Crystallizing galactocele: A rare case report and review of literature.

ABSTRACT: Crystallizing galactocele is an uncommon condition that produces a viscous, chalky substance on fine needle aspiration cytology. (FNAC). Both the diagnosis and the management of this illness include the use of FNAC. Here, we discuss the case of a 25-year-old nursing woman who experienced left breast edema lump for two years. The upper outer quadrant of the leftt breast was involved by the hard, small, non-tender, and movable enlargement. The lesion's FNAC produced a thick, milky, and chalky substance. Numerous semi-transparent crystals of various sizes and shapes with angulated edges could be seen in cytological smears against a background of granular and amorphous proteinaceous material. A diagnosis of crystallizing galactocele was made on the basis of the patient's clinical history of lactation and characteristic cytological findings. Due to the rarity of this condition-to the best of our knowledge, less than ten cases of crystallizing galactocele have been documented in medical literature.

Angle Stable Plate Fixation vs Hemicallotasis in Medial Opening Wedge High Tibial Osteotomy: A Comparative Study.

Background: Varus alignment associated with medial compartment degeneration is the most common presentation of knee osteoarthritis and often presents in young active adults where arthroplasty might be unsuitable. Purpose: To compare the accuracy of the angle stable medial high tibia plate and self-adjusting HTO (high tibial osteotomy) fixator in achieving correction of varus deformity of the knee by medial opening wedge HTO and to evaluate functionality between the groups. Study Design: Prospective randomized control study. Methods: Forty patients each underwent medial opening wedge high tibial osteotomy with acute correction and stabilization using the angle stable plate (ASP group) or with the hemicallotasis technique using the self-adjusting HTO external fixator (HCO group). Anatomical and functional outcomes were compared to the pre-operative values at the 6th and 12th month. Results: The FTA (femoro-tibial axis), mechanical axis, and functional scores improved significantly in both groups. There was also a significant change in the patellar height and tibial slope. Except for a better KOOS (Knee Injury and Osteoarthritis Outcome Score) in the angle stable plate group at the 6-month follow-up, there were no significant differences between the groups. Conclusion: Both methods of performing a medially based proximal tibial osteotomy gave equivalent outcomes at the 1-year follow-up.

An observational study on the presence of perilimbal conjunctival pigmentation in vernal keratoconjunctivitis.

Purpose: To evaluate presence of perilimbal pigmentation (PLP) in Indian patients with vernal keratoconjunctivitis (VKC). Methods: A cross sectional study was conducted from 2019 to 2020 at a tertiary eye care center in Western Maharashtra, India. In this study, 152 cases of VKC were identified. The presence, type, color, and extent of PLP were recorded. The incidence of presence of PLP was calculated. Its correlations with severity and duration of VKC were analyzed using Wilcoxon-Mann-Whitney U test and Chi square test. Results: Of 152 cases, 79.61% were males. Mean age at presentation was 11.4 ± 5.6 years. The characteristic PLP was present in 81 cases (53.29%; 95% confidence interval [CI]: 45.03%-61.42%; P < 0.001), of which 15 cases (18.5%) had this pigmentation in all the four quadrants. There was a significant difference between the groups with respect to quadrants involvement in terms of the extent of PLP in clock hours (χ2 = 73.85, P < 0.001). However, the extent did not correlate with age (rho = 0.08, P = 0.487), sex (P = 0.115), time since onset in months (rho = 0.03, P = 0.77), duration of VKC and type or color of PLP (P = 0.12). Conclusion: Perilimbal pigmentation seems to be a consistent clinical finding seen in a significant number of VKC cases. It may benefit ophthalmologists in treating VKC cases when the palpebral/limbal signs are elusive.

Evolutionary jumps in bacterial GC content.

Genomic GC (Guanine-Cytosine) content is a fundamental molecular trait linked with many key genomic features such as codon and amino acid use. Across bacteria, GC content is surprisingly diverse and has been studied for many decades; yet its evolution remains incompletely understood. Since it is difficult to observe GC content evolve on laboratory time scales, phylogenetic comparative approaches are instrumental; but this dimension is rarely studied systematically in the case of bacterial GC content. We applied phylogenetic comparative models to analyze GC content evolution in multiple bacterial groups across 2 major bacterial phyla. We find that GC content diversifies via a combination of gradual evolution and evolutionary "jumps." Surprisingly, unlike prior reports that solely focused on reductions in GC, we found a comparable number of jumps with both increased and decreased GC content. Overall, many of the identified jumps occur in lineages beyond the well-studied peculiar examples of endosymbiotic and AT-rich marine bacteria and do not support the predicted role of oxygen dependence. Our analysis of rapid and large shifts in GC content thus identifies new clades and novel contexts to further understand the ecological and evolutionary drivers of this important genomic trait.

Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays.

An epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus diseases (C0VID-19) initially reported in Wuhan, China has rapidly emerged into a global pandemic affecting millions of people worldwide. Molecular detection of SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR) forms the mainstay in screening, diagnosis and epidemiology of the disease. Since the virus evolves by accumulating base substitutions, mutations in the viral genome could possibly affect the accuracy of RT-PCR-based detection assays. The recent availability of genomes of SARS-CoV-2 isolates motivated us to assess the presence and potential impact of variations in target sites of the oligonucleotide primers and probes used in molecular diagnosis. We catalogued a total of 132 primer or probe sequences from literature and data available in the public domain. Our analysis revealed that a total of 5862 unique genetic variants mapped to at least one of the 132 primer or probe binding sites in the genome. A total of 29 unique variants were present in ≥ 1% of genomes from at least one of the continents (Asia, Africa, Australia, Europe, North America, and South America) that mapped to 36 unique primers or probes binding sites. Similarly, a total of 27 primer or probe binding sites had cumulative variants frequency of ≥ 1% in the global SARS-CoV-2 genomes. These included primers or probes sites which are used worldwide for molecular diagnosis as well as approved by national and international agencies. We also found 286 SARS-CoV-2 genomic regions with low variability at a continuous stretch of ≥ 20bps that could be potentially used for primer designing. This highlights the need for sequencing genomes of emerging pathogens to enable evidence-based policies for development and approval of diagnostics.

Weight of Schoolbags Among Indian Schoolchildren in Pune and Hyderabad.

OBJECTIVE: This study was done to determine proportion of children carrying heavy school bags and to compare new guidelines issued by Government of India on school bag weight limit, based on class of the child with previous guidelines based on child's weight. METHODS: A cross-sectional study was done among students of schools from two cities of India - Pune and Hyderabad. Weight of school bag of 1321 children was measured and classified as 'heavy' or 'normal' based on existing as well as new guidelines. Agreement between two guidelines was also calculated. RESULTS: In our study, 722 (77.2%) out of 935 students from class 1-10 were found to be carrying 'heavy' school bags. Kappa coefficient for agreement between two guidelines was 0.55 (0.47,0.60) indicating moderately strong agreement. CONCLUSIONS: Large proportion of school children are carrying school bags with weight beyond permissible limits. There is a need for all stake holders to take steps to reduce weight of school bags.

Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis.

The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of feedbacks from the metabolic network (MN) has received relatively little attention. Here we study the causal structure of the GRNs, namely the chain of influence of one component on the other, taking into account feedback from the MN. First we consider the GRNs of E. coli and B. subtilis without feedback from MN and illustrate their causal structure. Next we augment the GRNs with feedback from their respective MNs by including (a) links from genes coding for enzymes to metabolites produced or consumed in reactions catalyzed by those enzymes and (b) links from metabolites to genes coding for transcription factors whose transcriptional activity the metabolites alter by binding to them. We find that the inclusion of feedback from MN into GRN significantly affects its causal structure, in particular the number of levels and relative positions of nodes in the hierarchy, and the number and size of the strongly connected components (SCCs). We then study the functional significance of the SCCs. For this we identify condition specific feedbacks from the MN into the GRN by retaining only those enzymes that are essential for growth in specific environmental conditions simulated via the technique of flux balance analysis (FBA). We find that the SCCs of the GRN augmented by these feedbacks can be ascribed specific functional roles in the organism. Our algorithmic approach thus reveals relatively autonomous subsystems with specific functionality, or regulatory modules in the organism. This automated approach could be useful in identifying biologically relevant modules in other organisms for which network data is available, but whose biology is less well studied.

Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias.

Increasing growth rate across bacteria strengthens selection for faster translation, concomitantly increasing the total number of tRNA genes and codon usage bias (CUB: enrichment of specific synonymous codons in highly expressed genes). Typically, enriched codons are translated by tRNAs with higher gene copy numbers (GCN). A model of tRNA-CUB coevolution based on fast growth-associated selection on translational speed recapitulates these patterns. A key untested implication of the coevolution model is that translational selection should favor higher tRNA GCN for more frequently used amino acids, potentially weakening the effect of growth-associated selection on CUB. Surprisingly, we find that CUB saturates with increasing growth rate across γ-proteobacteria, even as the number of tRNA genes continues to increase. As predicted, amino acid-specific tRNA GCN is positively correlated with the usage of corresponding amino acids, but there is no correlation between growth rate associated changes in CUB and amino acid usage. Instead, we find that some amino acids-cysteine and those in the NNA/G codon family-show weak CUB that does not increase with growth rate, despite large variation in the corresponding tRNA GCN. We suggest that amino acid-specific variation in CUB is not explained by tRNA GCN because GCN does not influence the difference between translation times of synonymous codons as expected. Thus, selection on translational speed alone cannot fully explain quantitative variation in overall or amino acid-specific CUB, suggesting a significant role for other functional constraints and amino acid-specific codon features.

HIV-1 latency and virus production from unintegrated genomes following direct infection of resting CD4 T cells.

BACKGROUND: HIV-1 integration is prone to a high rate of failure, resulting in the accumulation of unintegrated viral genomes (uDNA) in vivo and in vitro. uDNA can be transcriptionally active, and circularized uDNA genomes are biochemically stable in non-proliferating cells. Resting, non-proliferating CD4 T cells are prime targets of HIV-1 infection and latently infected resting CD4 T cells are the major barrier to HIV cure. Our prior studies demonstrated that uDNA generates infectious virions when T cell activation follows rather than precedes infection. RESULTS: Here, we characterize in primary resting CD4 T cells the dynamics of integrated and unintegrated virus expression, genome persistence and sensitivity to latency reversing agents. Unintegrated HIV-1 was abundant in directly infected resting CD4 T cells. Maximal gene expression from uDNA was delayed compared with integrated HIV-1 and was less toxic, resulting in uDNA enrichment over time relative to integrated proviruses. Inhibiting integration with raltegravir shunted the generation of durable latency from integrated to unintegrated genomes. Latent uDNA was activated to de novo virus production by latency reversing agents that also activated latent integrated proviruses, including PKC activators, histone deacetylase inhibitors and P-TEFb agonists. However, uDNA responses displayed a wider dynamic range, indicating differential regulation of expression relative to integrated proviruses. Similar to what has recently been demonstrated for latent integrated proviruses, one or two applications of latency reversing agents failed to activate all latent unintegrated genomes. Unlike integrated proviruses, uDNA gene expression did not down modulate expression of HLA Class I on resting CD4 T cells. uDNA did, however, efficiently prime infected cells for killing by HIV-1-specific cytotoxic T cells. CONCLUSIONS: These studies demonstrate that contributions by unintegrated genomes to HIV-1 gene expression, virus production, latency and immune responses are inherent properties of the direct infection of resting CD4 T cells. Experimental models of HIV-1 latency employing directly infected resting CD4 T cells should calibrate the contribution of unintegrated HIV-1.

Suppression of Foxo1 activity and down-modulation of CD62L (L-selectin) in HIV-1 infected resting CD4 T cells.

HIV-1 hijacks and disrupts many processes in the cells it infects in order to suppress antiviral immunity and to facilitate its replication. Resting CD4 T cells are important early targets of HIV-1 infection in which HIV-1 must overcome intrinsic barriers to viral replication. Although resting CD4 T cells are refractory to infection in vitro, local environmental factors within lymphoid and mucosal tissues such as cytokines facilitate viral replication while maintaining the resting state. These factors can be utilized in vitro to study HIV-1 replication in resting CD4 T cells. In vivo, the migration of resting naïve and central memory T cells into lymphoid tissues is dependent upon expression of CD62L (L-selectin), a receptor that is subsequently down-modulated following T cell activation. CD62L gene transcription is maintained in resting T cells by Foxo1 and KLF2, transcription factors that maintain T cell quiescence and which regulate additional cellular processes including survival, migration, and differentiation. Here we report that HIV-1 down-modulates CD62L in productively infected naïve and memory resting CD4 T cells while suppressing Foxo1 activity and the expression of KLF2 mRNA. Partial T cell activation was further evident as an increase in CD69 expression. Several other Foxo1- and KLF2-regulated mRNA were increased or decreased in productively infected CD4 T cells, including IL-7rα, Myc, CCR5, Fam65b, S1P1 (EDG1), CD52, Cyclin D2 and p21CIP1, indicating a profound reprogramming of these cells. The Foxo1 inhibitor AS1842856 accelerated de novo viral gene expression and the sequella of infection, supporting the notion that HIV-1 suppression of Foxo1 activity may be a strategy to promote replication in resting CD4 T cells. As Foxo1 is an investigative cancer therapy target, the development of Foxo1 interventions may assist the quest to specifically suppress or activate HIV-1 replication in vivo.

