Modeling the Homeschool timetabling problem using Integer programming

Home schooling has steadily been increasing in the past decade. According to a survey in 2007, about 2.5 million children were being home schooled in the US. Typically, parents provide education at the convenience of their home and in some cases an instructor is appointed for the same. The Home School Timetabling problem (HSTP) deals with assigning subjects, timeslots and rooms to every student. In doing so, there are certain hard and specialty constraints that are to be satisfied. Integer programming (IP) has been used in solving the HSTP as it has the advantage of being able to provide information about the relative significance of each constraint with respect to the objective. A prototype in the form of a GUI has been built such that the parent can enter each student’s name, his/her subjects, duration, days and time for each subject, availability times of the parent etc. This data is then fed into the IP model so that it can generate a feasible timetable satisfying all of the constraints. When a solution is found it is formatted to provide the weekly timetable for each student, individually, as well as a complete timetable for all students each day

Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays

BACKGROUND: Second generation RNA sequencing technology (RNA-seq) offers the potential to interrogate genome-wide differential RNA splicing in cancer. However, since short RNA reads spanning spliced junctions cannot be mapped contiguously onto to the chromosomes, there is a need for methods to profile splicing from RNA-seq data. Before the invent of RNA-seq technologies, microarrays containing probe sequences representing exon-exon junctions of known genes have been used to hybridize cellular RNAs for measuring context-specific differential splicing. Here, we extend this approach to detect tumor-specific splicing in prostate cancer from a RNA-seq dataset. METHOD: A database, SPEventH, representing probe sequences of under a million non-redundant splice events in human is created with exon-exon junctions of optimized length for use as virtual microarray. SPEventH is used to map tens of millions of reads from matched tumor-normal samples from ten individuals with prostate cancer. Differential counts of reads mapped to each event from tumor and matched normal is used to identify statistically significant tumor-specific splice events in prostate. RESULTS: We find sixty-one (61) splice events that are differentially expressed with a p-value of less than 0.0001 and a fold change of greater than 1.5 in prostate tumor compared to the respective matched normal samples. Interestingly, the only evidence, EST (BF372485), in the public database for one of the tumor-specific splice event joining one of the intron in KLK3 gene to an intron in KLK2, is also derived from prostate tumor-tissue. Also, the 765 events with a p-value of less than 0.001 is shown to cluster all twenty samples in a context-specific fashion with few exceptions stemming from low coverage of samples. CONCLUSIONS: We demonstrate that virtual microarray experiments using a non-redundant database of splice events in human is both efficient and sensitive way to profile genome-wide splicing in biological samples and to detect tumor-specific splicing signatures in datasets from RNA-seq technologies. The signature from the large number of splice events that could cluster tumor and matched-normal samples into two tight separate clusters, suggests that differential splicing is yet another RNA phenotype, alongside gene expression and SNPs, that can be exploited for tumor stratification

Melanoma and Seborrheic Keratosis Differentiation using Texture Features

Purpose: To explore texture features in two-dimensional images to differentiate seborrheic keratosis from melanoma. Methods: A systematic approach to consistent classification of skin tumors is described. Texture features, based on the second-order histogram, were used to identify the features or a combination of features that could consistently differentiate a malignant skin tumor (melanoma) from a benign one (seborrheic keratosis). Two hundred and seventy-one skin tumor images were separated into training and test sets for accuracy and consistency. Automatic induction was applied to generate classification rules. Data analysis and modeling tools were used to gain further insight into the feature space. Result and Conclusions: In all, 85-90% of seborrheic keratosis images were correctly differentiated from the malignant skin tumors. The features correlation_average, correlation_range, texture_energy_average and texture_energy_range were found to be the most important features in differentiating seborrheic keratosis from melanoma. Overall, the seborrheic keratosis images were better identified by the texture features than the melanoma images

