Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds

In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.

Genome wide copy number variations using Porcine 60K SNP Beadchip in Landlly pigs

In the present study, Porcine 60K SNP genotype data from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) across the autosomes. A total of 386 CNVs were identified using Hidden Markov Model (HMM) in PennCNV software, which were subsequently aggregated to 115 CNV regions (CNVRs). Among the total detected CNVRs, 58 gain, 49 were loss type while remaining 8 events were both gain and loss types. Identified CNVRs covered 12.5 Mb (0.55%) of Sus scrofa reference 11.1 genome. Comparison of our results with previous investigations on pigs revealed that approximately 75% CNVRs were novel, which may be due to differences in genetic background, environment and implementation of artificial selection in Landlly pigs. Functional annotation and pathway analysis showed the significant enrichment of 267 well-annotated Sus scrofa genes in CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Additionally, KIT and FUT1 were two major genes detected on CNVR in our population. This investigation provided a comprehensive overview of CNV distribution in the Indian porcine genome for the first time, which may be useful for further investigating the association of important quantitative traits in Landlly pigs.Highlights115 CNVRs were identified in 69 Landlly pig population.Approximately 75% detected CNVRs were novel for Landlly population.Significant enrichment of 267 well-annotated Sus scrofa genes observed in these CNVRs.These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity.Comprehensive CNV map in the Indian porcine genome developed for the first time.

Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs

BACKGROUND

Genetic correlations between complex traits suggest that pleiotropic variants contribute to trait variation. Genome-wide association studies (GWAS) aim to uncover the genetic underpinnings of traits. Multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS enable detecting variants associated with multiple phenotypes. In this study, we used array-derived genotypes and phenotypes for 24 reproduction, production, and conformation traits to explore differences between the two methods and used imputed sequence variant genotypes to fine-map six quantitative trait loci (QTL).

RESULTS

We considered genotypes at 44,733 SNPs for 5,753 pigs from the Swiss Large White breed that had deregressed breeding values for 24 traits. Single-trait association analyses revealed eleven QTL that affected 15 traits. Multi-trait association testing and the meta-analysis of the single-trait GWAS revealed between 3 and 6 QTL, respectively, in three groups of traits. The multi-trait methods revealed three loci that were not detected in the single-trait GWAS. Four QTL that were identified in the single-trait GWAS, remained undetected in the multi-trait analyses. To pinpoint candidate causal variants for the QTL, we imputed the array-derived genotypes to the sequence level using a sequenced reference panel consisting of 421 pigs. This approach provided genotypes at 16 million imputed sequence variants with a mean accuracy of imputation of 0.94. The fine-mapping of six QTL with imputed sequence variant genotypes revealed four previously proposed causal mutations among the top variants.

CONCLUSIONS

Our findings in a medium-size cohort of pigs suggest that multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS provide very similar results. Although multi-trait association methods provide a useful overview of pleiotropic loci segregating in mapping populations, the investigation of single-trait association studies is still advised, as multi-trait methods may miss QTL that are uncovered in single-trait GWAS.

Exploring barriers to vaccine delivery in adult migrants: a qualitative study in primary care

Background

The COVID-19 pandemic has highlighted shortfalls in the delivery of vaccine programmes to older migrant groups. Guidelines exist, however, little is known around care pathways and engagement of these older cohorts in routine vaccinations in primary care, including catch-up programmes. We explored the views of primary care professionals around barriers and facilitators to catch-up vaccination in adult migrants (defined as foreign born; 18+ years) with incomplete or uncertain vaccination status.

Methods

We did a qualitative interview study with purposive sampling and thematic analysis in UK primary care (50 practices included nationally; 1 hour qualitative interviews) with 64 primary care professionals (PCPs): 48 clinical staff including GPs, Practice Nurses and healthcare assistants (HCAs); 16 administrative staff including practice managers and receptionists (mean age 45 years; 84.4% female; a range of ethnicities).

Results

Participants highlighted direct and indirect barriers to catch-up vaccines in adult migrants who may have missed vaccines as children, missed boosters, and not be aligned with the UK's vaccine schedule, from both a personal and service-delivery level, with themes including: lack of training and knowledge of guidance around catch-up vaccination among staff; unclear or incomplete vaccine records; and lack of incentivization (including financial reimbursement) and dedicated time and care pathways. Adult migrants were reported as being excluded from many vaccination initiatives, most of which focus exclusively on children. PCPs noted that migrants expressed to them a range of views around vaccines, from positivity to uncertainty, to refusal.

