphism is associated with CP in Dravidian ethnicity.

Weight gain with pizotifen therapy

OBJECTIVE

To describe the characteristics of weight gain occurring in children treated for migranous conditions with pizotifen

DESIGN

Retrospective case note review

SETTING

West Suffolk Hospital between 1999 and 2003 PATIENTS: 405 clinic attendances of 121 children receiving pizotifen treatment

MAIN OUTCOME MEASURES

Rates of change in weight for age z score between successive outpatient appointments were used to detect excessive weight gain.

RESULTS

The mean rate of weight z score increase for 105 patients receiving a constant dosage in 181 intervals between appointments was 0.79 standard deviations per year compared with 0.11 standard deviations per year for height z score increases. The rate of weight z score increase was not correlated with pizotifen dose per kg (r = -0.08), per m(2) (r = -0.05) or initial body mass index (r = -0.04). Mean rates of z score increase were similar in patients with a satisfactory and unsatisfactory therapeutic responses.

CONCLUSIONS

Excess weight gain in pizotifen therapy is not predicted by drug dosage or therapeutic response within the range of doses used in clinical practice.

FT-IR, FT-Raman spectra and ab initio HF, DFT vibrational analysis of p-chlorobenzoic acid

The infrared, the Fourier transform infrared and Fourier transform Raman spectra of p-chlorobenzoic acid (p-CBA) has been recorded in the region 4000-600 cm(-1), 4000-400 cm(-1) and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of p-CBA were obtained by the ab initio HF and DFT (B3LYP) methods with complete relaxation in the potential energy surface using 6-311+G(d,p) basis set. The harmonic-vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

Vibrational spectra and assignments of 3-aminobenzyl alcohol by ab initio Hartree-Fock and density functional method

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of 3-aminobenzyl alcohol. The FT-Raman and FT-IR spectra of 3-aminobenzyl alcohol were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by ab initio HF and density functional B3LYP method with 6-311+G(d,p) basis sets. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. A detailed interpretation of the infrared and Raman spectra of 3-aminobenzyl alcohol is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.

FT-IR, FT-Raman spectra and ab initio HF, DFT vibrational analysis of 2,3-difluoro phenol

The FT-IR and FT-Raman spectra of 2,3-difluoro phenol (2,3-DFP) has been recorded in the region 4000-400 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2,3-DFP were obtained by the ab initio HF and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-311+G(d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

Vibrational spectra and assignments of 2-amino-5-iodopyridine by ab initio Hartree-Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra of 2-amino-5-iodopyridine were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) methods with the 6-31G(d,p) basis set for C, N, H and LANL2DZ pseudopotential for I. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of 2-amino-5-iodopyridine is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 2-amino-5-methylphenol

The laser Raman and Fourier transform infrared spectra of 2-amino-5-methylphenol were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by HF and density functional B3LYP methods by using 6-311+G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-31G(d,p)/6-311+G(d,p) and B3LYP/6-31G(d,p)/6-311+G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of 2-amino-5-methylphenol is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.

FT-IR, FT-Raman spectra and ab initio DFT vibrational analysis of p-bromophenoxyacetic acid

The Fourier transform Raman and Fourier transform infrared spectra of p-bromophenoxyacetic acid were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) method with the 6-31G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of p-bromophenoxyacetic acid is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2,4-dichloro-6-nitrophenol

The FTIR and FT-Raman spectra of 2,4-dichloro-6-nitrophenol (2,4-DC6NP) has been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of (2,4-DC6NP) were obtained by the ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311+G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2-amino-5-chloropyridine

The FTIR and FT-Raman spectra of 2-amino-5-chloropyridine (ACP) has been recorded in the region 4000-400 and 3500-100 cm-1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of ACP were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311+G(2df,2p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

The culture of articular chondrocytes in hydrogel constructs within a bioreactor enhances cell proliferation and matrix synthesis

Bovine and human articular chondrocytes were seeded in 2% alginate constructs and cultured for up to 19 days in a rotating-wall-vessel (RWV) and under static conditions. Culture within the RWV enhanced DNA levels for bovine chondrocyte-seeded constructs when compared with static conditions but did not produce enhancement for human cells. There was a significant enhancement of glycosaminoglycans and hydroxyproline synthesis for both bovine and human chondrocytes. In all cases, histological analysis revealed enhanced Safranin-O staining in the peripheral regions of the constructs compared with the central region. There was an overall increase in staining intensity after culture within the RWV compared with static conditions. Type-II collagen was produced by both bovine and human chondrocytes in the peripheral and central regions of the constructs and the staining intensity was enhanced by culture within the RWV. A capsule of flattened cells containing type-I collagen developed around the constructs maintained under static conditions when seeded with either bovine or human chondrocytes, but not when cultured within the RWV bioreactor.

