PASBio: predicate-argument structures for event extraction in molecular biology

Background: The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas where sentence understanding is required like machine translation and text summarization. In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction. Results: We introduce PASBio by extending a model based on PropBank to the MB domain. The hypothesis we explore is that PAS holds the key for understanding relationships describing the roles of genes and gene products in mediating their biological functions. We chose predicates describing gene expression, molecular interactions and signal transduction events with the aim of covering a number of research areas in MB. Analysis was performed on sentences containing a set of verbal predicates from MEDLINE and full text journals. Results confirm the necessity to analyze PAS specifically for MB domain. Conclusions: At present PASBio contains the analyzed PAS of over 30 verbs, publicly available on the Internet for use in advanced applications. In the future we aim to expand the knowledge base to cover more verbs and the nominal form of each predicate

Structural Microstructural and Electrical Transport Studies of Ba(Fe0.25Eu0.25Nb0.5)O3

The complex multifunctional ceramic Ba(Fe0.25Eu0.25Nb0.5)O3 (BFEN) has been synthesized. The structural studies show two iso-structured phases related with BFN and BEN co-exists in the compound. The high dielectric constant and low dielectric loss of the compound below 575 K promises industrial applications. The activation energies obtained from the Arrhenius analysis of dc conductivity supports possible ferroelectric transition at elevated temperatures. Thus the desirable properties of two different compounds viz. multiferroic properties of BFN and high quality factor of BEN are successfully incorporated in a single compound. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/3101

Proteome-wide profiling of the MCF10AT breast cancer progression model

10.1371/journal.pone.0011030PLoS ONE56

Milk Yield Response of Bypass Protein on Smallholder Dairy Animals

Protein need for small holder dairy animals is very limited. Considering this problem one on-station and one on-farm trails were conducted in 2013 and 2014 in Nepal respectively. In on-station trial (2013) 15 milking buffaloes were randomly assigned to 5 dietary treatments (0, 0.5, 1, 1.5 and 2 kg de-oiled soybean meals/day/buffalo) and in on-farm trial (2014), 20 milking buffaloes were assigned to 0.5 kg de-oiled soybean meal/day/buffalo for two months dry period. From on-station trial, significantly higher (42 %) milk production was observed from 0.5 kg and 1 kg de-oiled soybean meal/day/buffalo feeding groups. From the on-farm trials in village dairy buffaloes 20 percent milk production increment was observed compared with the normal farmer's feeding practices (de-oiled soybean meals unfed condition). It was concluded that, in addition to normal diet, 0.5 to 1 kg de-oiled soybean meal (depending up on the body weight of animal and feeding situation) per day feeding as bypass protein sources could be beneficial during dry period where green fodder is scarce to maintain milk production from dairy animals

p31 comet acts to ensure timely spindle checkpoint silencing subsequent to kinetochore attachment

The spindle assembly checkpoint links the onset of anaphase to completion of chromosome-microtubule attachment and is mediated by the binding of Mad and Bub proteins to kinetochores of unattached or maloriented chromosomes. Mad2 and BubR1 traffic between kinetochores and the cytosol, thereby transmitting a "wait anaphase" signal to the anaphase-promoting complex. It is generally assumed that this signal dissipates automatically upon kinetochore-microtubule binding, but it has been shown that under conditions of nocodazole-induced arrest p31comet, a Mad2-binding protein, is required for mitotic progression. In this article we investigate the localization and function of p31 comet during normal, unperturbed mitosis in human and marsupial cells. We find that, like Mad2, p31 comet traffics on and off kinetochores and is also present in the cytosol. Cells depleted of p31 comet arrest in metaphase with mature bipolar kinetochore-microtubule attachments, a satisfied checkpoint, and high cyclin B levels. Thus p31 comet is required for timely mitotic exit. We propose that p31 comet is an essential component of the machinery that silences the checkpoint during each cell cycle

Biofilm production and antimicrobial resistance among uropathogens in pediatric cases: a hospital based study

Background: The study was designed to provide account of etiological agents of urinary tract infection in pediatric patients and the antimicrobial resistance pattern plus biofilm producing profile of the isolates. Methods: The prospective study was conducted in Alka Hospital, Nepal with 353 clean catch urine samples from children. It was obtained during July 2014 to January 2015 which were first cultured by semi-quantitative method, followed by antimicrobial susceptibility testing and biofilm production assay on Congo red agar. Multidrug- resistance, extensively drug- resistance and pandrug- resistance among isolates were considered as per international consensus. Results: Out of 353 samples, 64 (18.13%) showed positive growth in culture, confirming urinary tract infection. E. coli, 44 (68.8%) was the predominant organism followed by Klebsiella spp. 6 (14.1%). Most E. coli were sensitive to amikacin (93.2%) followed by nitrofurantoin (86.4%), and highly resistant to ampicillin (95.5%). Of 64 isolates, 23 (35.93%) were found to be multidrug- resistant strains. Biofilm was produced by 36 (56.25%) isolates. Conclusions: This study showed higher biofilm production and resistance to in-use antibiotics rendering ineffective for empirical use. Regular surveillance of resistance patterns should be done to regulate multidrug- resistant bugs and to ensure effective management of urinary tract infection in children in a tertiary care setups. Keywords: AMR; antimicrobial resistance; biofilm; urinary tract infection; UTI.Dhiraj Shrestha, Pratigya Thapa, Dinesh Bhandari, Hiramani Parajuli, Prakash Chaudhary, Kabi Thapa, Vijay Kumar Sharma, Pradeep Kumar Sha