bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three‐dimensional non‐planar crack growth by a coupled extended finite element and fast marching method
Authors: Sukumar N. , Chopp D. L. , Béchet E. , Moës N. 
Published: April 2008

AbstractA numerical technique for non‐planar three‐dimensional linear elastic crack growth simulations is proposed. This technique couples the extended finite element method (X‐FEM) and the fast marching method (FMM). In crack modeling using X‐FEM, the framework of partition of unity is used to enrich the standard finite element approximation by a discontinuous function and the two‐dimensional asymptotic crack‐tip displacement fields. The initial crack geometry is represented by two level set functions, and subsequently signed distance functions are used to maintain the location of the crack and to compute the enrichment functions that appear in the displacement approximation. Crack modeling is performed without the need to mesh the crack, and crack propagation is simulated without remeshing. Crack growth is conducted using FMM; unlike a level set formulation for interface capturing, no iterations nor any time step restrictions are imposed in the FMM. Planar and non‐planar quasi‐static crack growth simulations are presented to demonstrate the robustness and versatility of the proposed technique. Copyright © 2008 John Wiley & Sons, Ltd.
Robotic trajectory tracking for neurological rehabilitation
Authors: Hughes Ann‐Marie , Burridge Jane , Freeman Chris , Chappell Paul , Lewin Paul , Rogers Eric 
Published: April 2008

AbstractThe authors describe the initial phase of their work at the University of Southampton on testing an improved technique to help stroke patients regain the use of their arms.Useful arm movement is regarded as one of the most important factors for regaining functional independence among stroke patients. Copyright © 2008 Wiley Interface Ltd
Structure of YraM, a protein essential for growth of Haemophilus influenzae
Authors: Vijayalakshmi J. , Akerley Brian J. , Saper Mark A. 
Published: April 2008

AbstractNontypeable Haemophilus influenzae is an obligate human parasite that often causes middle ear infections in children and exacerbates chronic obstructive pulmonary disorder, the fourth leading cause of death in the United States. There are no effective vaccines available for this strain. The lipoprotein YraM (gene HI1655) was identified as essential for the growth and viability of H. influenzae but its function is unknown. Sequence comparisons showed that YraM is a fusion of two protein modules. We grew crystals of the carboxyl‐terminal module of YraM comprising residues 257–573 (YraM‐C), phased the diffraction data by the multiwavelength anomalous diffraction technique, and refined the model to a crystallographic R‐factor of 0.16 (Rfree = 0.19) with data to 1.35 Å resolution. The two‐domain structure of YraM‐C adopts a fold similar to that observed for the open, unliganded forms of several periplasmic binding proteins (PBPs) involved in bacterial active transport. Sequence alignments of YraM homologues from other Gram‐negative species showed that the most conserved residues of YraM‐C cluster between the two domains in the location where other PBPs bind their cognate ligand. Modeling of YraM‐C into a closed conformation similar to the leucine‐bound form of the Leu/Ile/Val‐binding protein (LIVBP) shows a putative binding pocket larger than the leucine‐binding site in LIVBP. The pocket has both polar and nonpolar surfaces, with the latter located in the same area where a leucine side chain binds to LIVBP. We discuss possible biological functions of YraM considering its predicted location in the outer membrane, a novel place for such a binding protein. Proteins 2008. © 2008 Wiley‐Liss, Inc.
A QM/MM study of proton transport pathways in a [NiFe] hydrogenase
Authors: Fdez. Galván Ignacio , Volbeda Anne , Fontecilla‐Camps Juan C. , Field Martin J. 
Published: April 2008

AbstractA theoretical QM/MM study of the [NiFe] hydrogenase from Desulfovibrio fructosovorans has been performed to investigate possible routes of proton transfer between the active site and the protein surface. We obtained the minimum energy paths, with a modified version of the nudged elastic band method, for a set of proposed pathways. The calculations were carried out for the crystallographic structure and for several structures of the protein obtained from a molecular dynamics simulation. The results show one of the studied pathways to be preferred for transport from the active site to the surface, but the preference is not so strong when transport occurs in the opposite direction. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Coarse‐grained dynamics of the receiver domain of NtrC: Fluctuations, correlations and implications for allosteric cooperativity
Authors: Liu Ming S. , Todd B. D. , Yao Shenggen , Feng Zhi‐Ping , Norton Raymond S. , Sadus Richard J. 
Published: April 2008