An HIV-1 replication pathway utilizing reverse transcription products that fail to integrate.

Integration is a central event in the replication of retroviruses, yet ≥ 90% of HIV-1 reverse transcripts fail to integrate, resulting in accumulation of unintegrated viral DNA in cells. However, understanding what role, if any, unintegrated viral DNA plays in the natural history of HIV-1 has remained elusive. Unintegrated HIV-1 DNA is reported to possess a limited capacity for gene expression restricted to early gene products and is considered a replicative dead end. Although the majority of peripheral blood CD4(+) T cells are refractory to infection, nonactivated CD4 T cells present in lymphoid and mucosal tissues are major targets for infection. Treatment with cytokine interleukin-2 (IL-2), IL-4, IL-7, or IL-15 renders CD4(+) T cells permissive to HIV-1 infection in the absence of cell activation and proliferation and provides a useful model for infection of resting CD4(+) T cells. We found that infection of cytokine-treated resting CD4(+) T cells in the presence of raltegravir or with integrase active-site mutant HIV-1 yielded de novo virus production following subsequent T cell activation. Infection with integration-competent HIV-1 naturally generated a population of cells generating virus from unintegrated DNA. Latent infection persisted for several weeks and could be activated to virus production by a combination of a histone deacetylase inhibitor and a protein kinase C activator or by T cell activation. HIV-1 Vpr was essential for unintegrated HIV-1 gene expression and de novo virus production in this system. Bypassing integration by this mechanism may allow the preservation of genetic information that otherwise would be lost.

Spatial and temporal sensing limits of microtubule polarization in neuronal growth cones by intracellular gradients and forces.

Neuronal growth cones are the most sensitive among eukaryotic cells in responding to directional chemical cues. Although a dynamic microtubule cytoskeleton has been shown to be essential for growth-cone turning, the precise nature of coupling of the spatial cue with microtubule polarization is less understood. Here we present a computational model of microtubule polarization in a turning neuronal growth cone. We explore the limits of directional cues in modifying the spatial polarization of microtubules by testing the role of microtubule dynamics, gradients of regulators, and retrograde forces along filopodia. We analyze the steady state and transition behavior of microtubules on being presented with a directional stimulus. Our model makes novel, to our knowledge, predictions about the minimal angular spread of the chemical signal at the growth cone and the fastest polarization times. A regulatory reaction-diffusion network based on the cyclic phosphorylation-dephosphorylation of a regulator predicts that the receptor-signal magnitude can generate the maximal polarization of microtubules and not feedback loops or amplifications in the network. Using both the phenomenological and network models, we have demonstrated some of the physical limits within which the microtubule polarization system works in turning the neuron.

Comparative evaluation of the sniffing position with simple head extension for laryngoscopic view and intubation difficulty in adults undergoing elective surgery.

The effect of patient position on mask ventilation, laryngoscopic view, intubation difficulty, and the stance adopted by the anesthesiologist during laryngoscopy and tracheal intubation was investigated in 546 anesthetized adults in this prospective, randomized study. Patients were randomly assigned to either the sniffing position group or the simple extension group. The distribution of Cormack grades was comparable between the two groups (P = 0.144). The IDS score [median (IQR)] was 0 (0-2) in the sniffing group and 1 (0-2) in the simple extension group; P = 0.002. There were significant differences between groups with regard to intensity of lifting force, external laryngeal manipulation, alternate techniques used, number of attempts, and the stance adopted by anesthesiologist. We conclude that the sniffing position is superior to simple head extension with regard to ease of intubation as assessed by IDS. An upright stance is adopted by more anesthesiologists performing intubation with patients in the sniffing position.

Management of a case of endobronchial blood clot in the post operative period.

SUMMARY: Endobronchial blood clot is an unusual cause of airway obstruction leading to lung collapse in the postoperative period. It is not always easy to pin point the exact etiology in the presence of multiple risk factors. Pulmonary collapse can herald the onset of severe haemodynamic derangements and hypoxemia. So, early identification and management is crucial for preventing catastrophic complications. Various modalities have been described in the literature for removing the obstructing clot and re-expansion of the lung. We present a case of postoperative left lung collapse by an obstructing endobronchial blood clot in a patient undergoing coronary artery bypass graft surgery.

Low levels of genetic divergence across geographically and linguistically diverse populations from India.

Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States-sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.

Clines, clusters, and the effect of study design on the inference of human population structure.

Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables--sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample--on the "clusteredness" of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions.