bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research Objects: Towards Exchange and Reuse of Digital Knowledge
Authors: Bechhofer Sean , De Roure David , Gamble Matthew , Goble Carole , Buchan Iain 
Published: October 2010

Abstract What will researchers be publishing in the future? Whilst there is little question that the Web will be the publication platform, as scholars move away from paper towards digital content, there is a need for mechanisms that support the production of self-contained units of knowledge and facilitate the publication, sharing and reuse of such entities. In this paper we discuss the notion of research objects, semantically rich aggregations of resources, that can possess some scientific intent or support some research objective. We present a number of principles that we expect such objects and their associated services to follow.
Impacts – The Key to Understand Earth
Authors: Huang Hua 
Published: October 2010

AbstractA significant factor, where are the major elements e.g. Mg, Fe, Si, Al, Ca, P, Ni that make up the asteroid or comet after the impact, has been ignored since the proposal of the impact events. In a striking contrast, there are many remaining unanswered or poorly answered questions regarding the formation and nature of banded iron formation (BIF), iron stone, phosphorite, bedded manganese ore, dolomite and carbonaceous black shales. The appearance of Lake Superior type banded ion formation associated with dolomite, quartzite, and black shale, the deposition of manganese ore and the occurrence of large phosphate repository during the Plaeoproterozoic; the onset of BIF with phosphate deposition and sedimentary manganese deposits and cap dolomite during the Neoproterozoic; the penecontemporary formation of oolitic iron stone taking place of the BIF, bedded manganese deposit, phosphorite, dolomite, and black shale during the Phanerozoic, which suggest a genetic link among them from the perspective of chemical elements. Actually, during hypervelocity impact cratering events, the main part of the asteroid or comet and target material are vaporizing, which forms a mushroom cloud of vapor in the atmosphere.The previous study shows that the calcite, magnetite, clay minerals and organic compounds condense from a solar gas at 10−4 atm with temperature less than 400 K, which provides an analog for the generation of the chemical sedimentary ore deposits. This also supported by table isotopes fractionation at small sacle (grain size, cm scale), all stable isotopes fractionation e.g. (Cr, Fe, S, Si, O,C) and mass-independent fractionation of sulphur isotopes following the rule of isotope fractionation during impacts: the earlier the condensed material, the more enriched in lighter isotopes. Thus, the impact of the asteroid or comet provides not only the elements source of chemical sedimentary ore deposits and the mechanism for their formation. The enrichment in iridium in BIFs and their associated impact spherule units are the other evidence to demonstrate that BIFs are the products of impacts. Impacts produce black shale, banded iron formation, limestone and dolomite. Based on the coeval sub-continental lithosphere mantle (SCLM) formation, juvenile crust generation, banded iron formations, mantle plumes and black shale, it seems that impacts maybe the driving force for Earth.
An approach able to escape the most common problem during protein Crystallization i.e. formation of salt crystal
Authors: Singh K. Awaneesh , Celie Patrick , Rao G. R. K. , Jagannatham M. 
Published: October 2010

AbstractFormation and differentiation of salt crystal is a most common as well as challenging problem during protein crystallography. Although there are some methods used for their differentiation i.e. physical manipulation, birefringence, dye absorption and run a gel but all of them are totally depends on own perception and expertise as well as also require a good crystal (final stage crystal). To escape this problem the screening was done with PACT, JCSG and other automated screens as everyone do. But during optimization the additives/salts were ignored at first and optimization screen was made just based on different buffers and precipitant. After selecting suitable buffer, the type and percentage of precipitant was optimized. We got some ugly crystals and with the help of previous screening the effective additives/salts were chosen. On the basis of relation between pH and additive/salt concentration, the additive/salt and their concentration were optimized. At last optimization of methods, protein and crystallization ratio and physical conditions were done to get good crystals better in size and shape. This approach is completely able to escape the risk of salt crystal formation which can reduce our wastage of time and money.
Targeting Human Dendritic Cells with Lewis X Modified Liposomes
Authors: Kalvodova Lucie , Zhang Yongmin 
Published: October 2010