Conclusions

Vaccine uptake in adult migrants could be improved through implementing new financial incentives, strengthening care pathways and training, and working directly with local community groups to improve understanding around the benefits of vaccination at all ages.

Key messages

Clinical correlation and assessment of olfactory dysfunction with n-butanol in COVID-19 patients: our experience

Background: Studies showed olfactory disturbances in COVID patients. This has attracted focus of clinicians as an easy clinical screening tool in suspected population. Material and methods: 70 mild and moderate category COVID-19 RT-PCR positive patients, more than 10 years of age were tested on day of admission for olfaction with serial dilution of n-butanol and asked to grade severity of their olfactory dysfunction according to visual analogue score from 1-10. Results: Fatigue 42 (93.33%), sore throat 37 (82.22%), fever 36 (80%) and dyspnea 23 (51.11%) were the most common symptoms in moderate patients. Diabetes, hypertension and allergy were the three prominent risk factors. At time of admission, n-butanol diagnosed 20 patients having olfactory dysfunction compared to 11 by VAS. Patients tend to grade their dysfunction higher on VAS whereas the n-butanol test classified their olfactory dysfunction lower. Viral load and high CRP were not found to be significantly related with olfactory dysfunction. d-Dimer and LDH levels were found statistically associated with higher grading of olfactory dysfunction detected by n-butanol. Conclusion: The majority of cases developed hyposmia before they were admitted to hospital even before they realized that they were having hyposmia as revealed by n-butanol testing. We should go for objective tests of olfaction.

Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India

India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and F _ST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and F _ST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.

Characterisation and comparison of immune response mechanisms in an indigenous and a commercial pig breed after classical swine fever vaccination

The live attenuated classical swine fever (CSF) vaccine has been successfully used to prevent and control CSF outbreaks for 6 decades. However, the immune response mechanisms against the vaccine remain poorly understood. Moreover, very few reports exist regarding the breed differences in the response to CSF vaccine. In this study, we generated the peripheral blood mononuclear cell transcriptomes of indigenous Ghurrah and commercial Landrace pig breeds, before and 7 days after CSF vaccination. Subsequently, between and within-breed differential gene expression analyses were carried out. Results revealed large differences in pre-vaccination peripheral blood mononuclear cell transcriptome profiles of the two breeds, which were homogenised 7 days after vaccination. Before vaccination, gene set enrichment analysis showed that pathways related to antigen sensing and innate immune response were enriched in Ghurrah, while pathways related to adaptive immunity were enriched in Landrace. Ghurrah exhibited greater immunomodulation compared to Landrace following the vaccination. In Ghurrah, cell-cycle processes and T-cell response pathways were upregulated after vaccination. However, no pathways were upregulated in Landrace after vaccination. Pathways related to inflammation were downregulated in both the breeds after vaccination. Key regulators of inflammation such as IL1A, IL1B, NFKBIA and TNF genes were strongly downregulated in both the breeds after vaccination. Overall, our results have elucidated the mechanisms of host immune response against CSF vaccination in two distinct breeds and revealed common key genes instrumental in the global immune response to the vaccine.

Analysis of selection signatures reveals important insights into the adaptability of high-altitude Indian sheep breed Changthangi

Changthangi is a high-altitude sheep breed of India that is adapted to cold and hypoxic climate of Himalayas. In the present study, we analysed population structure of Changthangi and contrasted it with selected Indian and European commercial sheep breeds to detect genomic regions under positive selection. The Illumina OvineSNP50v1 genotype data on 292 animals from seven different sheep breeds i.e., Changthangi (n = 29), Garole (n = 26), Deccani (n = 24), Tibetan (n = 37), Rambouillet (n = 102) and Australian Merino (n = 50) was used. European Mouflon (n = 24) was used as an out-group for studying the stratification and phylogenetic lineage. While the principal component analysis (PCA) revealed Changthangi to cluster with Tibetan sheep; TREEMIX and ADMIXTURE results also detected the introgression of lowland Indian sheep inheritance in Changthangi. Changthangi sheep were compared with other breed groups as reference i.e., commercial (Australian Merino and Rambouillet), Indian (Deccani, Garole and Tibetan) and breeds inhabiting plains (Australian Merino, Rambouillet, Deccani and Garole). Genomic comparisons of Changthangi using cross population extended haplotype homozygosity (XP-EHH) showed multiple functional regions present on Ovis aries (Oar) chromosomes 2, 3, 6 and 18 to be under selection in Changthangi sheep. These regions were related with adaptation to climatic and hypoxic stressors, fleece characteristics and functioning of immune and reproductive systems. UCP genes, associated with adaptation to cold and hypoxic conditions, were the main loci under positive selection in Changthangi sheep population. The selection signals in Indian and European commercial sheep breeds were mainly associated with body weight and carcass traits. Furthermore, selection signals found in different comparisons were found to be part of different quantitative trait loci (QTLs) associated with important traits in different breed classes. The genes present in these regions are suitable candidates for future studies on the genetic mechanisms underlying high-altitude adaptation.

Accurate assessment of body weights using morphometric measurements in Landlly pigs

The aim of the study was to evaluate 16 novel morphometric traits of Landlly piglets at weaning (6 weeks) and post weaning (8 weeks) stage and to predict corresponding body weight from the measurements. A total of 279 Landlly piglets (n = 279, 75% Landrace + 25% Ghurrah crosses) were enrolled in this study. Body length, heart girth, paunch girth, height at wither, height at back, rump width, thigh circumference, neck circumference, and body depth had high correlation coefficients (0.8-0.97) with body weight at both the stages. Stepwise regression showed that body length and heart girth contributed most in prediction of both body weights while height at wither for body weight at 6 weeks and neck circumference for body weight at 8 weeks was the next highest contributing trait. Akaike's information criterion, Bayesian information criteria, adjusted R², concordance correlation coefficient, bias correction factor, modeling efficiency, and coefficient of model determination were used to determine the most appropriate model for the prediction of body weight. Model containing body length and heart girth was fitted best to data for prediction of body weight at both weaning and post weaning stage with adjusted R² values of 0.94 and 0.96, respectively. Hence, 2 different models were proposed for accurately predicting body weight in Landlly pigs at 6 and 8 weeks.

Identification of genes affecting milk fat and fatty acid composition in Vrindavani crossbred cattle using 50 K SNP-Chip

The aim of this study was to identify candidate genes associated with milk fat per cent and fatty acid (FA) composition in Vrindavani cattle using the Illumina 50 K single-nucleotide polymorphism (SNP) array. After quality control, a total of 41,427 informative and high-quality SNPs were used for a genome-wide association study (GWAS) for milk fat percentage and 16 different types of fatty acids. Lactation stage, parity, test day milk yield, and proportion of exotic inheritance were included as fixed effects in the GWAS model. A total of 67 genome-wide significant (P < 1.20 × 10^-06) SNPs and 176 suggestive significant (P < 2.41 × 10^-05) SNPs were identified. Out of these, 15 SNPs were associated with more than one trait. The strongest associations were found on BTA14 for milk fat percentage and on BTA2 and BTA16 for polyunsaturated fatty acids. Several significant SNPs were identified close to or within the genes ELOVL6, FABP4, PMP2, PLIN1, MFGE8, GHRL2, and LDLRAD3 which are known to be associated with fat percentage and FA composition in dairy cattle breeds. This study is a step forward to better characterize the molecular mechanisms of phenotypic variation in milk fatty acids in a taurine-indicine composite cattle breed reared in tropical environments.

A 1.6 Mb region on SSC2 is associated with antibody response to classical swine fever vaccination in a mixed pig population

Classical Swine Fever (CSF) is a contagious viral disease of pigs which is endemic in several parts of the world, including India. Prophylactic vaccination using live attenuated vaccine is the preferred method of control. However, there is significant inter-individual variation in the antibody response to vaccination. In this study, we measured the E2 antibody blocking percentage after 21 days of CSF vaccination in a mixed pig population consisting of Landrace, indigenous Ghurrah pigs, and their crossbreds. A Genome Wide Association Study (GWAS) carried out using single-SNP and haplotype based methods detected a 1.6 Mb region on SSC2 (28.92-30.52 Mb) as significantly associated with antibody response to CSF vaccination. The significant region and 1 Mb flanking sequences encompass 3 genes - EIF3M, DNAJC24 and ARL14EP, which code for proteins involved in Pestivirus replication and host immune response system. Our results combined with previous studies on immune response of pigs present this region as a suitable candidate for future functional investigations.

Signatures of Selection in Composite Vrindavani Cattle of India

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (F_ST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.