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues

MOTIVATION

Position specific scoring matrices (PSSMs) corresponding to aligned sequences of homologous proteins are commonly used in homology detection. A PSSM is generated on the basis of one of the homologues as a reference sequence, which is the query in the case of PSI-BLAST searches. The reference sequence is chosen arbitrarily while generating PSSMs for reverse BLAST searches. In this work we demonstrate that the use of multiple PSSMs corresponding to a given alignment and variable reference sequences is more effective than using traditional single PSSMs and hidden Markov models.

RESULTS

Searches for proteins with known 3-D structures have been made against three databases of protein family profiles corresponding to known structures: (1) One PSSM per family; (2) multiple PSSMs corresponding to an alignment and variable reference sequences for every family; and (3) hidden Markov models. A comparison of the performances of these three approaches suggests that the use of multiple PSSMs is most effective.

CONTACT

ns@mbu.iisc.ernet.in.

Psychological autopsy of suicide-a cross-sectional study

BACKGROUND

Psychological autopsy is the reconstruction of events leading to death. There are few studies on psychological autopsy.

AIM

To understand the profile of suicide completers and find out ways of dealing with it.

METHODS

Fifty suicide cases were analysed. Using a semi-structured, self-designed questionnaire, the family, friends and relatives of the deceased were interviewed.

RESULTS

The presence of some type of psychiatric disorder and stressful life events are two important reasons for committing suicide.

CONCLUSION

Psychological autopsy is a very important tool for assessing the causes and precipitants of suicide. More and more studies in this field are required with a larger sample size for the evaluation of suicides.

SUPFAM: a database of sequence superfamilies of protein domains

BACKGROUND

SUPFAM database is a compilation of superfamily relationships between protein domain families of either known or unknown 3-D structure. In SUPFAM, sequence families from Pfam and structural families from SCOP are associated, using profile matching, to result in sequence superfamilies of known structure. Subsequently all-against-all family profile matches are made to deduce a list of new potential superfamilies of yet unknown structure.

DESCRIPTION

The current version of SUPFAM (release 1.4) corresponds to significant enhancements and major developments compared to the earlier and basic version. In the present version we have used RPS-BLAST, which is robust and sensitive, for profile matching. The reliability of connections between protein families is ensured better than before by use of benchmarked criteria involving strict e-value cut-off and a minimal alignment length condition. An e-value based indication of reliability of connections is now presented in the database. Web access to a RPS-BLAST-based tool to associate a query sequence to one of the family profiles in SUPFAM is available with the current release. In terms of the scientific content the present release of SUPFAM is entirely reorganized with the use of 6190 Pfam families and 2317 structural families derived from SCOP. Due to a steep increase in the number of sequence and structural families used in SUPFAM the details of scientific content in the present release are almost entirely complementary to previous basic version. Of the 2286 families, we could relate 245 Pfam families with apparently no structural information to families of known 3-D structures, thus resulting in the identification of new families in the existing superfamilies. Using the profiles of 3904 Pfam families of yet unknown structure, an all-against-all comparison involving sequence-profile match resulted in clustering of 96 Pfam families into 39 new potential superfamilies.

CONCLUSION

SUPFAM presents many non-trivial superfamily relationships of sequence families involved in a variety of functions and hence the information content is of interest to a wide scientific community. The grouping of related proteins without a known structure in SUPFAM is useful in identifying priority targets for structural genomics initiatives and in the assignment of putative functions. Database URL: http://pauling.mbu.iisc.ernet.in/~supfam.

A study of clinical efficacy of sildenafil in patients with primary pulmonary hypertension

BACKGROUND

Primary pulmonary hypertension is a disorder with limited treatment options and poor outcome. Sildenafil, a pulmonary vasodilator, is likely to be beneficial in primary pulmonary hypertension. We studied the clinical efficacy of sildenafil in patients with primary pulmonary hypertension.

