bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of near‐native structures by clustering protein docking conformations
Authors: Lorenzen Stephan , Zhang Yang 
Published: March 2007

AbstractMost state‐of‐the‐art protein–protein docking algorithms use the Fast Fourier Transform (FFT) technique to sample the six‐dimensional translational and rotational space. Scoring functions including shape complementarity, electrostatics, and desolvation are usually exploited in ranking the docking conformations. While these rigid‐body docking methods provide good performance in bound docking, using unbound structures as input frequently leads to a high number of false positive hits. For the purpose of better selecting correct docking conformations, we structurally cluster the docking decoys generated by four widely‐used FFT‐based protein–protein docking methods. In all cases, the selection based on cluster size outperforms the ranking based on the inherent scoring function. If we cluster decoys from different servers together, only marginal improvement is obtained in comparison with clustering decoys from the best individual server. A collection of multiple decoy sets of comparable quality will be the key to improve the clustering result from meta‐docking servers. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Microwave‐assisted RCM for the synthesis of carbocyclic peptides
Authors: Robinson Andrea J. , Elaridi Jomana , Van Lierop Bianca J. , Mujcinovic Selma , Jackson W. Roy 
Published: March 2007

AbstractMicrowave irradiation dramatically improves the efficiency of ring closing metathesis (RCM) reactions of resin‐attached peptides and the technology is illustrated by the highly selective synthesis of dicarba analogues of α‐conotoxin IMI. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Electrospray ionization mass spectrometric characterization of key Te(IV) cationic intermediates for the addition of TeCl4 to alkynes
Authors: Santos Leonardo S. , Cunha Rodrigo L. O. R. , Comasseto João V. , Eberlin Marcos N. 
Published: March 2007

AbstractTellurium tetrachloride adds to alkynes via two pathways: a concerted syn‐addition that yields Z‐tri‐ and ‐tetrasubstituted alkenes or an anti‐addition that yields E‐alkenes. The mechanistic aspects of these divergent pathways for TeCl4 addition to alkynes have been investigated by on‐line electrospray ionization (tandem) mass spectrometry (ESI‐MS(/MS)). Via ESI‐MS(/MS), we have been able to intercept and characterize the active electrophile TeCl in tetrahydrofuran (THF) solutions of TeCl4, as well as its THF complex and several TeClx(OH) derivatives. For the first time, also, key Te(IV) cationic intermediates of the electrophilic addition of TeCl4 to alkynes were captured for gas‐phase MS investigation. The detailed structural data of cyclic tellurane intermediates intercepted herein seems to provide insights into the coordinative behavior of the Te(IV) atom and its mode of action towards biological targets. Copyright © 2007 John Wiley & Sons, Ltd.
A survey and taxonomy of approaches for mining software repositories in the context of software evolution
Authors: Kagdi Huzefa , Collard Michael L. , Maletic Jonathan I. 
Published: March 2007

AbstractA comprehensive literature survey on approaches for mining software repositories (MSR) in the context of software evolution is presented. In particular, this survey deals with those investigations that examine multiple versions of software artifacts or other temporal information. A taxonomy is derived from the analysis of this literature and presents the work via four dimensions: the type of software repositories mined (what), the purpose (why), the adopted/invented methodology used (how), and the evaluation method (quality). The taxonomy is demonstrated to be expressive (i.e., capable of representing a wide spectrum of MSR investigations) and effective (i.e., facilitates similarities and comparisons of MSR investigations). Lastly, a number of open research issues in MSR that require further investigation are identified. Copyright © 2007 John Wiley & Sons, Ltd.
The application of product measures in directing software maintenance activity
Authors: Ware M. P. , Wilkie F. G. , Shapcott M. 
Published: March 2007

AbstractThis paper is concerned with enhancing aspects of project‐management techniques in relation to maintenance in commercial object‐oriented software. Maintenance forms a significant proportion of the lifecycle of a product and consequently its costs. Techniques such as lean production attempt to reduce cost by focusing team effort and to pre‐empt issues by the use of early detection and resolution strategies. This study involves a commercial application written in C++ and its evolution over a one‐year period. Software product measures are used in conjunction with Pareto analysis to determine effective predictive class targeting in a release cycle. We assess the capability of the measures and consider how the results can be used by the project team. The study extends the work of others in this field in three ways. First, other studies have analysed procedural code, whereas we use an object‐oriented code base. Second, most studies assess the predictive capability of measures against the number of software issues; we examine these factors, but uniquely test for change density using density modified measures and we also test for revision volume. Finally, we examine the implications of these results and offer a cohesive framework of recommendations placed within the lean management philosophy. Copyright © 2007 John Wiley & Sons, Ltd.
Remote stereocontrol using functionalized allylmetal reagents
Authors: Thomas Eric J. 
Published: March 2007

AbstractAlk‐2‐enyl(trialkyl)stannanes with heteroatom substituents at the 4‐, 5‐, and 6‐positions are transmetallated stereoselectively using tin(IV) halides to generate allyltin trihalides, which react with aldehydes to give (3Z)‐homoallylic alcohols with efficient 1,5‐, 1,6‐, and 1,7‐stereocontrol. This chemistry has been used to develop new strategies for natural product synthesis. Because of the toxicity of organotin reagents and the problems in removing organotin residues from reaction products, alternative procedures that avoid the use of organotin reagents have been investigated. To date, alk‐2‐enylgermanium reagents have been shown to deliver effective 1,5‐ and 1,6‐stereocontrol, which is analogous to that observed for the organotin compounds. Organobismuth intermediates, which can be generated from allyl bromides and zinc‐bismuth(III)iodide, react with aldehydes with efficient 1,5‐stereocontrol which is complementary to that observed with the organo‐stannanes or ‐germanes in that (3E)‐homoallylic alcohols are obtained. © 2007 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 7: 115–124; 2007: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20113
Formation and characterization of liposomes from lipid/proteic material extracted from pig stratum corneum
Authors: Lopez O. , de la Maza A. , Coderch L. , Parra J. L. 
Published: March 2007

AbstractThe formation and physicochemical properties of liposomes prepared from a mixture of lipids and proteins extracted from pig stratum corneum have been investigated. The extraction of this material was carried out with chloroform/methanol mixtures. The sonication of these mixtures at 80°C in water that contained piperazine‐1,4‐bis(2‐ethanesulfonic acid) led to the formation of bilayered structures (vesicle size of about 150 nm), which were stable to aggregation for more than 24 h. The interaction of these liposome suspensions (proteoliposomes) at a subsolubilizing level with surfactants indicates that the nonionic surfactant Triton X‐100 had the largest capacity for altering liposome permeability, whereas the amphoteric surfactant dodecyl betaine exhibited the smallest. The anionic surfactant sodium dodecyl sulfate showed an intermediate activity relative to that shown by the other surfactants tested. Despite the fact that the proteoliposomes showed negligible permeability in the absence of surfactants, compared with that of phosphatidylcholine liposomes, addition of identical amounts of surfactants resulted after 45 min in similar permeability effects for both. However, the proteoliposomes appeared to be more resistant to the action of surfactants in the initial interaction period.
Changes in the characteristics and composition of oils during deep‐fat frying
Authors: Tyagi V. K. , Vasishtha A. K. 
Published: March 2007

AbstractRefined, bleached, and deodorized soybean oil and vanaspati (partially hydrogenated vegetable oil blend consisting of peanut, cottonseed, nigerseed, palm, rapeseed, mustard, rice bran, soybean, sunflower, corn, safflower, sesame oil, etc., in varying proportions) were used for deep‐fat frying potato chips at 170, 180, and 190°C. Refractive index, specific gravity, color, viscosity, saponification value, and free fatty acids of soybean oil increased with frying temperature, whereas the iodine value decreased. The same trend was observed in vanaspati, but less markedly than in soybean oil, indicating a lesser degree of deterioration. Iodine values of soybean oil and vanaspati decreased from their initial values of 129.8 and 74.7 to 96.2 and 59.6, respectively, after 70 h of frying. Polyunsaturated fatty acids decreased in direct proportion to frying time and temperature. Losses were highest in soybean oil with a 79% decrease in trienoic acids and a 60% decrease in dienoic acids. Levels of nonurea adduct‐forming esters were proportional to the losses of unsaturated fatty acids. Butylated hydroxyanisole and tertiary butylhydroquinone did not affect deterioration of soybean oil at frying temperatures.
The effect of sodium carboxymethyl cellulose on synthetic detergent systems
Authors: Vaughn Thomas H. , Smith Clifton E. 
Published: March 2007

SummaryCertain forms of sodium carboxymethyl cellulose have been shown to be highly effective as synthetic detergent promoters. Formulations containing a sodium alkyl aryl sulfonate type of synthetic detergent, alkaline salts and a type of sodium carboxymethyl cellulose developed for high detergency promoting properties surpass high quality fatty acid soaps in both carbon soil removal and whiteness retention on cottons.Methods having a relatively high order of precision for the evaluation of detergency have been presented in detail. By these methods two fundamental characteristics of detergency—as applied to the laundering of cotton fabrics may be independently measured.
Solidification point curves of binary acid mixtures
Authors: Schuette H. A. , Maylott Asa O. , Roth D. A. 
Published: March 2007

SummaryWith the synthesis ofn‐hexatriacontanoic acid (sol. pt. 99.65°C.), this time coupling ω‐carbethoxynonoyl chloride with cadmium docosyl bromide, rather than with its zine iodide counterpart (5d), to formn‐dotriacontanoic acid, from which by malonic‐ester synthesis, the chain was lengthened in two stages, the series of solidification point eurves of binary mixtures of the homologous acids in question has been increased by one pair. Detailed descriptions of the several steps involved in these syntheses have been given. The curve, although slightly flatter—it is here drawn to a different scale than that previously used (5)−has the same general shape as those previously reported for the homologous fatty acids in this area.
Mono‐ and diglycerides in industrial fats
Authors: Schlenker Ernest , Gnaedinger Jean 
Published: March 2007

Summary

The presence of mono‐ and diglycerides in raw and hydrolyzed fats and their effect on the yields of fatty acids obtained by distillation is discussed.

Experiments carried out under conditions suitable for the esterification of mono‐ and diglycerides with fatty acids to form triglycerides indicate the presence of these mono‐ and diglycerides.
X‐ray diffraction by aluminum soaps
Authors: Marsden Sullivan S. , Mysels Karol J. , Smith Gerould H. , Ross Sydney 
Published: March 2007

Summary

The microphotometer tracings and Bragg spacings of typical x‐ray powder diffraction patterns are reported for aluminum dilaurates and distearates. Patterns for both extracted soaps and soaps containing uncombined acid are included. The extraction of molecular, uncombined fatty acid may produce either a complete recrystallization of the soap, or only minor changes in the diffraction pattern. At least two of the three types of extracted distearate are polymorphs whereas the two types of unextracted stearate are each mixtures of free fatty acid, together with what may be a solid solution of fatty acid in one of the extracted types.

Extracted aluminum dilaurate has been observed to exist in only one “crystalline form,” differing from that of the unextracted aluminum dilaurate. The latter consists of free fatty acid, together with dilaurate sorbing some acid with a slight but distinct change in the x‐ray powder pattern.

The presence of some free fatty acid in unextracted aluminum soaps is confirmed by x‐rays.

The sorption of moisture has no effect on the x‐ray diffraction pattern of aluminum di‐soaps, pointing to purely surface attachment of water.
Preparation of gossypol from cottonseed pigment glands
Authors: Castillon L. E. , Hall C. M. , Boatner C. H. 
Published: March 2007

SummaryCottonseed pigment glands, produced from whole cottonseed meal and defatted cottonseed meal by the gland flotation process, have been investigated as a raw material for the production of gossypol.Methods based on the previously reported properties of gossypol and cottonseed pigment glands have been developed for the relatively rapid isolation of gossypol from pigment glands.Extraction of gossypol from pigment glands with acetone followed by precipitation of gossypol acetic acid from the extract was found to be the preferable method for obtaining pure gossypol in good yields.The precautions which must be applied in order to produce gossypol on a large scale by the acetone‐acetic acid method are discussed together with methods for the purification and preservation of gossypol.
Autoxidation of fats. I. Preparation and oxidation of alkylbenzene‐maleic anhydride adducts
Authors: Bickford W. G. , Fisher G. S. , Dollear F. G. , Swift C. E. 
Published: March 2007

SummaryIt has been shown that certain alkylbenzenes having a hydrogen atom on the alpha carbon atom react with maleic anhydride to form compounds analogous to the hydroperoxides produced by autoxidation of the alkylbenzenes. The structure of these products has been determined by oxidation with aqueous permanganate and the results have been applied, together with other data, to demonstrate that the reaction proceeds by a free radical chain mechanism involving the abstraction of a hydrogen atom from the alpha carbon atom. In view of the analogy between the products obtained in this investigation and in autoxidation, it is suggested that autoxidation is propagated in a similar manner.
Fatty acid esters of methylglucoside prepared by the alcoholysis reaction
Authors: Wolff Hans , Hill W. H. 
Published: March 2007

Summary

Alcoholysis of triglycerides by methylglucoside gave an impure reaction mixture containing from 60–70% of glucoside‐monoesters.

The mono‐, di‐, and trioleoyl methylglucosides were prepared by alcoholysis of methyloleate with α‐methylglucoside.

Hydrolysis of the glucoside esters of fatty acids to dextrose esters could not be achieved. The ester linkage hydrolyzed in preference to the acetal linkage.
An introduction to biomarkers: applications to chronic kidney disease
Authors: Lemley Kevin V. 
Published: March 2007

Abstract
Diagnosis and management of chronic kidney disease (CKD) will be characterized in the future by an increasing use of biomarkers—quantitative indicators of biologic or pathologic processes that vary continuously with progression of the process. “Classical” biomarkers of CKD progression include quantitative proteinuria, the percentage of sclerotic glomeruli or fractional interstitial fibrosis. New candidate biomarkers (e.g., urinary proteomic patterns) are being developed based on both mechanistic and “shotgun” approaches. Validation of potential biomarkers in prospective studies as surrogate endpoints for hard clinical outcomes is often complicated by the long lag time to the ultimate clinical outcome (e.g., end-stage renal disease). The very dense data sets that result from shotgun approaches on small numbers of patients carry a significant risk of model overfitting, leading to spurious associations. New analytic methods can help to decrease this risk. It is likely that clinical practice will come to depend increasingly on multiplex (vector) biomarkers used in conjunction with risk markers in early diagnosis as well as to guide therapy.
Biomarkers for the early detection of acute kidney injury
Authors: Nguyen Mai T. , Devarajan Prasad 
Published: March 2007

AbstractAcute kidney injury (AKI), previously referred to as acute renal failure (ARF), represents a persistent problem in clinical medicine. Despite significant improvements in therapeutics, the mortality and morbidity associated with AKI remain high. A major reason for this is the lack of early markers for AKI, akin to troponins in acute myocardial disease, and hence an unacceptable delay in initiating therapy. Fortunately, the application of innovative technologies such as functional genomics and proteomics to human and animal models of AKI has uncovered several novel genes and gene products that are emerging as biomarkers. The most promising of these are chronicled in this article. These include a plasma panel [neutrophil gelatinase-associated lipocalin (NGAL) and cystatin C] and a urine panel [NGAL, interleukin 18 (IL-18), and kidney injury molecule 1 (KIM)-1]. As they represent sequentially expressed biomarkers, it is likely that the AKI panels will be useful for timing the initial insult and assessing the duration of AKI. Based on the differential expression of the biomarkers, it is also likely that the AKI panels will distinguish between the various types and etiologies of AKI. It will be important in future studies to validate the sensitivity and specificity of these biomarker panels in clinical samples from large cohorts and from multiple clinical situations.
Growth of prepubertal children on dialysis
Authors: Stefanidis Constantinos J. , Klaus Günter 
Published: March 2007

AbstractGrowth failure is a common and significant clinical problem for children on dialysis and often remains a major impediment to their rehabilitation. Early referral to a paediatric nephrology centre and appropriate management before the initiation of dialysis may significantly prevent growth deterioration. Growth in children on dialysis can be affected by nutritional, metabolic, and hormonal changes. Early diagnosis of malnutrition and aggressive management should be a priority. Gastrostomy feeding should be used when adequate oral intake to maintain normal height and weight velocity cannot be achieved. Active vitamin D metabolites should be used carefully, to prevent low-turnover bone disease. All children should have an adequate regimen of dialysis and an appropriate management of malnutrition, renal osteodystrophy, metabolic acidosis, salt wasting and anaemia, before recombinant human growth hormone (rhGH) administration is considered. The current challenge of reversing growth impairment in children on dialysis can only be achieved by optimization of their care.
Effects of acorn masting on population dynamics of three forest‐dwelling rodent species in Hokkaido, Japan
Authors: Saitoh Takashi , Osawa Jun , Takanishi Toshikazu , Hayakashi Shintaro , Ohmori Masaaki , Morita Toshio , Uemura Shigeru , Vik Jon Olav , Stenseth Nils Chr. , Maekawa Koji 
Published: March 2007

AbstractThe effects of the abundance of acorns of the oak, Quercus crispula, on the population dynamics of three rodent species (Apodemus speciosus, A. argenteus, and Clethrionomys rufocanus) were analyzed using time series data (1992–2006). The data were obtained in a forest in northern Hokkaido, Japan, by live trapping rodents and directly counting acorns on the ground. Apodemus speciosus generally increased in abundance following acorn masting. However, the clear effect of acorn abundance was not detected for the other two rodent species. Acorns of Q. crispula contain tannins, which potentially have detrimental effects on herbivores. Apodemus speciosus may reduce the damage caused by acorn tannins with tannin‐binding salivary proteins and tannase‐producing bacteria, whereas such physiological tolerance to tannins is not known in the other two rodent species. The differences in the effects of acorns between the three species may be due to differences in their physiological tolerance to tannins.
Plant regrowth response to a stem‐boring insect: a swift moth‐willow system
Authors: Utsumi Shunsuke , Ohgushi Takayuki 
Published: March 2007

AbstractTo examine plastic willow regrowth response to herbivory, we studied the effect of a boring insect, the swift moth Endoclita excrescens (Hepialidae: Lepidoptera), which does not remove apical meristems, on shoot growth in three willow species—Salix gilgiana, S. eriocarpa, and S. serissaefolia−by direct observations and experiments in the field. We hypothesized that the stem‐boring could initiate new lateral bud activation, and result in secondary shoot regrowth without the removal of the primary apical meristems. There were significantly more lateral shoots on naturally attacked than unattacked stems, and a significant positive correlation between lateral shoot density and the number of swift moth tunnels per tree was observed for all three willow species. Artificial boring, and larval infestation, resulted in an increase in the number of lateral shoots, but did not affect growth of current‐year shoots. The length of lateral shoots differed between species, being significantly longer in S. gilgiana than S. eriocarpa and S. serissaefolia. The results of this study show that compensatory regrowth can result even if herbivory does not remove the apical meristem. We argue that this type of plant compensatory response is probably widespread, given that the stem‐boring is a common feeding type of insect herbivores.
A pH sensor based on electric properties of nanotubes on a glass substrate
Authors: Takeda Seiji , Nakamura Motonori , Ishii Atsushi , Subagyo Agus , Hosoi Hirotaka , Sueoka Kazuhisa , Mukasa Koichi 
Published: March 2007

Abstract
We fabricated a pH-sensitive device on a glass substrate based on properties of carbon nanotubes. Nanotubes were immobilized specifically on chemically modified areas on a substrate followed by deposition of metallic source and drain electrodes on the area. Some nanotubes connected the source and drain electrodes. A top gate electrode was fabricated on an insulating layer of silane coupling agent on the nanotube. The device showed properties of ann-type field effect transistor when a potential was applied to the nanotube from the top gate electrode. Before fabrication of the insulating layer, the device showed that thep-type field effect transistor and the current through the source and drain electrodes depend on the buffer pH. The current increases with decreasing pH of the CNT solution. This device, which can detect pH, is applicable for use as a biosensor through modification of the CNT surface.