Time Series Modeling of Tuberculosis Cases in India from 2017 to 2022 Based on the SARIMA-NNAR Hybrid Model.

Tuberculosis (TB) is still one of the severe progressive threats in developing countries. There are some limitations to social and economic development among developing nations. The present study forecasts the notified prevalence of TB based on seasonality and trend by applying the SARIMA-NNAR hybrid model. The NIKSHAY database repository provides monthly informed TB cases (2017 to 2022) in India. A time series model was constructed based on the seasonal autoregressive integrated moving averages (SARIMA), neural network autoregressive (NNAR), and, SARIM-NNAR hybrid models. These models were estimated with the help of the Bayesian information criterion (BIC) and Akaike information criterion (AIC). These models were established to compare the estimation. A total of 12,576,746 notified TB cases were reported over the years whereas the average case was observed as 174,677.02. The evaluating parameters values of RMSE, MAE, and MAPE for the hybrid model were found to be (13738.97), (10369.48), and (06.68). SARIMA model was (19104.38), (14304.15), and (09.45) and the NNAR were (11566.83), (9049.27), and (05.37), respectively. Therefore, the NNAR model performs better with time series data for fitting and forecasting compared to other models such as SARIMA as well as the hybrid model. The NNAR model indicated a suitable model for notified TB incidence forecasting. This model can be a good tool for future prediction. This will assist in devising a policy and strategizing for better prevention and control.

Analysis of genetic diversity in indian natural populations of drosophila ananassae.

Forty five natural populations of Drosophila ananassae, collected from entire geo-climatic regions of the India were analyzed to determine the distribution of genetic diversity relative to different eco-geographic factors. Quantitative data on the frequencies of three cosmopolitan inversions in the sampled populations were utilized to deduce Nei's gene diversity estimates. Populations were grouped according to the time of collection (years and month); collection-regions like coastal and mainland regions, and collection-seasons. Further, data was subjected to network analysis to detect community structure in the populations and Modularity analysis to quantify the strength in community structure. Gene-diversity statistics revealed the presence of significant variability in the Indian natural populations of D.ananassae. Off all the parameters used to group the populations, geographical attributes seems to have maximum, while the time of collection and seasons have minimum influence on the genetic variability in Indian natural populations of D.ananassae. The results clearly link the association of genetic variability with environmental heterogeneity, elucidating the role of environment specific natural selection. The homogenizing effects could be due to genetic hitchhiking and canalization.

Diagnosis of TB: From conventional to modern molecular protocols.

Tuberculosis (TB) is an infectious disease caused by different strains of Mycobacterium tuberculosis complex. TB is a curable infection if diagnosed correctly and timely. Late diagnosis and improper treatment may lead to relapse or its escalation to MDR / XDR-TB. TB with HIV co-infection is difficult to diagnose by conventional set-up. Also, detection of child TB and extrapulmonary TB has its own set of problems and is not straightforward to diagnose. The increasing complexity of TB due to the advent of new circulating strains and invasion to the regions where it was non-existent or thought to be eradicated is putting a severe strain on the health management services and making it an unmanageable pandemic. This increasing complexity has led to the spurt in the development of TB diagnostics platforms. This review focuses on the new emerging technologies that have changed the diagnostics landscape.

Design, display and immunogenicity of HIV1 gp120 fragment immunogens on virus-like particles.

The broadly neutralizing antibody against HIV-1, b12, binds to the CD4 binding site (CD4bs) on the outer domain (OD) of the gp120 subunit of HIV-1 Env. We have previously reported the design of an E. coli expressed fragment of HIV-1 gp120, b122a, containing about 70% of the b12 epitope with the idea of focusing the immune response to this structure. Since the b122a structure was found to be only partially folded, as assessed by circular dichroism and protease resistance, we attempted to stabilize it by the introduction of additional disulfide bonds. One such mutant, b122a1-b showed increased stability and bound b12 with 30-fold greater affinity as compared to b122a. Various b122a and OD fragment proteins were displayed on the surface of Qß virus-like particles. Sera raised against these particles in six-month long rabbit immunization studies could neutralize Tier1 viruses across different subtypes with the best results observed with b122a1-b displayed particles. Significantly higher amounts of antibodies directed towards the CD4bs were also elicited by particles displaying b122a1-b. This study highlights the ability of fragment immunogens to focus the antibody response to the conserved CD4bs of HIV-1.

Surface plasmon resonance (SPR) based binding studies of refolded single chain antibody fragments.

Recent advances in Recombinant antibody technology / Antibody Engineering has given impetus to the genetic manipulation of antibody fragments that has paved the way for better understanding of the structure and functions of immunoglobulins and also has escalated their use in immunotherapy. Bacterial expression system such as Escherichia coli has complemented this technique through the expression of recombinant antibodies. Present communication has attempted to optimize the expression and refolding protocol of single chain fragment variable (ScFv) and single chain antigen binding fragment (ScFab) using E.coli expression system. Efficiency of refolding protocol was validated by structural analysis by CD, native folding by fluorescence and functional analysis by its binding with full length HIV-1 gp120 via SPR. Results show the predominant ß-sheet (CD) as secondary structural content and native folding via red shift (tryptophan fluorescence). The single chain fragments have shown good binding with HIV-1 gp120 thus validating the expression and refolding strategy and also reinstating E.coli as model expression system for recombinant antibody engineering. SPR based binding analysis coupled with E.coli based expression and purification will have implication for HIV therapeutics and will set a benchmark for future studies of similar kind.

Identifying ADHD in adults using the international personality disorder examination screening questionnaire.

BACKGROUND: Attention deficit hyperactivity disorder (ADHD) is frequently diagnosed concurrently with a personality disorder (PD) in adulthood. Both are trait-like chronic disorders with substantial similarities. AIM: To measure the accuracy of the International Personality Disorder Examination screening questionnaire (IPDE-SQ) in identifying ADHD in adults from a psychiatric population. METHOD: Participants (n = 119) from mental health services completed an ADHD interview and the IPDE-SQ. MAIN RESULTS: Although many IPDE-SQ subscales demonstrated good sensitivity in identifying ADHD, a potential 11-item scale from IPDE-SQ components had excellent sensitivity (84%) and specificity (82%). CONCLUSIONS: An 11-item subscale from the IPDE-SQ shows potential as a screening instrument for ADHD in an adult psychiatric population.

Critical Analysis of Psychiatrists' Opinion in GP Referral letter.

BACKGROUND: Primary and secondary care communication is the cornerstone of patient's care. Proper dialogue should be established. The shared care protocol was an attempt to try to fill gaps and build bridges. METHODS: A special form was designed to collect information about psychiatrists' opinion on GPs' referral letter to psychiatric services. It contained 14 items, each item was marked as essential, can be included or irrelevant. This form was sent electronically to psychiatrists in South Essex University NHS Trust. They are 98 in total. It was inputted on Excel data sheet and was analysed. RESULTS: 44 psychiatrists responded. All respondents agreed that reason for referral is essential. Concise description of the condition, risks and current medication were rated as essential in more than 90%. Past medical history, past psychiatric history and current physical health were essential in 79%. DISCUSSION: All professionals involved should participate in evaluating and refining communication. Psychiatrists' opinion in GPs letters is paramount as they are the recipients and their assessments and future management plan should be geared to address the GP's concerns. This is shown clearly by the psychiatrists agreeing that reason for referral should be included in all letters, followed by what the GP has already done and what risks the patient presents. CONCLUSION: Improving communication between health professionals, improves patient's care, saves time and money, and in addition prevents duplication of investigation and procedures.

Antipsychotic prescribing before clozapine in a community psychiatric hospital: a case note review.

OBJECTIVES: To examine whether prescribing Clozapine was delayed in Treatment Resistant Schizophrenia (TRS), and elucidate possible reasons for this. METHODS: A retrospective Case note review was done. The main outcome measured was the mean maximum theoretical delay in starting Clozapine. In analyses, mean values were compared using an unpaired, 2-sided Student t-test. The association between duration of illness and theoretical delay was analysed by scatterplot and Pearson correlation coefficient. RESULTS: 42 case notes were reviewed. Mean age of subjects was 40.1 years. The mean maximum theoretical delay in all patients was 5 years. A statistically significant longer delay was found in patients over 30 years, patients diagnosed with TRS before 1991,and for patients before the introduction of Risperidone. Delay was significantly shorter for patients admitted to a psychiatric hospital more than once a year. CONCLUSION: There is a strong indication that Clozapine was not introduced at the earliest opportunity. Factors contributing to the delay include the patient's age, using sequential antipsychotic trials, and the failure to identify TRS. The use of Clozapine appears to have been adopted more in recent years, with a delay of five years to Clozapine for those diagnosed pre-1991, reducing to two years for those diagnosed pre-2003. SIGNIFICANT OUTCOMES: Mean average delay of prescribing clozapine was 5 years. Statistically significant delays in patients over 30 years of age. LIMITATIONS: There was no evaluation of: Reasons for co-prescribing of antipsychotics. Reasons for delay in prescribing Clozapine, e.g. prescriber inexperience, patient choice, risk of non-compliance etc. Evidence of treatment resistance, and whether primary or secondary in onset.

