Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia

Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by differentiation block at the promyelocyte stage. Besides the presence of chromosomal rearrangement t(15;17), leading to the formation of PML-RARA (promyelocytic leukemia-retinoic acid receptor alpha) fusion, other genetic alterations have also been implicated in APL. Here, we performed comprehensive mutational analysis of primary and relapse APL to identify somatic alterations, which cooperate with PML-RARA in the pathogenesis of APL. We explored the mutational landscape using whole-exome (n=12) and subsequent targeted sequencing of 398 genes in 153 primary and 69 relapse APL. Both primary and relapse APL harbored an average of eight non-silent somatic mutations per exome. We observed recurrent alterations of FLT3, WT1, NRAS and KRAS in the newly diagnosed APL, whereas mutations in other genes commonly mutated in myeloid leukemia were rarely detected. The molecular signature of APL relapse was characterized by emergence of frequent mutations in PML and RARA genes. Our sequencing data also demonstrates incidence of loss-of-function mutations in previously unidentified genes, ARID1B and ARID1A, both of which encode for key components of the SWI/SNF complex. We show that knockdown of ARID1B in APL cell line, NB4, results in large-scale activation of gene expression and reduced in vitro differentiation potential.

Loss of B Cells in Patients with Heterozygous Mutations in IKAROS

BACKGROUND

Common variable immunodeficiency (CVID) is characterized by late-onset hypogammaglobulinemia in the absence of predisposing factors. The genetic cause is unknown in the majority of cases, and less than 10% of patients have a family history of the disease. Most patients have normal numbers of B cells but lack plasma cells.

METHODS

We used whole-exome sequencing and array-based comparative genomic hybridization to evaluate a subset of patients with CVID and low B-cell numbers. Mutant proteins were analyzed for DNA binding with the use of an electrophoretic mobility-shift assay (EMSA) and confocal microscopy. Flow cytometry was used to analyze peripheral-blood lymphocytes and bone marrow aspirates.

RESULTS

Six different heterozygous mutations in IKZF1, the gene encoding the transcription factor IKAROS, were identified in 29 persons from six families. In two families, the mutation was a de novo event in the proband. All the mutations, four amino acid substitutions, an intragenic deletion, and a 4.7-Mb multigene deletion involved the DNA-binding domain of IKAROS. The proteins bearing missense mutations failed to bind target DNA sequences on EMSA and confocal microscopy; however, they did not inhibit the binding of wild-type IKAROS. Studies in family members showed progressive loss of B cells and serum immunoglobulins. Bone marrow aspirates in two patients had markedly decreased early B-cell precursors, but plasma cells were present. Acute lymphoblastic leukemia developed in 2 of the 29 patients.

CONCLUSIONS

Heterozygous mutations in the transcription factor IKAROS caused an autosomal dominant form of CVID that is associated with a striking decrease in B-cell numbers. (Funded by the National Institutes of Health and others.).

The prevalence and risk factors for age-related macular degeneration in rural-urban India, Sankara Nethralaya Rural-Urban Age-related Macular degeneration study, Report No. 1

PurposeTo report the age- and gender-adjusted prevalence rates of early and late age-related maculopathy (ARM) and associated risk factors in rural and urban Indian population.MethodsA population-based cross-sectional study was carried out in South India between 2009 and 2011. Of the 6617 subjects ≥60 years enumerated ones, 5495 (83.04%) participated in the eye examination. A detailed history including data on demographic, socioeconomic, and ocular history was obtained. Participants underwent detailed ophthalmic evaluation including 30° 3-field photograph as per Age-Related Eye Disease Study protocol. The ARM was graded according to the International ARM Epidemiological Study Group.ResultsAge- and gender-adjusted prevalence of early ARM was 20.91% (20.86-20.94) in the rural population and 16.37% (16.32-16.42) in the urban population. Similarly, the prevalence of late ARM was 2.26% (2.24-2.29) and 2.32% (2.29-2.34) in the rural and urban population, respectively. In both rural and urban populations, risk factors that were related to both early and late ARM were age, per year increase (OR, range 1.00-1.08); middle socioeconomic status (OR, range 1.05-1.83); and smokeless tobacco (OR, range 1.11-2.21). Protective factor in both was the presence of diabetes mellitus in all ARM (OR, range 0.34-0.83). Risk factors, only in the rural arm, were female gender (OR, range 1.06-1.64), past smoker (OR, 1.14), and serum low-density lipoprotein cholesterol level (OR, 1.03).ConclusionsThe study reports smokessless tobacco as a risk factor for both early and late ARM and identified a higher prevalence of early ARM in the rural population compared with urban population.

Abstract P5-07-12: Local nuclear architecture features from H&E images predict early versus distant recurrence in lymph node negative, ER+ breast cancers

Introduction: Breast cancer (BCa) Patients with ER+ tumors that are lymph node negative (LN-) typically receive hormonal therapy. There is a need to identify ER+ LN- patients that will not benefit from adjuvant chemotherapy and will respond to hormonal therapy alone. Oncotype DX, a quantitative prognostic and predictive gene assay, provides a recurrence score that has been correlated with distant and early recurrence. In this work we present an approach that employ computer extracted features of nuclear architecture and morphology from routine H&E slides alone that can distinguish early and distant recurrence in ER+ breast cancers. By constructing graph networks within epithelium and stroma regions, built using nuclei as vertices and edge connections between proximal nuclei, local nuclear architecture can be quantitatively characterized. Hosoya index (HI) (originally introduced for analysis of chemical bonds) is a measure of a bond (in this context nuclei connections in a graph). In this work, we leverage HI to measure structural similarities of graphs across the populations that are indicative of recurrence in LN- ER+ breast cancer tissue microarray (TMA) images.

Design: In this study we considered two tissue microarrays (TMAs) comprising 453 early-stage lymph-node negative (LN-) estrogen receptor positive (ER+) breast cancer (BCa) patients (diagnosed with invasive ductal carcinoma), with a total of N=90 patients experiencing lifetime distant recurrence and N=343 patients who did not. All TMA cores were digitized at 20x magnification (0.33 um/pixel spatial resolution) using a digital whole-slide scanner. Each nucleus was identified via an automated computerized image analysis algorithm developed by our group. Then, using a cluster cell graph that encodes a link between a pair of nodes based on proximity, a series of graphs are constructed for a TMA. A HI value was then assigned to each local graph. A support vector machine classifier was trained in conjunction with the distribution of HI values for the early and distant recurrence cases on the training TMA (n=243, 50 early recurrences). Independent validation of the SVM classifier was performed on the second TMA (n=210, 40 early recurrences).

Results: For the LN- ER+ breast cancer dataset, our method was able to distinguish tumors with early and distant recurrence with an accuracy of 75.4%, a positive predictive value of 78.6% and a negative predictive value of 76.4%. The separation between the Kaplan-Meier curves for early and distant recurrence of LN-, ER+ breast cancers on the validation set was statistically significant (p < 0.00102).

Conclusion: Based only on tiny H&E punches, a computer-aided morphometric classifier appears to identify lymph node negative, ER+ breast cancers with a low likelihood of recurrence. With further validation, this approach could be developed into an image based assay which could serve as a lower cost alternative to Oncotype DX.

Citation Format: Ali S, Rimm D, Ganesan S, Madabhushi A. Local nuclear architecture features from H&E images predict early versus distant recurrence in lymph node negative, ER+ breast cancers. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-07-12.

Salivary pH and Buffering Capacity as Risk Markers for Early Childhood Caries: A Clinical Study

Background: The diagnostic utility of saliva is currently being explored in various branches of dentistry, remarkably in the field of caries research. This study was aimed to determine if assessment of salivary pH and buffering capacity would serve as reliable tools in risk prediction of early childhood caries (ECC).

Materials and methods: Paraffin-stimulated salivary samples were collected from 50 children with ECC (group I) and 50 caries free children (group II). Salivary pH and buffering capacity (by titration with 0.1 N hydrochloric acid) were assessed using a handheld digital pH meter in both groups. The data obtained were subjected to statistical analysis.

Results: Statistically, no significant difference was observed between both the groups for all salivary parameters assessed, except for the buffering capacity level at 150 μl titration of 0.1 N hydrochloric acid (p = 0.73; significant at 1% level).

Conclusion: Salivary pH and buffering capacity may not serve as reliable markers for risk prediction of ECC.

How to cite this article: Jayaraj D, Ganesan S. Salivary pH and Buffering Capacity as Risk Markers for Early Childhood Caries: A Clinical Study. Int J Clin Pediatr Dent 2015;8(3):167-171.

Combined heat and power dispatch by grey wolf optimization

Purpose

– The combined heat and power dispatch (CHPD) aims to optimize the outputs of online units in a power plant consisting thermal generators, co-generators and heat-only units. Identifying the operating point of a co-generator within its feasible operating region (FOR) is difficult. This paper aims to solve the CHPD problem in static and dynamic environments.

Design/methodology/approach

– The CHPD plant operation is formulated as an optimization problem under static and dynamic load conditions with the objectives of minimizations of cost and emissions subject to various system and operational constraints. A novel bio-inspired search technique, grey wolf optimization (GWO) algorithm is used as an optimization tool.

Findings

– The GWO-based algorithm has been developed to determine the preeminent power and heat dispatch of operating units within the FOR region. The proposed methodology provides fuel cost savings and lesser pollutant emissions than those in earlier reports. Particularly, the GWO always keeps the co-generator’s operating point within the FOR, whereas most of the existing methods fail.

Originality/value

– The GWO is applied for the first time to solve the CHPD problems. New dispatch schedules are reported for 7-unit system with the objectives of total fuel cost and emission minimizations, 24-unit system for economic operation and 11-unit system in dynamic environment. The simulation experiments reveal that GWO converges quickly, consistent and the statistical performance clears its applicability to CHPD problems.

Infantile developmental thoracolumbar kyphosis with segmental subluxation of the spine

Acute angulation at the thoracolumbar junction with segmental subluxation of the spine occurring at the level above an anteriorly hypoplastic vertebra in otherwise normal children is a rare condition described as infantile developmental thoracolumbar kyphosis. Three patient series with total of 18 children have been reported in the literature. We report five children who presented with thoracolumbar kyphosis and discuss the treatment algorithm. We reviewed the medical records and spinal imaging at initial clinical presentation and at minimum two-year follow-up. The mean age at presentation was eight months (two to 12). All five children had L2 anterior vertebral body hypoplasia. The kyphosis improved spontaneously in three children kept under monitoring. In contrast, the deformity was progressive in two patients who were treated with bracing. The kyphosis and segmental subluxation corrected at latest follow-up (mean age 52 months; 48 to 60) in all patients with near complete reconstitution of the anomalous vertebra. The deformity and radiological imaging on a young child can cause anxiety to both parents and treating physicians. Diagnostic workup and treatment algorithm in the management of infantile developmental thoracolumbar kyphosis is proposed. Observation is indicated for non-progressive kyphosis and bracing if there is evidence of kyphosis and segmental subluxation deterioration beyond walking age. Surgical stabilisation of the spine can be reserved for severe progressive deformities unresponsive to conservative treatment.

Cite this article: Bone Joint J 2015;97-B:982–7.

FT-IR and micro-Raman spectroscopic studies of archaeological potteries recently excavated in Poompuhar, Tamilnadu, India

Ancient ceramics are the abundant artifacts that give the knowledge of the past societies. Therefore it is of great importance to acquire knowledge about the chemical composition of the clay in archaeological artifacts. The spectroscopic techniques represent one of the most powerful tools to investigate the structure of all the materials and chemical composition of the cultural object like potteries. An attempt has been made in the present work to estimate the firing temperature of the archaeological pottery shreds excavated from the archaeological site Poompuhar in the state of Tamilnadu in India. The firing temperature of the archaeological pottery shreds were estimated by recording the corresponding FT-IR spectra in the range 4000-450 cm(-1) and Micro Raman spectra in the range 1800-400 cm(-1). The clay mineral present in the pottery samples are identified through FT-IR method and was confirmed with Micro Raman spectroscopy as both are complement to each other. The major primary mineral present in the samples is Kaolinite and the secondary mineral present is quartz and the accessory minerals present in the samples are hematite, magnetite and feldspar. The results of Raman spectra showed that the potters of this site used a mixture of clays as raw materials. The firing temperature for some of the samples did not exceed 800°C which suggests the use of open fire.

Investigation on the effectiveness of ABC algorithm for hydrothermal energy management considering emission aspects

Purpose

– The purpose of the paper is to solve hydrothermal scheduling (HTS) problem for energy-efficient management by allocating the optimal real power outputs for thermal and hydroelectric generators.

Design/methodology/approach

– HTS can be formulated as a complex and non-linear optimization problem which minimizes the total fuel cost and emissions of thermal generators subject to various physical and operational constraints. As the artificial bee colony algorithm has proven its ability to solve various engineering optimization problems, it has been used as a main optimization tool to solve the fixed-head HTS problem.

Findings

– A meta-heuristic search technique-based algorithm has been implemented for hydrothermal energy management, and the simulation results show that this approach can provide trade-off between conflict objectives and keep a rapid convergence speed.

Originality/value

– The proposed methodology is implemented on the standard test system, and the numerical results comparison indicates a considerable saving in total fuel cost and reduction in emission.

Prenatal diagnosis of ductus arteriosus aneurysm

The ductus arteriosus holds major functional importance within the fetal circulation, and anomalies within the ductus arteriosus may interfere with the integrity of the fetal circulation. Ductus arteriosus aneurysm, previously considered a rare lesion, is now a well-reported finding in infancy with some reports describing this finding in the prenatal period. Postnatally, most ductus arteriosus aneurysms resolve spontaneously; however, a small group of infants show complications such as connective-tissue disorders, thrombo-embolism, compression of surrounding thoracic structures and life-threatening spontaneous rupture requiring surgical correction. As such, postnatal assessment in this group is recommended.

Crystal structure of 3-methyl-2,6-bis-(4-methyl-1,3-thia-zol-5-yl)piperidin-4-one

In the title compound, C₁₄H₁₇N₃OS₂, the central piperidinone ring adopts a chair conformation and the thia­zole rings are inclined to its mean plane by 80.16 (12) and 67.15 (12)°. The O atom and methyl group C atom deviate significantly from the mean plane of the central piperidinone ring, by 0.8138 (2) and 0.3175 (2) Å, respectively. The dihedral angle between the thia­zole rings is 51.88 (13)°. In the crystal, mol­ecules are linked via C—H⋯O hydrogen bonds, forming zigzag C(10) chains running parallel to [001].