A SURVEY ON ANT COLONY OPTIMIZATION ALGORITHM

A novel Ant Colony Optimization algorithm (ACO) combined for the hierarchical multi- label classification problem of protein function prediction. This kind of problem is mainly focused on biometric area, given the large increase in the number of uncharacterized proteins available for analysis and the importance of determining their functions in order to improve the current biological knowledge. Because it is known that a protein can perform more than one function and many protein functional-definition schemes are organized in a hierarchical structure, the classification problem in this case is an instance of a hierarchical multi-label problem. In this classification method, each class might have multiple class labels and class labels are represented in a hierarchical structure—either a tree or a directed acyclic graph (DAG) structure. A more difficult problem than conventional flat classification in this approach, given that the classification algorithm has to take into account hierarchical relationships between class labels and be able to predict multiple class labels for the same example. The proposed ACO algorithm discovers an ordered list of hierarchical multi-label classification rules

New features of collective motion of intrinsic degrees of freedom. Toward a possible way to classify the intrinsic states

Three exactly solvable Hamiltonians of complex structure are studied in the framework of a semi-classical approach. The quantized trajectories for intrinsic coordinates correspond to energies which may be classified in collective bands. For two of the chosen Hamiltonians the symmetry SU2xSU2 is the appropriate one to classify the eigenvalues in the laboratory frame. Connections of results presented here with the molecular spectrum and Moszkowski model are pointed out. The present approach suggests that the intrinsic states, which in standard formalisms are heading rotational bands, are forming themselves "rotational" bands, the rotations being performed in a fictious boson space.Comment: 33 pages, 9 figure

The GALNT9, BNC1 and CCDC8 genes are frequently epigenetically dysregulated in breast tumours that metastasise to the brain.

Tumour metastasis to the brain is a common and deadly development in certain cancers; 18-30 % of breast tumours metastasise to the brain. The contribution that gene silencing through epigenetic mechanisms plays in these metastatic tumours is not well understood

Human BRCA1-BARD1 ubiquitin ligase activity counters chromatin barriers to DNA resection

The opposing activities of 53BP1 and BRCA1 influence pathway choice of DNA double-strand break repair. How BRCA1 counters the inhibitory effect of 53BP1 on DNA resection and homologous recombination is unknown. Here we identify the site of BRCA1-BARD1 required for priming ubiquitin transfer from E2~ubiquitin. We demonstrate that BRCA1-BARD1’s ubiquitin ligase activity is required for repositioning 53BP1 on damaged chromatin. We confirm H2A ubiquitylation by BRCA1-BARD1 and show that an H2A-ubiquitin fusion protein promotes DNA resection and repair in BARD1 deficient cells. We show BRCA1-BARD1 function in homologous recombination requires the chromatin remodeler SMARCAD1. SMARCAD1 binding to H2A-ubiquitin, optimal localization to sites of damage and activity in DNA repair requires its ubiquitin-binding CUE domains. SMARCAD1 is required for 53BP1 repositioning and the need for SMARCAD1 in Olaparib or camptothecin resistance is alleviated by 53BP1 loss. Thus BRCA1- BARD1 ligase activity and subsequent SMARCAD1-dependent chromatin remodeling are critical regulators of DNA repair

Selection of Metastatic Breast Cancer Cells Based on Adaptability of Their Metabolic State

A small subpopulation of highly adaptable breast cancer cells within a vastly heterogeneous population drives cancer metastasis. Here we describe a function-based strategy for selecting rare cancer cells that are highly adaptable and drive malignancy. Although cancer cells are dependent on certain nutrients, e.g., glucose and glutamine, we hypothesized that the adaptable cancer cells that drive malignancy must possess an adaptable metabolic state and that such cells could be identified using a robust selection strategy. As expected, more than 99.99% of cells died upon glutamine withdrawal from the aggressive breast cancer cell line SUM149. The rare cells that survived and proliferated without glutamine were highly adaptable, as judged by additional robust adaptability assays involving prolonged cell culture without glucose or serum. We were successful in isolating rare metabolically plastic glutamine-independent (Gln-ind) variants from several aggressive breast cancer cell lines that we tested. The Gln-ind cells overexpressed cyclooxygenase-2, an indicator of tumor aggressiveness, and they were able to adjust their glutaminase level to suit glutamine availability. The Gln-ind cells were anchorage-independent, resistant to chemotherapeutic drugs doxorubicin and paclitaxel, and resistant to a high concentration of a COX-2 inhibitor celecoxib. The number of cells being able to adapt to non-availability of glutamine increased upon prior selection of cells for resistance to chemotherapy drugs or resistance to celecoxib, further supporting a linkage between cellular adaptability and therapeutic resistance. Gln-ind cells showed indications of oxidative stress, and they produced cadherin11 and vimentin, indicators of mesenchymal phenotype. Gln-ind cells were more tumorigenic and more metastatic in nude mice than the parental cell line as judged by incidence and time of occurrence. As we decreased the number of cancer cells in xenografts, lung metastasis and then primary tumor growth was impaired in mice injected with parental cell line, but not in mice injected with Gln-ind cells