Effect of signal peptide on stability and folding of Escherichia coli thioredoxin.

The signal peptide plays a key role in targeting and membrane insertion of secretory and membrane proteins in both prokaryotes and eukaryotes. In E. coli, recombinant proteins can be targeted to the periplasmic space by fusing naturally occurring signal sequences to their N-terminus. The model protein thioredoxin was fused at its N-terminus with malE and pelB signal sequences. While WT and the pelB fusion are soluble when expressed, the malE fusion was targeted to inclusion bodies and was refolded in vitro to yield a monomeric product with identical secondary structure to WT thioredoxin. The purified recombinant proteins were studied with respect to their thermodynamic stability, aggregation propensity and activity, and compared with wild type thioredoxin, without a signal sequence. The presence of signal sequences leads to thermodynamic destabilization, reduces the activity and increases the aggregation propensity, with malE having much larger effects than pelB. These studies show that besides acting as address labels, signal sequences can modulate protein stability and aggregation in a sequence dependent manner.

Design of an Escherichia coli expressed HIV-1 gp120 fragment immunogen that binds to b12 and induces broad and potent neutralizing antibodies.

b12, one of the few broadly neutralizing antibodies against HIV-1, binds to the CD4 binding site (CD4bs) on the gp120 subunit of HIV-1 Env. Two small fragments of HIV-1 gp120, b121a and b122a, which display about 70% of the b12 epitope and include solubility-enhancing mutations, were designed. Bacterially expressed b121a/b122a were partially folded and could bind b12 but not the CD4bs-directed non-neutralizing antibody b6. Sera from rabbits primed with b121a or b122a protein fragments and boosted with full-length gp120 showed broad neutralizing activity in a TZM-bl assay against a 16-virus panel that included nine Tier 2 and 3 viruses as well as in a five-virus panel previously designed to screen for broad neutralization. Using a mean IC50 cut-off of 50, sera from control rabbits immunized with gp120 alone neutralized only one virus of the 14 non-Tier 1 viruses tested (7%), whereas sera from b121a- and b122a-immunized rabbits neutralized seven (50%) and twelve (86%) viruses, respectively. Serum depletion studies confirmed that neutralization was gp120-directed and that sera from animals immunized with gp120 contained lower amounts of CD4bs-directed antibodies than corresponding sera from animals immunized with b121a/b122a. Competition binding assays with b12 also showed that b121a/2a sera contained significantly higher amounts of antibodies directed toward the CD4 binding site than the gp120 sera. The data demonstrate that it is possible to elicit broadly neutralizing sera against HIV-1 in small animals.

Simultaneous refolding and purification of recombinant proteins by macro-(affinity ligand) facilitated three-phase partitioning.

A strategy called macro-(affinity ligand) facilitated three-phase partitioning (MLFTPP) is described for refolding of a diverse set of recombinant proteins starting from the solubilized inclusion bodies. It essentially consists of: (i) binding of the protein with a suitable smart polymer and (ii) precipitating the polymer-protein complex as an interfacial layer by mixing in a suitable amount of ammonium sulfate and t-butanol. Smart polymers are stimuli-responsive polymers that become insoluble on the application of a suitable stimulus (e.g., a change in the temperature, pH, or concentration of a chemical species such as Ca(2+) or K(+)). The MLFTPP process required approximately 10min, and the refolded proteins were found to be homogeneous on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The folded proteins were characterized by fluorescence emission spectroscopy, circular dichroism spectroscopy, biological activity, melting temperature, and surface hydrophobicity measurements by 8-anilino-1-naphthalenesulfonate fluorescence. Two refolded antibody fragments were also characterized by measuring K(D) by Biacore by using immobilized HIV-1 gp120. The data demonstrate that MLFTPP is a rapid and convenient procedure for refolding a variety of proteins from inclusion bodies at high concentration. Although establishing the generic nature of the approach would require wider trials by different groups, its success with the diverse kinds of proteins tried so far appears to be promising.