Measures of Neural Similarity

One fundamental question is what makes two brain states similar. For example, what makes the activity in visual cortex elicited from viewing a robin similar to a sparrow? One common assumption in fMRI analysis is that neural similarity is described by Pearson correlation. However, there are a host of other possibilities, including Minkowski and Mahalanobis measures, with each differing in its mathematical, theoretical, and neural computational assumptions. Moreover, the operable measures may vary across brain regions and tasks. Here, we evaluated which of several competing similarity measures best captured neural similarity. Our technique uses a decoding approach to assess the information present in a brain region, and the similarity measures that best correspond to the classifier’s confusion matrix are preferred. Across two published fMRI datasets, we found the preferred neural similarity measures were common across brain regions but differed across tasks. Moreover, Pearson correlation was consistently surpassed by alternatives.

A systematic review of left unilateral electroconvulsive therapy

OBJECTIVE

To systematically review the published clinical trials, case series, and case reports on left unilateral (LUL) electrode placement for clinical electroconvulsive therapy (ECT).

METHOD

PubMed, Ovid Medline, and the Cochrane Library were searched for articles concerning LUL ECT. Number of patients, efficacy, and cognitive outcomes were extracted from the papers that met our inclusion criteria.

RESULTS

A total of 52 articles were included in this review, consisting of 33 clinical trials, seven case series, and 12 case reports.

CONCLUSION

Overall, the efficacy of LUL electrode placement for the treatment of depression and psychosis is similar to that of right unilateral (RUL) and bilateral (BL) electrode placements. Patients receiving LUL ECT tend to experience more verbal memory impairment than patients receiving RUL ECT, but less verbal impairment than patients receiving BL ECT. In contrast, patients receiving LUL ECT tended to experience the least visual and nonverbal memory impairment, compared to patients receiving RUL or BL ECT.

Who and how in the regulation of mitochondrial cristae shape and function

Mitochondrial adaptation to different physiological conditions highly relies on the regulation of mitochondrial ultrastructure, particularly at the level of cristae compartment. Cristae represent the membrane hub where most of the respiratory complexes embed to account for OXPHOS and energy production in the form of adenosine triphosphate (ATP). Changes in cristae number and shape define the respiratory capacity as well as cell viability. The identification of key regulators of cristae morphology and the understanding of their contribution to the mitochondrial ultrastructure and function have become an strategic goal to understand mitochondrial disorders and to exploit as therapeutic targets. This review summarizes the known regulators of cristae ultrastructure and discusses their contribution and implications for mitochondrial dysfunction.

Timing of Pregnancy After Kidney Transplantation and Risk of Allograft Failure

The optimal timing of pregnancy after kidney transplantation remains uncertain. We determined the risk of allograft failure among women who became pregnant within the first 3 posttransplant years. Among 21 814 women aged 15-45 years who received a first kidney-only transplant between 1990 and 2010 captured in the United States Renal Data System, n = 729 pregnancies were identified using Medicare claims. The probability of allograft failure from any cause including death (ACGL) at 1, 3, and 5 years after pregnancy was 9.6%, 25.9%, and 36.6%. In multivariate analyses, pregnancy in the first posttransplant year was associated with an increased risk of ACGL (hazard ratio [HR]: 1.18; 95% confidence interval [CI] 1.00, 1.40) and death censored graft loss (DCGL) (HR:1.25; 95% CI 1.04, 1.50), while pregnancy in the second posttransplant year was associated with an increased risk of DCGL (HR: 1.26; 95% CI 1.06, 1.50). Pregnancy in the third posttransplant year was not associated with an increased risk of ACGL or DCGL. These findings demonstrate a higher incidence of allograft failure after pregnancy than previously reported and that the increased risk of allograft failure extends to pregnancies in the second posttransplant year.

Decontamination of heavy metal laden sewage sludge with simultaneous solids reduction using thermophilic sulfur and ferrous oxidizing species