GIS Based Mapping for a Better Crop Planning for Perumpadappu Block of Ponnani Kole Lands in Kerala

Kole lands are one of the biggest saline, humid tropical wetland ecosystems. It spreads across  Thrissur and Malappuram districts of Kerala state. They serve as a water storage structure during  rainy season. After rains, the stored water is dewatered and circulated in various Kole padasekarams and channels to cultivate paddy. However, the problem is the lack of a proper water management plan resulting in crop loss. The current study is conducted in the Perumpadappu block of Ponnani Kole lands in Malappuram district. In this study, both GIS and Remote sensing technology have been collaborated to plan the crop calendar. The cropping calendar of Ponnai Kole was developed mainly for 37 Kole padashekharams of Perumpadappu block. Data about elevation, transportation, irrigation, weather and soil were collected to arrive at the crop calendar. Together, by adopting participatory rural appraisal methods and local knowledge were integrated. The final crop calendar was wetted with farmers and experts

An unusual mutation in RECQ4 gene leading to Rothmund-Thomson syndrome

Rothmund-Thomson syndrome (OMIM #268400) is a severe autosomal recessive genodermatosis: characterised by growth retardation, hyperpigmentation and frequently accompanied by congenital bone defects, brittle hair and hypogonadism. Mutations in helicase RECQ4 gene are responsible for a subset of cases of RTS. Only six mutations have been reported, thus, far and each affecting the coding sequence or the splice junctions. We report the first homozygous mutation in RECQ4 helicase: 2746-2756-delTGGGCTGAGGC in IVS8 responsible for the severe phenotype associated with RTS in a Malaysian pedigree. We report also a 5321 G-->A transition in exon 17 and the updated list of the RECQ4 gene mutations

Study of water supply & sanitation practices in India using geographic information systems: some design & other considerations in a village setting

Background & objectives: Availability of clean water and adequate sanitation facilities are of prime importance for limiting diarrhoeal diseases. We examined the water and sanitation facilities of a village in southern India using geographic information system (GIS) tools. Methods: Places of residence, water storage and distribution, sewage and places where people in the village defaecated were mapped and drinking water sources were tested for microbial contamination in Nelvoy village, Vellore district, Tamil Nadu. Results: Water in the village was found to be microbiologically unfit for consumption. Analysis using direct observations supplemented by GIS maps revealed poor planning, poor engineering design and lack of policing of the water distribution system causing possible contamination of drinking water from sewage at multiple sites. Interpretation & conclusions: Until appropriate engineering designs for water supply and sewage disposal to suit individual village needs are made available, point-of-use water disinfection methods could serve as an interim solution

Assessment of variability in physical and chemical composition of Cuminum cyminum seeds from arid and semiarid India

Cumin (Cuminum cyminum L.) is an important spice commodity cultivated under large areas in arid and semiarid India. It has attained a valuable importance due to its immense aromatic, culinary and medicinal values. Due to its very selective dry and cool climate requirement, cumin is mainly being grown in western regions of India. The present study accounts for the variability observed in physical and chemical properties of cumin seed samples collected from cumin growing areas located in the 7 districts of Rajasthan and 5 districts of Gujarat classified under Agro-Ecological Sub Regions (AESR) of India. Quantity of essential oil (EO) in cumin seeds from various districts revealed that the overall EO content ranged between 28.4 to 39.1 g/kg. In Rajasthan, highest EO content was recorded in the cumin samples from Nagaur (38.5 ± 0.37), followed by Jaisalmer (37.4 ± 0.31) and was least in Ajmer (28.6 ± 0.27) whereas, in Gujarat, samples from Patan possessed highest EO content (39.1± 0.17) with least values in Amreli (28.4 ±1.08). The average flavonoid content expressed as mg QE/g seeds was highest in Nagaur (39.72), followed by Amreli (36.03) and lowest in Ajmer district (23.71), similarly the estimated phenol content (mg GAE/g seeds) was maximum in Jalore (73.61), followed by Nagaur (63.77) and least in Amreli district (41.50). The carbohydrates content and total protein content ranged between 15.86-28.88 and 19.30-21.89 per cent respectively. This study also provides basic information in understanding cumin composition and its value as a commodity for business based on interstices parameters reflecting quality assessment for regional produce harvested from India

Insights from global data for use of rotavirus vaccines in India

Rotavirus vaccines are being introduced in several low- and middle-income countries across the world with and without support from the GAVI Alliance. India has the highest disease burden of rotavirus based on morbidity and mortality estimates and several indigenous vaccine manufacturers are developing rotavirus vaccines. One candidate has undergone phase III testing and others have completed evaluation in phase II. Global data on licensed vaccine performance in terms of impact on disease, strain diversity, safety and cost-effectiveness has been reviewed to provide a framework for decision making in India