AbstractIn this short report, we demonstrate that liposomes bearing the Lewis X trisaccharide on the surface (“Awesosomes”) efficiently target human dendritic cells. We chose a glycolipid with Lewis X trisaccharide headgroup to facilitate the targeted liposome uptake via the DC-SIGN internalization pathway. While no uptake of Awesosomes was detected with wild-type human HEK293 cells, HEK293 cells transfected with human DC-SIGN internalized Awesosomes extensively. In samples of human blood-derived leukocytes, the extent of uptake of Awesosomes correlated with the expression of DC-SIGN, which is a dendritic cells marker. There was a marked difference in the uptake of Awesosomes and plain liposomes by DC-SIGN expressing dendritic cells. There was no difference in uptake of Awesosomes and plain liposomes by wt HEK293 cells or macrophages. These results indicate that Lewis X trisaccharide can “sweet-talk” dendritic cells into internalizing a delivery vehicle, and that Awesosomes are promising as “magic bullets” for specific delivery of drugs, antigens, or immunostimulatory molecules to human dendritic cells without influencing other cell types.
Studies on Utilizing the Three Famous International Index Systems to Evaluate Scientific Research Level of Higher Learning Institutions
Authors: Liu Xun , Huang Changyu , Qian Wei-Liang , Huang Yong-Chang 
Published: October 2010

AbstractScience Citation Index (SCI), The Engineering Index (EI) and Index to Scientific & Technical Proceeding (ISTP) are widely accepted and used to evaluate the scientific research level of higher learning institutions by many country's science and technology field currently. After research, we point out the blemishes in this method and put forward the problems that need to be noticed, and then, under current conditions, bring forward brand-new standard and method to estimate research level, efficiency, fund exploitation and so on. One shouldn't over-emphasize the total amount of papers collected in SCI, EI & ISTP when evaluating the scientific research level of higher learning institutions, whereas using ‘comprehensive factor’ analysis method can make it more scientific and efficient.
Cloning and expression of first gene for biodegrading microcystins by Sphingopyxis sp. USTB-05
Authors: Yan Hai , Wang Junfeng , Chen Jian , Wei Wei , Wang Hui 
Published: October 2010

AbstractHarmful cyanobacterial blooms (HCBs) in natural waters are a growing environmental problem worldwide because microcystins (MCs) produced by cyanobacteria are potent hepatotoxins and tumor promoters. MCs are resistant against physical and chemical factors. Thus, biodegradation is the most efficient method for removing MCs, and a number of bacterial strains, especially genus Sphingomonas, have been isolated for biodegrading MCs. Although the pathway, enzyme, and gene for biodegrading MCs by Sphingomonas sp. have been widely identified recently, no gene concerned with the biodegradation of MCs has been successfully cloned and expressed. In this study, we show that the first and most important gene of mlrA, containing 1,008 bp nucleotides in length, in the biodegradation pathway of MCs by Sphingopyxis sp. USTB-05, which encodes an enzyme MlrA containing 336 amino acid residues, is firstly cloned and expressed in E. coli DH5&x03B1;, with a cloning vector of pGEM-T easy and an expression vector of pGEX-4T-1. The encoded and expressed enzyme MlrA is responsible for cleaving the target peptide bond between 3-amino-9-methoxy-2,6,8-trimethyl-10-phenyl-deca-4,6-dienoic acid (Adda) and Arg in the cyclic structure of microcystin-RR &xFF08;MC-RR&xFF09;and microcystin-LR&xFF08;MC-LR), two typical and toxic types of MCs. Linear MC-RR and MC-LR are produced as the first products. These findings are important in constructing a new genetic bacterial strain for the efficient removal of MCs from the important water supplies and resolving the controversy on the biodegradation pathway of different types of MCs by genus Sphingomonas.
Without magic bullets: the biological basis for public health interventions against protein folding disorders
Authors: Wallace Rodrick 
Published: October 2010

AbstractProtein folding disorders of aging like Alzheimer's and Parkinson's diseases currently present intractable medical challenges. 'Small molecule' interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary 'physics' or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty's (2010a) elegant exploration of the genetic code. The formalism produces large-scale, quasi-equilibrium 'resilience' states representing normal and pathological protein folding regulation under a cellular-level cognitive paradigm similar to that proposed by Atlan and Cohen (1998) for the immune system. Generalization to long times produces diffusion models of protein folding disorders in which epigenetic or life history factors determine the rate of onset of regulatory failure, in essence, a premature aging driven by familiar synergisms between disjunctions of resource allocation and need in the context of socially or physiologically toxic exposures and chronic powerlessness at individual and group scales. Application of an HPA axis model is made to recent observed differences in Alzheimer's onset rates in White and African American subpopulations as a function of an index of distress-proneness.
A novel mathematical tool for generating highly conserved protein domain via different organismal genomic landscapes
Authors: Goswami Arunava , Pal Choudhury Pabitra , Singh Rajneesh , Hassan Sk. Sarif 
Published: October 2010