AbstractReceiver domains are key molecular switches in bacterial signaling. Structural studies have shown that the receiver domain of the nitrogen regulatory protein C (NtrC) exists in a conformational equilibrium encompassing both inactive and active states, with phosphorylation of Asp54 allosterically shifting the equilibrium towards the active state. To analyze dynamical fluctuations and correlations in NtrC as it undergoes activation, we have applied a coarse‐grained dynamics algorithm using elastic network models. Normal mode analysis reveals possible dynamical pathways for the transition of NtrC from the inactive state to the active state. The diagonalized correlation between the inactive and the active (phosphorylated) state shows that most correlated motions occur around the active site of Asp54 and in the region Thr82 to Tyr101. This indicates a coupled correlation of dynamics in the “Thr82‐Tyr101” motion. With phosphorylation inducing significant flexibility changes around the active site and α3 and α4 helices, we find that this activation makes the active‐site region and the loops of α3/β4 and α4/β5 more stable. This means that phosphorylation entropically favors the receiver domain in its active state, and the induced conformational changes occur in an allosteric manner. Analyses of the local flexibility and long‐range correlated motion also suggest a dynamics criterion for determining the allosteric cooperativity of NtrC, and may be applicable to other proteins. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Discriminative learning for protein conformation sampling
Authors: Zhao Feng , Li Shuaicheng , Sterner Beckett W. , Xu Jinbo 
Published: April 2008

AbstractProtein structure prediction without using templates (i.e., ab initio folding) is one of the most challenging problems in structural biology. In particular, conformation sampling poses as a major bottleneck of ab initio folding. This article presents CRFSampler, an extensible protein conformation sampler, built on a probabilistic graphical model Conditional Random Fields (CRFs). Using a discriminative learning method, CRFSampler can automatically learn more than ten thousand parameters quantifying the relationship among primary sequence, secondary structure, and (pseudo) backbone angles. Using only compactness and self‐avoiding constraints, CRFSampler can efficiently generate protein‐like conformations from primary sequence and predicted secondary structure. CRFSampler is also very flexible in that a variety of model topologies and feature sets can be defined to model the sequence‐structure relationship without worrying about parameter estimation. Our experimental results demonstrate that using a simple set of features, CRFSampler can generate decoys with much higher quality than the most recent HMM model. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Antiinflammatory effect of Daesiho, a Korean traditional prescription for cerebral infarct patients
Authors: Kim Yunha , So Hong‐Seob , Kim Se‐Jin , Youn Myung‐Ja , Lee Jeong‐Han , Kim Nam‐Song , Lee Jeong‐Ho , Woo Won‐Hong , Lee Dong Wook , Cho Kwang‐Ho , Moon Byung‐Soon , Park Raekil 
Published: April 2008

AbstractDaesiho, a prescription composed of eight herbal mixtures, has been widely used in the treatment of cerebral infarct in Oriental medicine. However, the mechanisms by which the formula affects the production of pro‐inflammatory cytokines in cerebral infarct patients remains unknown. The levels of secretory protein pro‐inflammatory cytokines, including tumor necrosis factor (TNF)‐α, interleukin (IL)‐1β and IL‐6, were significantly increased in both lipopolysaccharide (LPS) and phytohemagglutinin (PHA)‐stimulated peripheral blood mononuclear cells (PBMCs) from cerebral infarct patients and LPS‐stimulated THP‐1 differentiated macrophage‐like cells (THP‐1/M). However, pretreatment with Daesiho significantly inhibited the secretion of pro‐inflammatory cytokines, including TNF‐α, IL‐1β, and IL‐6, in stimulated PBMCs and THP‐1/M cells. In addition, Daesiho significantly suppressed mRNA expression of pro‐inflammatory cytokines. Therefore, these data indicate that Daesiho may be beneficial in the cessation of inflammatory processes of cerebral infarction through suppression of the production of pro‐inflammatory cytokines via inhibition of mRNA expression. Copyright © 2008 John Wiley & Sons, Ltd.
Multi‐class, multi‐residue liquid chromatography/tandem mass spectrometry screening and confirmation methods for drug residues in milk
Authors: Turnipseed Sherri B. , Andersen Wendy C. , Karbiwnyk Christine M. , Madson Mark R. , Miller Keith E. 
Published: April 2008

AbstractThis paper describes the development and optimization of a multi‐residue veterinary drug screening method for whole milk. The drug residues of regulatory interest in milk include β‐lactams, sulfonamides, tetracyclines, fluoroquinolones, and macrolides. Milk samples were extracted with acetonitrile and the samples were then subjected to a clean‐up procedure using a bonded solid‐phase extraction cartridge and a molecular weight cut‐off filter. Liquid chromatography/tandem mass spectrometry (LC/MS/MS) triple quadrupole electrospray methods were developed to monitor for the drugs in milk. Since established tolerance levels are set for most of these drugs in milk, the initial screening procedure was semi‐quantitative, where samples were compared to the response of a positive control. The positive control, consisting of an extract from a portion of milk fortified with the drugs at half their allowed levels, was used to set the laboratory's minimum response criteria for unknown samples. Confirmatory analyses, with additional ion transitions for each residue, were performed on the same extracts. Published in 2008 by John Wiley & Sons, Ltd.
New amphoteric surfactants containing a 2‐hydroxyalkyl group: IV. Performance of amphoteric surfactant/soap blends
Authors: Takai M. , Hidaka H. , Ishikawa S. , Takada M. , Moriya M. 
Published: April 2008

AbstractThe performance of new amphoteric surfactants,N‐(2‐hydroxyethyl)‐N‐(2‐hydroxyalkyl)‐β‐alanines (HAA) and their oxyethylated derivatives (HAA‐nEO) was studied in blends with a fatty acid soap. The solubility, foaming power and fabric detergency were measured for blends of (Na‐HAA or Na‐HAA‐nEO)/soap. Furthermore, lime soap dispersing power, toxicity to fish and biodegradability for HAA or HAA‐nEO homologs were examined and evaluated. The blend of tallow soap and not less than 10% of C12–14‐Na‐HAA exhibited better solubility behavior than tallow soap or tallow/coconut oil soap alone. Fabric detergency was improved by blending Na‐HAA with soap. Soil deposition in Na‐HAA/soap or Na‐HAA/soap/Na2CO3 solution was measured. On the basis of the results for: (a) the measurements of redeposition; (b) interfacial tension between oil and water and (c) contact angle between oil and fabric in water, it was presumed that since Na‐HAA adsorbed more or less in preference to soap on the surface of fabric in water, soil redeposition would be prevented in the Na‐HAA/soap detergent solution.
Gas chromatography‐mass spectrometry of methyl esters of unsaturated oxygenated fatty acids
Authors: Kleiman R. , Spencer G. F. 
Published: April 2008

AbstractSilylation of hydroxyl groups in methyl esters of unsaturated hydroxy acids provides compounds that give mass spectra which can be readily interpreted, whereas spectra of underivatized esters are extremely difficult to evaluate. The relationship of the double bond(s) to the trimethylsiloxy (TMS) group results in specific mass spectral patterns. In esters that have the TMS group separated from the double bond by one methylene group, the ions caused byα‐cleavage at the TMS group on the side closest to the olefinic group are much more abundant than those produced fromα‐cleavage on the other side of the TMS group. In esters that have the TMS group and the double bond separated by two methylene groups,α‐cleavage ions are approximately equal. When the TMS group and the double bond are allylic, no fragmentation results between them. Cleavage does occur on either side of this system, and those ions resulting from cleavage alpha to the TMS group are in greatest abundance. Silylation of esters that have a conjugated diene or ene‐yne system adjacent to a hydroxyl group also gives derivatives amenable to gas chromatographymass spectrometry. In these esters, large peaks are observed that arise fromα‐cleavage at the TMS group and at the other end of the olefinic system. No fragmentation between the TMS group and the sites of unsaturation occurs. Unsaturated epoxy methyl esters produce spectra difficult to interpret. When the epoxide is converted to methoxy‐hydroxy derivatives by BF3‐methanol, the spectrum locates the position of the epoxide group. Silylation of the hydroxyl group produces a compound that gives a less complicated spectrum which also locates the original epoxy group. Mass spectrometry of a series of unsaturated keto‐esters, without derivatization, provides spectra that are easily interpretable.
INFLUENCE OF SOWING DATE AND ENVIRONMENTAL FACTORS ON THE DEVELOPMENT AND YIELD OF BAMBARA GROUNDNUT (VIGNA SUBTERRANEA) LANDRACES IN A SUB-TROPICAL REGION
Authors: SESAY A. , MAGAGULA C. N. , MANSUETUS A. B. 
Published: April 2008