A possibility of using simultaneous sewage sludge digestion and metal leaching (SSDML) process at the thermophilic temperature to remove heavy metals and suspended solids from sewage sludge is explored in this study. Though thermophilic sludge digestion efficiently produces a stable sludge, its inability to remove heavy metals requires it to be used in tandem with another process like bioleaching for metal reduction. Previously, different temperature optima were known for the heterotrophs (thermophilic) responsible for the sludge digestion and the autotrophs involved in bioleaching (mesophilic), because of which the metal concentration was brought down separately in a different reactor. In our study, SSDML process was carried out at 50 °C (thermophilic) by using ferrous sulfate (batch-1) and sulfur (batch-2) as the energy source in two reactors. The concentration of volatile suspended solids reduced by >40% in both batches, while that of heavy metals zinc, copper, chromium, cadmium and nickel decreased by >50% in both batch-1 and batch-2. Lead got leached out only in batch-1. Using 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis analysis, Alicyclobacillus tolerans was found to be the microorganism responsible for lowering the pH in both the reactors at thermophilic temperature. The indicator organism count was also below the maximum permissible limit making sludge suitable for agricultural use. Our results indicate that SSDML at thermophilic temperature can be effectively used for reduction of heavy metals and suspended solids from sewage sludge.

Getting England to be more physically active: are the Public Health Responsibility Deal's physical activity pledges the answer?

BACKGROUND

The Public Health Responsibility Deal (RD) in England is a public-private partnership involving voluntary pledges between government, industry, and other organisations to improve public health by addressing alcohol, food, health at work, and physical activity. This paper analyses the RD physical activity (PA) pledges in terms of the evidence of their potential effectiveness, and the likelihood that they have motivated actions among organisations that would not otherwise have taken place.

METHODS

We systematically reviewed evidence of the effectiveness of interventions proposed in four PA pledges of the RD, namely, those on physical activity in the community; physical activity guidelines; active travel; and physical activity in the workplace. We then analysed publically available data on RD signatory organisations' plans and progress towards achieving the physical activity pledges, and assessed the extent to which activities among organisations could be attributed to the RD.

RESULTS

Where combined with environmental approaches, interventions such as mass media campaigns to communicate the benefits of physical activity, active travel in children and adults, and workplace-related interventions could in principle be effective, if fully implemented. However, most activities proposed by each PA pledge involved providing information or enabling choice, which has limited effectiveness. Moreover, it was difficult to establish the extent of implementation of pledges within organisations, given that progress reports were mostly unavailable, and, where provided, it was difficult to ascertain their relevance to the RD pledges. Finally, 15 % of interventions listed in organisations' delivery plans were judged to be the result of participation in the RD, meaning that most actions taken by organisations were likely already under way, regardless of the RD.

CONCLUSIONS

Irrespective of the nature of a public health policy to encourage physical activity, targets need to be evidence-based, well-defined, measurable and encourage organisations to go beyond business as usual. RD physical activity targets do not adequately fulfill these criteria.

SWI/SNF chromatin remodeling enzymes in melanocyte differentiation and melanoma

Epidermal melanocytes are pigment-producing cells derived from the neural crest that protects skin from the damaging effects of solar radiation. Malignant melanoma, a highly aggressive cancer, arises from melanocytes. SWI/SNF enzymes are multiprotein complexes that remodel chromatin structure and have extensive roles in cellular differentiation. Components of the complex have been found to be mutated or lost in several human cancers. This review focuses on studies that implicate SWI/SNF enzymes in melanocyte differentiation and in melanoma.

The Kidney Donor Profile Index (KDPI) of marginal donors allocated by standardized pretransplant donor biopsy assessment: distribution and association with graft outcomes

Pretransplant donor biopsy (PTDB)-based marginal donor allocation systems to single or dual renal transplantation could increase the use of organs with Kidney Donor Profile Index (KDPI) in the highest range (e.g. >80 or >90), whose discard rate approximates 50% in the United States. To test this hypothesis, we retrospectively calculated the KDPI and analyzed the outcomes of 442 marginal kidney transplants (340 single transplants: 278 with a PTDB Remuzzi score<4 [median KDPI: 87; interquartile range (IQR): 78-94] and 62 with a score=4 [median KDPI: 87; IQR: 76-93]; 102 dual transplants [median KDPI: 93; IQR: 86-96]) and 248 single standard transplant controls (median KDPI: 36; IQR: 18-51). PTDB-based allocation of marginal grafts led to a limited discard rate of 15% for kidneys with KDPI of 80-90 and of 37% for kidneys with a KDPI of 91-100. Although 1-year estimated GFRs were significantly lower in recipients of marginal kidneys (-9.3, -17.9 and -18.8 mL/min, for dual transplants, single kidneys with PTDB score<4 and =4, respectively; p<0.001), graft survival (median follow-up 3.3 years) was similar between marginal and standard kidney transplants (hazard ratio: 1.20 [95% confidence interval: 0.80-1.79; p=0.38]). In conclusion, PTDB-based allocation allows the safe transplantation of kidneys with KDPI in the highest range that may otherwise be discarded.