CONTRIBUTIONS OF EAG PROTEIN TO NEURONAL EXCITABILITY IN IDENTIFIED THORACIC MOTONEURONS OF DROSOPHILA

Diversity in the expression of ion channel proteins among neurons allows a wide range of excitability, growth and functional regulation. Ether-a-go-go (EAG), a member of the voltage-gated K+ channels, was characterized by spontaneous firing in nerve terminals and enhanced neurotransmitter release. In situ whole-cell patch-clamp recordings performed from the somata of Drosophila larval thoracic aCC motoneurons revealed spontaneous spike-like events in eag mutants. Spontaneous events were absent in wild type motoneurons. Spikes evoked by somatic current injection in to the cell body were not altered and comparable to wild type. Spontaneous spike-like events could be due to increased synaptic drive or altered intrinsic excitability of the motoneuron. Reduction of EAG function with selective expression of eag double stranded RNAi transgene in motoneurons only did not cause spontaneous spike-like events or alter evoked firing. This suggests increased synaptic drive contributes to spontaneous events.Both transient and sustained voltage-activated K+ currents, each with Ca++-sensitive (IA(Ca) and IK(Ca)) and Ca++ -insensitive components (IA and IK), were isolated in thoracic aCC motoneurons. In wild type motoneurons, IA was larger than IA(Ca). Conversely, IK(Ca) was larger than IK. Both eag mutants and eag RNAi expression resulted in a decrease in IA , IK and a slow sustained K+ current. Further, EAG and Shal demonstrate a potential functional interaction and contribute to IA. The voltage sensitivity for inactivation was reduced in Shal only and EAG-Shal double knock down compared to controls and EAG only knock down. In addition, a Ca++ sensitive EAG dependent K+ current was blocked by cAMP. Thus, both voltage-dependent and modulatory functions of EAG influence excitability in motoneurons.Firing properties and K+ currents distinguish aCC motoneurons in thoracic segments, T1 and T3. T3aCC had a shorter delay to spike, higher input resistance and were more easily recruited than T1aCC. T1aCC had a larger IA than T3aCC, but comparable IA(Ca). IK(Ca) was larger in T3aCC compared to T1aCC. These differences reflect cell-specific ion channel distribution that could contribute to patterned segmental motor output

The role of the glucocorticoids in developing resilience to stress and addiction

There is emerging evidence that individuals have the capacity to learn to be resilient by developing protective mechanisms that prevent them from the maladaptive effects of stress that can contribute to addiction.The emerging field of the neuroscience of resilience is beginning to uncover the circuits and molecules that protect against stress-related neuropsychiatric diseases, such as addiction. Glucocorticoids (GCs) are important regulators of basal and stress-related homeostasis in all higher organisms and influence a wide array of genes in almost every organ and tissue. GCs, therefore, are ideally situated to either promote or prevent adaptation to stress. In this review, we will focus on the role of GCs in the hypothalamic-pituitary adrenocortical axis and extra-hypothalamic regions in regulating basal and chronic stress responses. GCs interact with a large number of neurotransmitter and neuropeptide systems that are associated with the development of addiction. Additionally, the review will focus on the orexinergic and cholinergic pathways and highlight their role in stress and addiction. GCs play a key role in promoting the development of resilience or susceptibility and represent important pharmacotherapeutic targets that can reduce the impact of a maladapted stress system for the treatment of stress-induced addiction

Thromboxane A2 and thrombin receptors mediate platelet activation through P2Y12-independent mechanisms.

Thromboxane A2 and thrombin receptors mediate platelet activation through P2Y12-independent mechanisms

PULMONARY TUBERCULOSIS - A PROSPECTIVE ANALYSIS OF HEMATOLOGICAL CHANGES

 Objective: This study was a prospective analysis of hematological changes in pulmonary tuberculosis (TB). The objectives of this study are (1) to study the changes in different parameters of hemogram in association of sputum-positive pulmonary TB, (2) to evaluate the disease severity and patient infectivity, (3) to determine the most common type and severity of anemia in pulmonary TB patients, and (4) to count platelets in pulmonary TB patients. TB is an important communicable disease in the world and is a major public health problem in India. Hematogical abnormalities associated with TB have been completely investigated in the literature though it is a common condition in India.Methods: A total of 150 patients of acid-fast bacilli-positive cases were included, and disseminated TB, childhood TB, and patients receiving anti-TB drugs were excluded from this study.Results: Among the 150 patients, anemia was observed in 116 cases, normocytic normchromic and microcytic hypochromic picture, leukocytosis in 68 patients, thrombocytosis in 50 patients, thrombocytopenia in 5 patients, and ESR levels were elevated in more than 82% of patients.Conclusion: A complete hemogram has been demonstrated in patients with acid-fast bacilli-positive cases in the present study. Since there was a paucity of literature in the hematological changes associated with TB, this study aimed at reinforcing the fact that they can be valuable tools in monitoring pulmonary TB