Smart polymer mediated purification and recovery of active proteins from inclusion bodies.

Obtaining correctly folded proteins from inclusion bodies of recombinant proteins expressed in bacterial hosts requires solubilization with denaturants and a refolding step. Aggregation competes with the second step. Refolding of eight different proteins was carried out by precipitation with smart polymers. These proteins have different molecular weights, different number of disulfide bridges and some of these are known to be highly prone to aggregation. A high throughput refolding screen based upon fluorescence emission maximum around 340 nm (for correctly folded proteins) was developed to identify the suitable smart polymer. The proteins could be dissociated and recovered after the refolding step. The refolding could be scaled up and high refolding yields in the range of 8 mg L(-1) (for CD4D12, the first two domains of human CD4) to 58 mg L(-1) (for malETrx, thioredoxin fused with signal peptide of maltose binding protein) were obtained. Dynamic light scattering (DLS) showed that polymer if chosen correctly acted as a pseudochaperonin and bound to the proteins. It also showed that the time for maximum binding was about 50 min which coincided with the time required for incubation (with the polymer) before precipitation for maximum recovery of folded proteins. The refolded proteins were characterized by fluorescence emission spectra, circular dichroism (CD) spectroscopy, melting temperature (T(m)), and surface hydrophobicity measurement by ANS (8-anilino1-naphthalene sulfonic acid) fluorescence. Biological activity assay for thioredoxin and fluorescence based assay in case of maltose binding protein (MBP) were also carried out to confirm correct refolding.

Population genetics of Drosophila ananassae.

Drosophila ananassae Doleschall is a cosmopolitan and domestic species. It occupies a unique status among Drosophila species due to certain peculiarities in its genetic behaviour and is of common occurrence in India. Quantitative genetics of sexual and non-sexual traits provided evidence for genetic control of these traits. D. ananassae exhibits high level of chromosomal polymorphism in its natural populations. Indian natural populations of D. ananassae show geographic differentiation of inversion polymorphism due to their adaptation to varying environments and natural selection operates to maintain three cosmopolitan inversions. Populations do not show divergence on temporal scale, an evidence for rigid polymorphism. D. ananassae populations show substantial degree of sub-structuring and exist as semi-isolated populations. Gene flow is low despite co-transportation with human goods. There is persistence of cosmopolitan inversions when populations are transferred to laboratory conditions, which suggests that heterotic buffering is associated with these inversions in D. ananassae. Populations collected from similar environmental conditions that initially show high degree of genetic similarity have diverged to different degrees in laboratory environment. This randomness could be due to genetic drift. Interracial hybridization does not lead to breakdown of heterosis associated with cosmopolitan inversions, which shows that there is lack of genetic co-adaptation in D. ananassae. Linkage disequilibrium between independent inversions in laboratory populations has often been observed, which is likely to be due to suppression of crossing-over and random genetic drift. No evidence for chromosomal interactions has been found in natural and laboratory populations of D. ananassae. This strengthens the previous suggestion that there is lack of genetic co-adaptation in D. ananassae.

Population genetics of Drosophila ananassae: genetic differentiation among Indian natural populations at the level of inversion polymorphism.

The present study, which is one of the longest temporal (two decades) and largest spatial (different parts of India covered) investigations on inversion polymorphism in natural populations of D. ananassae, was undertaken to understand the dynamics of inversion polymorphism in a broad and comprehensive manner. Forty-five natural populations from different ecogeographic regions of the country (covering the regions from Kashmir to Kanniyakumari and Gujarat to Nagaland) were analysed for chromosomal inversions. All the populations show the presence of the three cosmopolitan inversions, frequencies of which vary among the populations analysed. Simple correlations between frequencies of different inversions and regression analysis of inversion frequencies with latitude, longitude and altitude were insignificant. This reinforces the concept of rigid polymorphism in D. ananassae. Genetic divergence (spatial and temporal) at the level of chromosomal polymorphism among natural populations was calculated. Results show spatial divergence but no temporal divergence. Rigid polymorphic systems of D. ananassae did not show long-term directional trends. On the basis of the present study, and after including comparisons with the studies conducted more than two decades ago, the most important conclusion to be drawn is that the three cosmopolitan inversions in D. ananassae segregate within populations at fairly similar frequencies, and the general geographic pattern has remained constant.