METHODS AND RESULTS

A registry of patients with primary pulmonary hypertension has been maintained in our hospital since January 1999. Of a total of 60 patients. 29 (M:16, F:13) consented to try sildenafiL. New York Heart Association functional class, six-minute walk test and Doppler echocardiographic evaluation of pulmonary artery pressure was done before and after treatment with sildenafil. Sildenafil was initiated at a dose of 25 mg thrice a day and increased up to 100 mg thrice a day as tolerated. There was a significant improvement in the functional class. The six-minute walked distance increased from 297.07+/-130.69 m at baseline to 427.68+/-85.35 m after 3 months of sildenafil therapy (p<0.0003). The mean of the pulmonary artery systolic pressure before starting sildenaffil was 109.26+/-24.15 mmHg (mean+/-SD) and it decreased to 95.15+/-24.64 mmHg (p<0.008). While 19 of the 31 historical controls in whom sildenafil was not given died during follow-up (11-44 months), only 1 of the 29 patients given sildenafil died (in an accident) during follow-up (5-20 months).

CONCLUSIONS

Sildenafil, a pulmonary vasodilator, has a beneficial effect in patients with primary pulmonary hypertension in improving the functional class, six-minute walked distance and in decreasing the pulmonary artery pressures.

A case-control study of plasma homocysteine levels in South Indians with and without coronary artery disease

BACKGROUND

An increased level of plasma homocysteine is being recognized as a new risk factor for coronary artery disease. Since there are not enough data about its importance in Indians with coronary artery disease, we aimed to assess the significance of plasma homocysteine as a coronary risk factor in South Indian patients.

METHODS AND RESULTS

In a case-control study, fasting plasma homocysteine levels were estimated in 565 subjects, of whom 221 were cases and 344 were controls. Of the 221 clinically defined cases, 112 underwent coronary angiography while 107 of the 344 controls had angiographically proven normal coronary arteries. Ninety healthy volunteers from the community were also included as controls. Fluorescent polarization immunosorbent assay was used to measure plasma homocysteine levels. In 12 patients, this method was compared to high pressure liquid chromatography and was found to give comparable results. The mean plasma homocysteine level was 18.30 +/- 10.08 micromol/L in clinically defined cases and 18.04 +/- 10.69 micromol/L in controls. Similarly, in angiographicallyproven coronary arterydisease patients, the mean plasma homocysteine levelwas 18.49 +/- 10.04 micromol/L and in individuals with angiographically normal coronary arteries, it was 19.16 +/- 11.38 micromol/L.

CONCLUSIONS

There is no statistically significant difference in plasma homocysteine levels between controls and cases with coronary artery disease. The mean plasma homocysteine levels in controls as assessed by fluorescent polarization immunosorbent assay in the present study population are higher as compared to other published reports.

Responses to time-varying stimuli in rat auditory cortex

Responses to frequency modulated (FM) sweeps were recorded in rat primary auditory cortex. Forty-four percent of the cells were direction-selective. For speed selectivity, the majority of the cells preferred faster sweeps. The results suggest that rat auditory cortex may be used for processing communication signals of their predators or for detecting spectral changes in acoustic signals.

CD14 mediated endogenous TNF-alpha release in HL60 AML cells: a potential model for CD14 mediated endogenous cytokine release in the treatment of AML

In previous studies, HL60 AML cells treated with tumor necrosis factor-alpha (TNF), interferon-gamma (IFN), and lipopolysaccharides (LPS) displayed decreased growth and viability, enhanced monocytic pathway differentiation and endogenous TNF release. Endogenous TNF release by LPS/TNF/IFN treated HL60 cells was postulated to play a role with the above findings. In these studies, HL60 cells expressed CD14 when treated with TNF, IFN, and LPS. CD14 mediates TNF release in monocytes/macrophages in response to binding of LPS with LPS binding protein (LBP). CD14 was not expressed in either untreated or LPS only treated HL60 cells. CD14 expression was present and greater with HL60 cells cultured with LPS/TNF/IFN vs TNF/IFN (47.47% vs 9.07% positive, respectively) suggesting synergism for LPS in CD14 induction. CD14 expression was associated with endogenous TNF release, and with significantly higher levels by HL60 cells treated with LPS/TNF/IFN vs TNF/IFN (p < 0.001). Addition of anti-CD14 antibody significantly reduced release of TNF in TNF/IFN (p < 0.001) and LPS/TNF/IFN (p = 0.0013) treated cells. KG1 and U937 AML cells treated with LPS, TNF, and IFN did not express CD14, nor release TNF. A model for inducing release of endogenous growth inhibitory cytokines by CD14 bearing AML cells is proposed as an approach to AML therapy.