Congenital paediatric atlantoaxial dislocation: clinico-radiological profile and surgical outcome

INTRODUCTION

Congenital atlantoaxial dislocation (AAD) is the most common bony abnormality affecting the craniovertebral junction. The paediatric population has specific problems like preoperative diagnostic difficulties, precise neurological examination, radiological diagnosis, surgical problems including physical fitness to tolerate surgery (including problems of anaesthesia), technical difficulties in surgery and problems related to immobilization.

MATERIAL AND METHODS

A total of 229 consecutive paediatric (≤18 years) patients of AAD visited our centre from the period of January 1997 to August 2011. Twenty-nine cases were excluded from the study as these cases were diagnosed as CVJ tuberculosis, 31 cases were excluded as they were traumatic and the remaining 169 cases were retrospectively analysed. These patients were operated by a single experienced surgeon (the senior author) at the Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow. The preoperative and the postoperative clinical evaluation of the patient was done by the Kumar and Kalra myelopathic scoring system. The score was recorded in the preoperative period, at the time of discharge, at 3 months follow-up and at 6 months follow-up.

RESULTS

Ninety-four were males and 75 were females. The age range was 4 to 18 years with mean age 9.96±3.78 years. The follow-up ranged from 3 to 120 months with mean follow-up being 39.03±13.38 months. One hundred five cases were of fixed/irreducible AAD, and 64 were cases of mobile/reducible AAD. Majority of these cases presented with features of pyramidal tract involvement, and 108 cases had compromised pulmonary function test. One hundred thirty-seven cases had improved outcome, and 18 cases were in the same grade in the postoperative period with only 14 cases either deteriorated or died.

CONCLUSIONS

Congenital paediatric AAD are a different subset of abnormalities and have a satisfactory outcome. Preoperative evaluation must also include identification of various syndromes associated with paediatric AAD and respiratory reserve. Cormack-Lehane grade can be helpful in selecting borderline cases for postoperative need of tracheostomy. Majority of the cases have a good outcome, and therefore, surgery should be offered even in severe grade.

Deterministic characterization of phase noise in biomolecular oscillators

On top of the many external perturbations, cellular oscillators also face intrinsic perturbations due the randomness of chemical kinetics. Biomolecular oscillators, distinct in their parameter sets or distinct in their architecture, show different resilience with respect to such intrinsic perturbations. Assessing this resilience can be done by ensemble stochastic simulations. These are computationally costly and do not permit further insights into the mechanistic cause of the observed resilience. For reaction systems operating at a steady state, the linear noise approximation (LNA) can be used to determine the effect of molecular noise. Here we show that methods based on LNA fail for oscillatory systems and we propose an alternative ansatz. It yields an asymptotic expression for the phase diffusion coefficient of stochastic oscillators. Moreover, it allows us to single out the noise contribution of every reaction in an oscillatory system. We test the approach on the one-loop model of the Drosophila circadian clock. Our results are consistent with those obtained through stochastic simulations with a gain in computational efficiency of about three orders of magnitude.

Late post-transplant erythrocytosis in a hepatitis C-positive allograft recipient on sirolimus

Hematological complications in renal transplant recipients include anemia, leukopenia, and post-transplant erythrocytosis (PTE). There are numerous causes for these which include immunosuppressive drugs, viral infections, etc. We report here a hepatitis C (HCV)-positive case who developed PTE while receiving rapamycin. As both HCV infection and rapamycin through different mechanisms can produce anemia, this case report highlights the rarity of erythrocytosis.

Jail inmates and HIV care: provision of antiretroviral therapy and Pneumocystis carinii pneumonia prophylaxis

The objective of this study was to examine prescription and acceptance of antiretroviral therapy (ART) and Pneumocystis carinii pneumonia (PCP) prophylaxis in jail and at release. A retrospective cross sectional design was used, by record review, of 77 inmates receiving HIV-related care in the San Francisco City and County Jail and released to the community in 1997. Average CD4 cell count was 335/microl. Fifteen had undectable HIV RNA, and average viral load was 19,826 copies/ml. Fifty-eight per cent were put on ART in jail. Lower CD4 cell count was associated with ART (P=0.017). All inmates with CD4 cell counts less than 200/microl received PCP prophylaxis. According to 1996 guidelines, 72% of those eligible for ART were on therapy. Of 24 inmates released on ART, 71% followed medical advice and picked up medication at release. HIV care in the San Francisco Jail met high standards and exceeded levels reported in other populations.