AbstractDarwinian evolution hypothesizes that a short stretch of DNA was first constructed and then it expanded to give rise to a long strand. This long strand then produced a mix of exons, introns and repetitive DNA sequence. The order of production of above three kinds of DNA sequence is unknown. Reshuffling of stretches of DNA like above within organisms has given rise to different chromosomes. Till date it is not known how this process is governed. In this paper we show that starting with a sixteen base-pair human olfactory DNA sequence one can form a highly conserved protein domain. Once this domain is formed repetitive DNA sequences of a particular kind starts generating which signifies that this particular conserved protein domain will be unique in nature. The entire mathematical exercise presented in this paper is based on simplest possible context free L-System which we think has been adopted by biological system in general.
Wikis as platforms for scholarly publishing
Authors: Mietchen Daniel 
Published: October 2010

AbstractWhile scholarly publishing has traditionally focused on stand-alone articles describing how a specific act of research advanced knowledge in a particular area for once, wikis and similar collaborative online environments provide the technical means to focus on contextually interlinked concepts instead and to update them continuously as new research results come in. Some platforms based totally or in part on these principles have already been put to practical tests whose relevance for Open Access publishing are discussed here, paying special attention to implementations of the review process. The presentation was given "on-wiki":http://en.citizendium.org/wiki/User:Daniel_Mietchen/Talks/COASP_2010/Start .
An attempt to understand Barstar, Barnase and Olfactory receptor protein folding problems using mathematical biological approach
Authors: Goswami Arunava , Hassan Sk Sarif , Pal Choudhury Pabitra 
Published: October 2010

AbstractProtein folding problem as attracted structural biologists immensely (1). Till date, correlation between X-ray crystallographic and NMR data are considered to be the best methods for determining structure of intra-cellular proteins. Generating crystals and finding correct experimental conditions for NMR are largly a gamble and resultant data processing highly time consuming. Even if, a large number of laboratories around the world and India make crystals of protein but majority of them fail to generate crystallographic data less than or equal to 10A resolution with currently available instruments. This means that X-ray crystallographic data have been generated from protein crystals with non-uniform lattices. We believe that a large portion of (chain of amino acids) all proteins, be it an intra-cellular, transmembrane or extra-cellular proteins form uniform lattices following precise deterministic mathematical rules in natural condition inside cells or membranes or in extra-cellular conditions. This hypothesis has several advantages. First, stacking of protein chains like lattices (lattices of helix or beta-sheet etc.) allows a particular protein to resist forces of compression and relaxation. Secondly, it will be easier to expose hydrophobic and hydrophilic domains following a mathematical rule described in this paper. Barstar, Barnase and olfactory receptors (ORs) have 90, 110 and ~312 amino acids respectively. Using Young-Fibonacci graph area model, here we show that all naturally available protein folding problems can be solved or a preliminary idea about their secondary and tertiary structures can be predicted. This is absolutely necessary considering the fact that there are zillions of proteins present in the animal and plant world. The process of X-ray crystallography and NMR followed by computer modeling for elucidating the secondary and tertiary structures of these vast numbers of proteins might take hundreds of years.
Identification of Potent Leads for Human cAMP Dependent Protein Kinase Catalytic Subunit Alpha: A Strategic Application of Virtual Screening for Cancer Therapeutics
Authors: Swargam Sandeep , Pradhan Dibyabhaba , Umamaheswari Amineni 
Published: October 2010