SUMMARYBambara groundnut (Vigna subterranea) is a grain legume crop, which is increasingly popular as food in rural areas across the African continent. However, reliable information pertaining to management of the crop is limited. Field experiments were conducted in Swaziland in the 1998/99 and 1999/2000 cropping seasons to determine the influence of sowing date and environmental factors on the growth, development and yield of bambara groundnut. In the 1998/99 season, seeds of one local landrace were sown on six dates between mid-September 1998 and mid-February 1999. In 1999/2000, seeds of two local landraces were sown on six dates between mid-October 1999 and late January 2000. The highest pod yield and total dry matter production were achieved in November sowings, with maximum pod yields of 1.3 and 0.64 t ha−1 for the 1998/99 and 1999/2000 seasons, respectively. Earlier sowing and successive delays in sowing from November caused substantial yield declines of as much as 72–75%. Sowing date influenced yields of bambara groundnut through the effect of temperature and daylength on plant development. For the landraces used in the study, while the rate of progress from sowing to flowering was influenced by temperature, the rate of progress from flowering to podding was influenced largely by daylength. The practical implications of the results for increased bambara groundnut production are discussed.
BREEDING NEW COTTON VARIETIES TO FIT THE DIVERSITY OF CROPPING CONDITIONS IN AFRICA: EFFECT OF PLANT ARCHITECTURE, EARLINESS AND EFFECTIVE FLOWERING TIME ON LATE-PLANTED COTTON PRODUCTIVITY
Authors: SEKLOKA EMMANUEL , LANÇON JACQUES , GOZE ERIC , HAU BERNARD , LEWICKI-DHAINAUT SYLVIE , THOMAS GRÉGOIRE 
Published: April 2008

SUMMARYIn most cotton-growing regions of West and Central Africa where rainfed conditions prevail, cropping conditions are highly diversified since the crop is planted over an extended period. We studied production and development patterns in 10 cotton (Gossypium hirsutum) varieties to determine the most efficient strategies that could be transformed into breeding traits. Four trials were carried out between 2002 and 2003 in two cotton-growing areas in Benin to compare the 10 varieties at three stand densities and two planting dates. The parameters monitored were the mean first flower opening date (FF), effective flowering time (EFT), plant height at harvest (HH), height to node ratio (HNR), length of fruiting branch (LFB), number of vegetative branches (NVB) and average boll retention at the first position of the fruiting branches (RP1). We identified two ideotypes that yielded better than the others: (i) Mar 88-214 performed well under late planting–high stand density conditions and was characterized by low vegetative growth and early flowering onset, a short flowering period and low RP1; (ii) H 279-1 performed especially well under early planting–low stand density conditions and was characterized by high vegetative growth, late flowering, long EFT and high RP1. We propose a breeding strategy for both ideotypes based on seven indicators with high heritability (FF, HH, HNR, and LFB) or medium heritability (NVB, EFT, and RP1).
ROOT DISTRIBUTION OF YAM (DIOSCOREA ALATA) DETERMINED BY STRONTIUM TRACER
Authors: O'SULLIVAN JANE N. 
Published: April 2008

SUMMARYStrontium was used as a tracer to detect root activity of yam (Dioscorea alata) at distances from 0.5 to 5.5 m from the plant's crown, and at depths of 7, 15, 25 and 40 cm, in field plantings separated by plastic root barriers. Tracer bands were installed at planting, and leaves were sampled at intervals throughout the growing season. Background Sr concentrations in leaves were found to be closely related to leaf Ca concentrations, allowing the expected background Sr to be calculated from the Ca concentration in each sample. The ratio of observed to expected Sr did not alter significantly with time of sampling or leaf age for control plants providing a robust parameter for comparison across harvests. Plants at all horizontal distances from the Sr placement up to 5.5 m showed significant elevation of leaf Sr by 13 weeks after planting (WAP). The depth placement at 15 cm showed earliest Sr elevation, followed by the 7 cm placement. However, both 25 cm and 40 cm placements resulted in significant leaf Sr elevation by 13 WAP, and their final Sr concentrations at 27 WAP did not differ significantly from those of shallower placements. Three fertilizer placement options were compared with respect to Sr uptake by the treated plants and by those in adjacent rows. Placement in a ring around the crown of the seed sett resulted in high leaf Sr concentration at 5 WAP, declining considerably at subsequent samplings. Placement underneath the seed sett produced a similar pattern but at lower concentrations. Banding midway between the plant rows, 0.5 m from plants, yielded a small increase at 5 WAP increasing to 13 WAP, and ultimately attaining similar concentrations to the other two placements. Plants in adjacent rows significantly accessed all three placements by 13 WAP. The results indicate greater reach of yam roots, both horizontally and vertically, than has been previously reported, and raise concerns about the adequacy of treatment separation in previously published fertilizer experiments with yams.
INTEGRATING GENETICS AND NATURAL RESOURCE MANAGEMENT FOR TECHNOLOGY TARGETING AND GREATER IMPACT OF AGRICULTURAL RESEARCH IN THE SEMI-ARID TROPICS
Authors: TWOMLOW STEVE , SHIFERAW BEKELE , COOPER PETER , KEATINGE J. D. H. 
Published: April 2008

SUMMARYGood management of natural resources is the key to good agriculture. This is true everywhere – and particularly in the semi-arid tropics, where over-exploitation of fragile or inherently vulnerable agro-ecosystems is leading to land and soil degradation, productivity decline, and increasing hunger and poverty. Modern crop varieties offer high yields, but the larger share of this potential yield can only be realized with good crop management. The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), working over a vast and diverse mandate area, has learned one key lesson: that technologies and interventions must be matched not only to the crop or livestock enterprise and the biophysical environment, but also with the market and investment environment, including input supply systems and policy. Various Natural Resource Management (NRM) technologies have been developed over the years, but widespread adoption has been limited for various reasons: technical, socio-economic and institutional. To change this, ICRISAT hypothesizes that ‘A research approach, founded on the need to integrate a broad consideration of technical, socio-economic and institutional issues into the generation of agricultural innovations will result in a higher level of adoption and more sustainable and diverse impacts in the rainfed systems of the semi-arid tropics.’ Traditionally, crop improvement and NRM were seen as distinct but complementary disciplines. ICRISAT is deliberately blurring these boundaries to create the new paradigm of IGNRM or Integrated Genetic and Natural Resource Management. Improved varieties and improved resource management are two sides of the same coin. Most farming problems require integrated solutions, with genetic, management-related and socio-economic components. In essence, plant breeders and NRM scientists must integrate their work with that of private and public sector change agents to develop flexible cropping systems that can respond to rapid changes in market opportunities and climatic conditions. The systems approach looks at various components of the rural economy – traditional food grains, new potential cash crops, livestock and fodder production, as well as socio-economic factors such as alternative sources of employment and income. Crucially the IGNRM approach is participatory, with farmers closely involved in technology development, testing and dissemination. ICRISAT has begun to use the IGNRM approach to catalyse technology uptake and substantially improve food security and incomes in smallholder farm communities at several locations in India, Mali, Niger, Vietnam, China, Thailand and Zimbabwe.
Dual task performance in early Alzheimer's disease, amnestic mild cognitive impairment and depression
Authors: Lonie J. A. , Tierney K. M. , Herrmann L. L. , Donaghey C. , O'Carroll R. E. , Lee A. , Ebmeier K. P. 
Published: April 2008

BackgroundThe dual task paradigm (Baddeleyet al.1986; Della Salaet al.1995) has been proposed as a sensitive measure of Alzheimer's dementia, early in the disease process.MethodWe investigated this claim by administering the modified dual task paradigm (utilising a pencil-and-paper version of a tracking task) to 33 patients with amnestic mild cognitive impairment (aMCI) and 10 with very early Alzheimer's disease, as well as 21 healthy elderly subjects and 17 controls with depressive symptoms. All groups were closely matched for age and pre-morbid intellectual ability.ResultsThere were no group differences in dual task performance, despite poor performance in episodic memory tests of the aMCI and early Alzheimer's disease groups. In contrast, the Alzheimer patients were specifically impaired in the trail-making test B, another commonly used test of divided attention.ConclusionsThe dual task paradigm lacks sensitivity for use in the early differential diagnosis of Alzheimer's disease.