An experimental study of some indigenous drugs with special reference to hydraulic permeability

The effect of commonly used indigenous drugs for hepatic disorders i.e. Tinospora cordifolia, (Guduchi/Amrita), Andrographis paniculata (Kalmegha), Picrorhiza kurroa (Kutki), Phyllantnus niruri (Bhoomyamalaki) and Berberis aristata (Daruharidra) was tested on the hydraulic permeability of water in the presence of bile salt through a transport cell model. The data on hydraulic permeability were calculated as t (time). JV = Lp x AP, where Lp = hydraulic conductivity and AP is the pressure difference. It was observed that the value of controlled hydraulic permeability (0.49 x 10(-8) M3 S(-1) N(-1)) decreased in the presence of indigenous drugs and bile salt. The results suggest that these drugs might have the cell membrane stabilizing property which may lead to prevention of the toxic effect of bile salts in various hepatic disorders.

Polymerase chain reaction vs. conventional diagnosis in fine needle aspirates of tuberculous lymph nodes

OBJECTIVE

To compare four conventional methods of diagnosing tuberculous lymphadenophathy (TL)--namely fine needle aspiration cytology (FNAC), Zeihl-Neelsen staining of smears for acid-fast bacilli (AFB), culture for Mycobacterium tuberculosis (MTB) and lymph node biopsies--with the polymerase chain reaction (PCR) in order to assess the practicability and advantage of its use in routine diagnosis in a developing country.

STUDY DESIGN

Fine needle aspirates from 142 consecutive patients presenting with lymphadenopathy (mainly cervical) without any known systemic involvement underwent cytomorphologic diagnosis, AFB smears, culture for MTB, confirmatory biopsy and PCR for MTB. The aspirates from cases other than TL served as controls for PCR.

RESULTS

Correct diagnosis of tuberculosis could be made in 94.87% of cases by a combination of the four methods. PCR was done in 52 cases, 39 confirmed TL and 13 controls. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value of PCR were 94.44%, 38.23%, 44.73% and 92.85%, respectively, when culture alone was considered the gold standard. However, specificity (38.23-92.30%) and PPV (44.73-97.36%) of PCR increased remarkably when response to treatment was taken as the final arbiter.

CONCLUSION

The four conventional tests were found to be the methods of choice for the diagnosis of TL in developing countries. PCR should be reserved for problem cases.

Immunohistochemical localization of transferrin in human breast cancer tissue

The present study was planned to detect the iron binding protein, transferrin (TR) in paraffin sections of the human breast tumors. The distribution of transferrin has been studied in 153 cases (63 benign lesions and 90 malignant tumors). The extent of staining reaction was determined by semiquantitative grading (weak, moderate and consistent). Positivity rate for transferrin was higher (92.2%) in malignant tumors as compared to benign breast lesions (28.5%) with significant p value (P = .0001) for both the groups. The intensity was variable in both the groups, being more intense in the malignant tumors. Tumors with higher grade of malignancy presented consistent positive staining along with the lymph nodes involved. The extent of immunoreactivity revealed a significant positive correlation with axillary lymph node status. However, no significant correlation was found with the age of the patients. Thus the study of transferrin in breast tumors besides being of prognostic significance helps in the further management of malignant lesions of the breast.

Adenosine-induced ventricular fibrillation

The use of adenosine has been suggested as a diagnostic tool in the evaluation of wide ORS complex tachycardia. However, adenosine shortens the antegrade refractoriness of accessory atrioventricular connections and may cause acceleration of the ventricular rate during atrial fibrillation. We observed ventricular fibrillation in 2 patients who presented to the emergency department with pre-excited atrial fibrillation and were given 12 mg of adenosine.

Immunohistochemical localization of transferrin in human breast cancer tissue

The present study was planned to detect the iron binding protein, transferrin (TR) in paraffin sections of the human breast tumors. The distribution of transferrin has been studied in 153 cases (63 benign lesions and 90 malignant tumors). The extent of staining reaction was determined by semiquantitative grading (weak, moderate and consistent). Positivity rate for transferrin was higher (92.2%) in malignant tumors as compared to benign breast lesions (28.5%) with significant p value (p = 0.0001) for both the groups. The intensity was variable in both the groups, being more intense in the malignant tumors. Tumors with higher grade of malignancy presented consistent positive staining along with the lymph nodes involved. The extent of immunoreactivity revealed a significant positive correlation with axillary lymph node status. However, no significant correlation was found with the age of the patients. Thus the study of transferrin in breast tumors besides being of prognostic significance helps in the further management of malignant lesions of the breast.

Immunohistochemical localization and correlation of p53 and PCNA expression in breast carcinoma

The object of the present study is to detect the p53 tumour suppressor gene and proliferation cell nuclear antigen (PCNA) expression in breast carcinoma by immunohistochemistry and correlate them with the prognostic parameters. Total 35 cases of primary breast carcinoma were studied and classified histologically. Paraffin sections were stained by using monoclonal antibody D07 for p53 protein and PC-10 for PCNA. Out of 35 cases, 16 (45.7%) were p53 positive and 25 (71.4%) were PCNA positive. The mean PCNA labelling index (PCNA LI +/- SD) was 58.97 +/- 22.72 in tumors positive for both p53+ and PCNA+ while cases negative for p53- and positive for PCNA+ has higher PCNA LI +/- SD (59.24 +/- 18.97). The difference in the two groups was not significant. Most cases were positive for both p53+ and PCNA+ in the age group < 30 with higher mean PCNA LI +/- SD (62.20 +/- 27.13) than in the group > 30 (57.88 +/- 18.47). In the pre-menopausal group 57.1% cases were positive for p53+ with higher PCNA LI +/- SD (59.94 +/- 24.22). Maximum p53 and PCNA positivity was observed in grade III tumors (63.2% and 84.2%). The mean PCNA LI +/- SD was also highest in grade III carcinomas (66.83 +/- 13.97). No significant correlation was found between p53 and PCNA status with morphological type and tumour size except that logistic regression showed a positive correlation with tumour grade. Therefore the present study suggests that both p53 expression and PCNA are markers of poor differentiation in breast cancer.

Cytopathology and AgNOR counts in fine-needle aspiration cytology smears of thyroid lesions

The object of the present work is to study the cytomorphological features and the value of silver colloidal staining method in distinguishing the non-neoplastic, benign, and malignant neoplasm in fine-needle aspiration cytology (FNAC) smears of thyroid nodules. One hundred forty histologically confirmed aspirated samples of thyroid lesions were studied and classified cytologically. These smears were stained for AgNOR counts. The number and location of AgNOR dots as well as clusters in nuclei were studied by two different observers independently. Lower AgNOR counts were recorded in cases of thyroiditis (1.375 +/- 0.414), whereas follicular carcinoma had a higher number of AgNOR counts (5.04 +/- 0.52). The clusters of AgNOR dots were centrally located in colloid goitre, but no cluster arrangement was observed in cases of carcinomas. Increased nuclear size, nucleoli, and chromocentres were helpful in the diagnosis of follicular carcinoma. AgNOR counting cannot be reliably used on an individual case basis to differentiate adenoma from carcinoma. Therefore, AgNOR study in thyroid lesions can be used as an additional diagnostic method with cytomorphological features to differentiate benign and malignant follicular neoplasms.

Statistical significance of AgNOR counts in FNAC smears and corresponding histopathological sections

The object of the present study was to determine the statistical significance of AgNOR counts in fine needle aspiration cytology (FNAC) smears and corresponding paraffin sections by using an one step silver colloidal staining method. Ninety five cases (31 benign and 64 malignant) were taken and a correlation between smears and sections was studied by two different observers. The total number of mean (SD) AgNOR counts was significantly higher in FNAC smears in benign (3.081 +/- .753) and malignant (7.101 +/- 1.544) neoplasms in comparison to paraffin sections in the same group of cases. FNAC smears had a cut off point 4 with proliferation index 1% in benign tumors and 97.5% in malignant tumors. Sections had an overlapping of AgNOR counts (5-7) with proliferation index 3.8 and 82% for benign and malignant groups respectively. The difference in the coefficient of variations was 3% in benign group and 2% in malignant group in FNAC smears while sections had 6 and 8% difference in the coefficient of variations. Smears present a superior staining and accurate number of AgNOR dots in nucleus as compared to paraffin sections. Therefore the results suggest that AgNOR technique can be successfully used in FNAC smears in comparison to paraffin sections to differentiate benign and malignant tumors in routine laboratory diagnosis.