AbstractThe advancement in therapeutic applications focused on specific macromolecular compounds of deregulated cell signaling pathways bestowed novel approach to design the ligands as drug molecules against several life threatening diseases such as Cancer. In humans, protein kinase A is one of the important kinases those were involved in cell signaling mechanism. cAMP, G-proteins and ATP molecules were required for activation of protein kinase A (PKA), upon activation, PKA catalytic subunits (PRKACA,PRKACB and PRKACG) undergoes many cellular functions like cell proliferations, cell cycle regulation, and survival of cells through acting on many substrates. Overexpression of extracellular cAMP dependent protein kinase A catalytic subunits (PRKACA) causes severe tumorgenesis in different organs (prostate gland, breast, lungs and pancreas) leading to cancer. High throughput virtual screening was implemented herein to identify the potent leads for human PRKACA that stimulates chronic form of cancers. In silico functional and phylogenetic analysis of PRKACA protein provided enough evidences towards its cancer stimulating nature. The human PRKACA crystal structure in complex with inhibitor ‘796’ (PDB ID: 2GU8) was optimized in Maestro v9.0 and the amino acid residues constituting inhibitor interaction site were determined. Fifteen published inhibitors were selected including HA1077, Flavopiridol, Roscovitine, MLN-518, PP2 and Gleevec which were already in clinical trials for high throughput screening at Ligand.Info database. An in house library of 5388 compounds was designing from the above screening procedure were prepared in LigPrep for molecular docking with human PRKACA. Maestro Glide docking from lesser to higher stringency towards minor steric classes were applied subsequently to the prepared ligand dataset against a grid around centroid of the identified inhibitor interaction site of human PRKACA and 21 lead molecules with good docking scores were obtained. Lead ‘1’ (Leptosidin) with relatively least docking score (-11.02 Kcal/mol) compared to other 20 lead molecules and 15 published inhibitors delineates it as potentially the best competitive inhibitor among all. The promising inhibitory activity of Leptosidin is further supported from analysis of binding orientations of human PRKACA- Leptosidin complex deciphering the Lead 1 blocks the active site residues Thr51, Glu121, Val123, Glu127 and Thr183 by forming hydrogen bond. Thus, Leptosidin could be futuristic perspective chemical compound to design drug molecule against human PRKACA in numerous cancers, however, further in vitro and in vivo studies were required to verify the computational strategic prediction of PKA holoenzyme against cancer therapeutics.
The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish
Authors: Fraser-Liggett Claire , Shuldiner Alan 
Published: October 2010

AbstractEmerging evidence that the gut microbiota may contribute in important ways to human health and disease has led us and others to hypothesize that both symbiotic and pathological relationships between gut microbes and their host may by key contributors to obesity and the metabolic complications of obesity. Our “Thrifty Microbiome Hypothesis” posits that gut microbiota play a key role in human energy homeostasis. Specifically, constituents of the gut microbial community may introduce a survival advantage to its host in times of nutrient scarcity, promoting positive energy balance by increasing efficiency of nutrient absorption and improving metabolic efficiency and energy storage. However, in the presence of excess nutrients, fat accretion and obesity may result, and in genetically predisposed individuals, increased fat mass may result in preferential abdominal obesity, ectopic fat deposition (liver, muscle), and metabolic complications of obesity (insulin resistance, hypertension, hyperlipidemia). Furthermore, in the presence of excess nutrients, a pathological transition of the gut microbial community may occur, causing leakage of bacterial products into the intestinal lymphatics and portal circulation, thereby inducing an inflammatory state, further aggravating metabolic syndrome traits and accelerating atherosclerosis. This pathological transition and the extent to which antimicrobial leakage occurs and causes inflammatory and other maladaptive sequelae of obesity may also be influenced by host factors, including genetics. In the proposed study, we will directly test the Thrifty Mirobiome Hypothesis by performing detailed genomic and functional assessment of gut microbial communities in intensively phenotyped and genotyped human subjects before and after intentional manipulation of the gut microbiome. To address this hypothesis, we will enroll three age- and sex-matched groups from the Old Order Amish: (i) 50 obese subjects (BMI > 30 kg/m2) with one or more dysmetabolic manifestations (malignant obesity), (ii) 50 obese subjects (BMI > 30 kg/m2) without any dysmetabolic manifestations (benign obesity), and (iii) 50 nonobese subjects (BMI < 25 kg/m2) without any features of the metabolic syndrome and characterize the architecture of the gut microbiota from the subjects enrolled in this study by high-throughput sequencing of 16S rRNA genes. These studies will provide a deeper understanding of the role of gut microbes in terms of ‘who’s there?’, ‘what are they doing?’, and ‘how are they influencing host energy homeostasis, obesity and its metabolic complications?’
Report on the status of SBGN ER and proposed extensions
Authors: Le Novere Nicolas 
Published: October 2010

AbstractThe Systems Biology Graphical Notation (SBGN) is an effort to standardize the graphical notation used in maps of biochemical and cellular processes studied in systems biology. SBGN is made up of three orthogonal languages, representing different visions of biological systems. Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules how maps are to be interpreted. In this presentation I recapitulated why SBGN was developed, and discuss the current state of the Entity Relationships language. I then describe the coming evolutions and the pending issues.
Composition of Biochemical Networks using Domain Knowledge
Authors: Goodfellow Martin , Wilson John , Hunt Ela 
Published: October 2010

AbstractGraph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain.