bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity
Authors: Milanesi Luciano , Petrillo Mauro , Sepe Leandra , Boccia Angelo , D'Agostino Nunzio , Passamano Myriam , Di Nardo Salvatore , Tasco Gianluca , Casadio Rita , Paolella Giovanni 
Published: December 2005

Abstract

Background
Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular processes, such as proliferation, maintenance of cell shape, apoptosys. In many members of the family, additional non-kinase domains contribute further specialization, resulting in subcellular localization, protein binding and regulation of activity, among others. About 500 genes encode members of the kinase family in the human genome, and although many of them represent well known genes, a larger number of genes code for proteins of more recent identification, or for unknown proteins identified as kinase only after computational studies.

Results
A systematic in silico study performed on the human genome, led to the identification of 5 genes, on chromosome 1, 11, 13, 15 and 16 respectively, and 1 pseudogene on chromosome X; some of these genes are reported as kinases from NCBI but are absent in other databases, such as KinBase. Comparative analysis of 483 gene regions and subsequent computational analysis, aimed at identifying unannotated exons, indicates that a large number of kinase may code for alternately spliced forms or be incorrectly annotated. An InterProScan automated analysis was perfomed to study domain distribution and combination in the various families. At the same time, other structural features were also added to the annotation process, including the putative presence of transmembrane alpha helices, and the cystein propensity to participate into a disulfide bridge.

Conclusion
The predicted human kinome was extended by identifiying both additional genes and potential splice variants, resulting in a varied panorama where functionality may be searched at the gene and protein level. Structural analysis of kinase proteins domains as defined in multiple sources together with transmembrane alpha helices and signal peptide prediction provides hints to function assignment. The results of the human kinome analysis are collected in the KinWeb database, available for browsing and searching over the internet, where all results from the comparative analysis and the gene structure annotation are made available, alongside the domain information. Kinases may be searched by domain combinations and the relative genes may be viewed in a graphic browser at various level of magnification up to gene organization on the full chromosome set.
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms
Authors: Persico Maria , Ceol Arnaud , Gavrila Caius , Hoffmann Robert , Florio Arnaldo , Cesareni Gianni 
Published: December 2005

Abstract

Background
The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms. Until now, however, such genome-wide approaches have not been applied to the human proteome.

Results
In order to fill this gap we have assembled an inferred human protein interaction network where interactions discovered in model organisms are mapped onto the corresponding human orthologs. In addition to a stringent assignment to orthology classes based on the InParanoid algorithm, we have implemented a string matching algorithm to filter out orthology assignments of proteins whose global domain organization is not conserved. Finally, we have assessed the accuracy of our own, and related, inferred networks by benchmarking them against i) an assembled experimental interactome, ii) a network derived by mining of the scientific literature and iii) by measuring the enrichment of interacting protein pairs sharing common Gene Ontology annotation.

Conclusion
The resulting networks are named HomoMINT and HomoMINT_filtered, the latter being based on the orthology table filtered by the domain architecture matching algorithm. They contains 9749 and 5203 interactions respectively and can be analyzed and viewed in the context of the experimentally verified interactions between human proteins stored in the MINT database. HomoMINT is constantly updated to take into account the growing information in the MINT database.
A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure
Authors: Armano Giuliano , Mancosu Gianmaria , Milanesi Luciano , Orro Alessandro , Saba Massimiliano , Vargiu Eloisa 
Published: December 2005

Abstract

Background
Due to the strict relation between protein function and structure, the prediction of protein 3D-structure has become one of the most important tasks in bioinformatics and proteomics. In fact, notwithstanding the increase of experimental data on protein structures available in public databases, the gap between known sequences and known tertiary structures is constantly increasing. The need for automatic methods has brought the development of several prediction and modelling tools, but a general methodology able to solve the problem has not yet been devised, and most methodologies concentrate on the simplified task of predicting secondary structure.

Results
In this paper we concentrate on the problem of predicting secondary structures by adopting a technology based on multiple experts. The system performs an overall processing based on two main steps: first, a "sequence-to-structure" prediction is enforced by resorting to a population of hybrid (genetic-neural) experts, and then a "structure-to-structure" prediction is performed by resorting to an artificial neural network. Experiments, performed on sequences taken from well-known protein databases, allowed to reach an accuracy of about 76%, which is comparable to those obtained by state-of-the-art predictors.

Conclusion
The adoption of a hybrid technique, which encompasses genetic and neural technologies, has demonstrated to be a promising approach in the task of protein secondary structure prediction.
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
Authors: Burgarella Sarah , Cattaneo Dario , Pinciroli Francesco , Masseroli Marco 
Published: December 2005

Abstract

Background
Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results.

Results
We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services.

Conclusion

MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.
The impact of age on post-operative outcomes of colorectal cancer patients undergoing surgical treatment
Authors: Latkauskas Tadas , Rudinskaitė Giedrė , Kurtinaitis Juozas , Jančiauskienė Rasa , Tamelis Algimantas , Saladžinskas Žilvinas , Pavalkis Dainius 
Published: December 2005

Abstract

Background
the purpose of study was to evaluate the impact of age on outcomes in colorectal cancer surgery.

Methods
patients on hospital database treated for colorectal cancer during the period 1995 – 2002 were divided into two groups: Group 1 – patients of 75 years or older (n = 154), and Group 2 – those younger than 75 years (n = 532).

Results
In Group 1, for colon cancers, proximal tumors were significantly more common (23% vs. 13.5%, p < 0.05), complicated cases were more frequent (46 % vs. 33%, p = 0.002), bowel obstruction more common at presentation (40% vs. 26.5%, p = 0.001), and more frequent emergency surgery required (24% vs. 14%, p = 0.003). Postoperative overall morbidity was higher in the elderly group, but with no differences in surgical complications rate. Overall 5 year survival was 39% vs. 55% (p = 0.0006) and cancer related 5 year survival was 44% vs. 62% (p = 0.0006). Multivariate Cox analysis showed that age was not an independent risk factor for postoperative mortality.

Conclusion
Preoperative complications and co-morbidities, more advanced disease, and higher postoperative nonsurgical complication rates adversely affect postoperative outcomes after surgery for colorectal cancer in the elderly.
SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study
Authors: Muin Michael , Fontelo Paul , Liu Fang , Ackerman Michael 
Published: December 2005

Abstract

Background
With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded.

Results
Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features.

Conclusion
SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine.
Patterns of strain and activation in the thigh muscles of goats across gaits during level locomotion
Authors: Gillis Gary B. , Flynn John P. , McGuigan Polly , Biewener Andrew A. 
Published: December 2005

SUMMARYUnlike homologous muscles in many vertebrates, which appear to function similarly during a particular mode of locomotion (e.g. red muscle in swimming fish, pectoralis muscle in flying birds, limb extensors in jumping and swimming frogs), a major knee extensor in mammalian quadrupeds, the vastus lateralis, appears to operate differently in different species studied to date. In rats, the vastus undergoes more stretching early in stance than shortening in later stance. In dogs, the reverse is true; more substantial shortening follows small amounts of initial stretching. And in horses, while the vastus strain trajectory is complex, it is characterized mainly by shortening during stance. In this study, we use sonomicrometry and electromyography to study the vastus lateralis and biceps femoris of goats,with three goals in mind: (1) to see how these muscles work in comparison to homologous muscles studied previously in other taxa; (2) to address how speed and gait impact muscle actions and (3) to test whether fascicles in different parts of the same muscle undergo similar length changes. Results indicate that the biceps femoris undergoes substantial shortening through much of stance,with higher strains in walking and trotting [32–33% resting length(L0)] than galloping (22% L0). These length changes occur with increasing biceps EMG intensities as animals increase speed from walking to galloping. The vastus undergoes a stretch–shorten cycle during stance. Stretching strains are higher during galloping (15% L0) than walking and trotting (9%L0). Shortening strains follow a reverse pattern and are greatest in walking (24% L0), intermediate in trotting(20% L0) and lowest during galloping (17%L0). As a result, the ratio of stretching to shortening increases from below 0.5 in walking and trotting to near 1.0 during galloping. This increasing ratio suggests that the vastus does relatively more positive work than energy absorption at the slower speeds compared with galloping,although an understanding of the timing and magnitude of force production is required to confirm this. Length-change regimes in proximal, middle and distal sites of the vastus are generally comparable, suggesting strain homogeneity through the muscle. When strain rates are compared across taxa, vastus shortening velocities exhibit the scaling pattern predicted by theoretical and empirical work: fascicles shorten relatively faster in smaller animals than larger animals (strain rates near 2 L s–1 have been reported for trotting dogs and were found here for goats, versus0.6–0.8 L s–1 reported in horses). Interestingly, biceps shortening strain rates are very similar in both goats and rats during walking (1–1.5 L s–1) and trotting (1.5–2.5 L s–1, depending on speed of trot), suggesting that the ratio of in vivo shortening velocities(V) to maximum shortening velocities (Vmax) is smaller in small animals (because of their higher Vmax).
Maturation sutures for the paediatric tracheostomy – an extra safety measure
Authors: Craig M F , Bajaj Y , Hartley B E J 
Published: December 2005

Objective: Displacement of the tracheostomy tube in paediatric patients is a potentially fatal complication. We describe an extra safety measure which facilitates tube replacement.Setting: Tertiary referral specialist paediatric centre.Materials and methods: The method involves the placement of sutures between the anterior tracheal wall and skin to hasten the formation of a mature stoma (maturation sutures). We also undertook a retrospective case note review on patients from an academic tertiary referral centre. Thirty-five notes were reviewed. The most common indication for tracheostomy was airway obstruction (65 per cent). Fourteen patients had early and 10 had late complications with three tube displacements occurring. No added complications due to the use of sutures were found.Conclusions: Our complication rates compare well with those in the literature, and we recommend considering the use of such a technique.
Metallurgy, Extractive
Authors: Duby Paul F. 
Published: December 2005

Abstract
Extractive metallurgy that involves chemical production of metals from their naturally occurring compounds, follows mining of the ore, and the processing of the minerals. The essential extractive process, the reduction of a metallic compound to the metal, is often preceded by preparatory steps and followed by a refining one to achieve suitable properties.Pyrometallurgy, processing at high temperature, often yields a molten metal, but may produce a vapor or a solid. Refining is the removal of impurities by volatilization, precipitation, or by transfer into a molten slag phase as in steelmaking. Hydrometallurgy, processing through an aqueous solution, consists of leaching, purification of the pregnant solution, and recovery of the valuable metal by reduction or precipitation of one of its compounds. Electrometallurgy is the use of electrical energy for reducing the metal either from an aqueous electrolyte or from a high temperature melt. Examples are given for all processes.
Minerals Recovery and Processing
Authors: Nagaraj D. R. 
Published: December 2005

Abstract
Minerals recovery from the earth’s crust and the subsequent processing of economic mineral deposits, ie, ores, constitutes a wide variety of steps. Taken together these represent one of the world’s largest industries. Liberation of the value minerals from the ore matrix is a significant undertaking as is the disposal of the gangue materials or tailings once processing is complete. Materials handling is a significant problem in minerals processing as is process or plant control. Massive quantities of material, ie, ores, solvents, additives, and gangue, must be handled for separation procedures. Most mined ore undergoes size reduction, ie, grinding or crushing, and size separation and classification prior to minerals concentration.
Minerals separation or concentration methods may include ore sorting, gravity concentration, magnetic or electrostatic separations, flotation, or combinations of these methods, depending on the ore, the mineral, and economic considerations. These methods are described as are the various solid–liquid separation, ie, dewatering, procedures, which may include thickening, filtration, centrifugal dewatering, or thermal drying. The methods of choice for several minerals are given as examples.
Nitrogen Fixation
Authors: Newton William E. 
Published: December 2005

AbstractNitrogen fixation converts inert atmospheric molecular nitrogen gas into reduced forms whereby the nitrogen may be used by all life forms for protein and nucleic acid production. The biological process occurs only in microorganisms and is the principal contributor of fixed nitrogen to the biosphere. Fixed nitrogen is also derived from nonbiological processes, eg, fires, volcanoes, and lightning, and from commercial fertilizer production. The Haber‐Bosch ammonia process is highly energy efficient and is the most economical industrial process available. The most important source of biologically fixed nitrogen for agriculture is the symbiotic system that involves leguminous plants, which harbor rhizobia bacteria in nodules on their roots. Smaller contributions are made by other, less formal systems and by free‐living microbes. All of the biological systems use a similar metalloenzyme complex, called nitrogenase. Biological nitrogen fixation is discussed from a biochemical‐genetic viewpoint, as well as in terms of model chemistry and comparisons with the commercial process. Chemical approaches aimed at duplicating the biological process are also presented.
Polyamides, Aromatic
Authors: Gallini J. 
Published: December 2005

Abstract

This article describes the preparation and properties of aromatic polyamides and the fibers and films made from those polymers. A number of such polymers are identified, but the main focus is on the relatively few polymers that have achieved commercial status, namely, poly(
m
‐phenylene isophthalamide), poly(
p
‐phenylene terephthalamide), and copoly(
p
‐phenylene/3,4′‐diphenyl ether terephthalamide). The processes for manufacture of the corresponding monomers for these three polymers are described briefly. Both laboratory and commercial scale processes for the preparation of the polymers are presented and the processes for the commercial production of the fibers and films from these polymers are described. Properties of the polymers and the commercial fibers and films are tabulated. These products include Teijinconex®, Nomex®, Kevlar®, Twaron®, Technora®, Aramica®, and Mictron®. The principal end uses are described. Estimates of current sales volumes are cited, along with price ranges for the products. Health and safety concerns are identified.
Propylene
Authors: Calamur Narasimhan , Carrera Martin ,   Updated by Staff
Published: December 2005

AbstractPropylene is an important industrial chemical used as a feedstock in the production of polypropylene, acrylonitrile, propylene oxide, 2‐propanol, alkylated fuels, and other chemicals. It is obtained from steam cracking in pyrolysis furnaces in olefins plants and in refinery catalytic‐cracking reactors. Distillation in multitray columns yields purities in excess of 99.5 wt%. The physical and chemical properties of propylene are well characterized. Under ambient conditions, it is a colorless gas and has anesthetic properties at high concentrations. Propylene is usually transported in the liquid state at high pressures. Proper precautions must be taken when handling propylene.
Microwave‐Assisted Fast Cyclohexane Oxygenation Catalyzed by Iron‐Substituted Polyoxotungstates
Authors: Bonchio Marcella , Carraro Mauro , Scorrano Gianfranco , Kortz Ulrich 
Published: December 2005

AbstractUnder microwave irradiation, iron‐substituted polyoxotungstates (Fe‐POMs) catalyze cyclohexane oxygenation to A/K oil with 90–95% selectivity, unmatched turnover frequencies (40–400 h−1), and multi‐turnover regime (>1000 TON). Such a rapid reaction protocol allowed the screening of so‐called inorganic Fe‐synzymes with 1–4 nuclearity, including a family of Krebs‐type isostructural complexes. Product distribution, kinetic analysis, mechanistic probes and fitting calculations, are consistent with a radical chain oxidation propagated by Fe‐catalysed decomposition of organic peroxides which ultimately depends on the redox‐properties and structural arrangement of the iron moiety within the POM cage.
Improved Turnover Numbers in Palladium‐Catalyzed Bisdiene Cyclization‐Trapping using N‐Heterocyclic Carbene Ligands
Authors: Takacs James M. , Layek Suman , Palencia Hector , Andrews Ross N. 
Published: December 2005

AbstractAn optimized palladium‐N‐heterocyclic carbene catalyst system effects the palladium‐catalyzed bisdiene cyclization‐trapping with phenol at the 0.01% catalyst loading level with a TON of 7.6×103and TOF of 280 h−1, values much higher than typically found for this and related carbocyclizations. The reaction scales well and thetrans‐substituted six‐membered ring product is obtained in excellent yield on a 10‐mmole scale without further optimization of the catalyst system or reaction conditions.
Layered Double Hydroxide Supported Nanoplatinum and Nanopalladium Catalyzed Allylation of Aldehydes: A Mechanistic Study
Authors: Choudary B. M. , Roy Moumita , Roy Sarabindu , Lakshmi Kantam M. , Jyothi Karangula , Sreedhar Bojja 
Published: December 2005

AbstractLayered double hydroxide (LDH)‐supported nanoplatinum(0) and nanopalladium(0) catalysts were prepared by a simple ion exchange technique and subsequent reduction with hydrazine hydrate and used for the allylation of aldehydes to give moderate to good yields of homoallylic alcohols. Detailed mechanistic studies of LDH‐Pd(0)‐catalyzed allylation using XPS and TGA‐MS reveal that a monoallyl‐palladium complex is the key intermediate for the catalytic cycle.