bluuebunny/crossref_metadata_2025_split huggingface dataset:
Density functional theory study of contribution of many‐body energies to binding energy for alanine‐(water)4 complex
Authors: Chaudhari Ajay , Lee Shyi‐Long 
Published: November 2004

AbstractThe lowest energy conformer of alanine‐(water)4 complex (Spectrochim. Acta A, 59, 2619, 2003) was studied in more detail using Density Functional Theory methods B3LYP/6‐31+G*. The total energy and binding energy for this complex is –629.514437 hartrees and –41.02 kcal/mol, respectively. Relaxation energy and many‐body energies, i.e., two‐, three‐, four‐, and five‐body energies, were obtained for this complex using many‐body analysis to elucidate their contribution to the binding energy of the complex. It was found that relaxation energy as well as all many‐body energies had significant contributions to the total binding energy. The highest contribution is from two‐body energies. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Periodic DFT approach to benzotrifuroxan crystal
Authors: Ju Xue‐Hai , Xiao He‐Ming , Chen Li‐Tao 
Published: November 2004

AbstractDensity Functional Theory (DFT) calculations at the B3LYP/6‐21G* level were performed on crystalline benzotrifuroxan (BTF). The frontier bands are generally quite flat. The energy gap between the highest occupied crystal orbital (HOCO) and the lowest unoccupied crystal orbital (LUCO) is 3.89 eV, indicating that the crystal is an electrical insulator. All the atoms of BTF make up both the lower and the higher energy bands. The projection of density of state (DOS) indicates that there exists no region with much higher reactivity as other explosives, since the coplanar rings of BTF are conjugated. An anisotropic impact on the bulk makes the electron transfer from carbon atoms to nitrogen and oxygen atoms, which lowers the strength of the C–C bond. The crystal lattice energy is predicted to be –47.39 kJ/mol. The elastic constants C11, C22, and C33 are predicted to be 191.48 GPa, 94.39 GPa, and 347.42 GPa, respectively. The large differences of C11, C22, and C33 indicate the anisotropic properties of BTF upon impacting. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Density functional study of O2 adsorption on (100) surface of γ‐uranium
Authors: Huda M. N. , Ray A. K. 
Published: November 2004

AbstractChemisorption of the oxygen molecule on the (100) surface of γ‐uranium was investigated using the generalized gradient approximation to Density Functional Theory. Dissociative adsorptions of O2 are found to be significantly favored compared to molecular adsorptions. Interstitial adsorptions of molecular oxygen are less probable, as no bound states are found in this case. Only after dissociation of O2 is atomic oxygen diffusion through the surface possible. The O 2p orbitals are found to hybridize with U 5f bands, and some of the U 5f electrons become more localized. A significant charge transfer from the first layer of the uranium surface to the oxygen atoms is found to occur, making the bonding partly ionic. For the most favored site, the dissociative chemisorption energy is ∼9.5 eV, which indicates a strong reaction of uranium surface with oxygen. Spin polarization does not have a significant effect on the chemisorption process. For most of the sites and approaches, chemisorption configurations are almost same for both spin‐polarized and non‐spin‐polarized cases. For the most favored chemisorption sites of oxygen on uranium, paramagnetic adsorption is slightly stronger, by 0.304 eV, compared to magnetic adsorption. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Hydratases involved in nitrile conversion: Screening, characterization and application
Authors: Yamada Hideaki , Shimizu Sakayu , Kobayashi Michihiko 
Published: November 2004

AbstractThe discovery of new enzymes with greater activity and specificity opens new, simple routes for synthetic processes, and consequently, new methods to solve environmental problems. A number of nitrile‐related enzymes have been screened over the past few years for use in developing synthetic applications. Microbial nitrile hydratase (NHase) has great potential as a catalyst in organic chemical processing because the enzyme can convert nitriles to the corresponding higher value amides under mild conditions, and has now been applied to the industrial productions of acrylamide and nicotinamide. Particularly, the former production is the first successful example of a bioconversion process for the manufacture of a commodity chemical. The characterization of the enzyme at the molecular level has provided new insights into how the molecular structure determines the enzyme function, and how the regulatory system controls the expression of the enzyme genes to improve the enzyme and the NHase‐dependent process. © 2001 John Wiley & Sons, Inc. and The Japan Chemical Journal Forum Chem Rec 1: 152–161, 2001
Interactions of target population size, population parameters, and program management on viability of captive populations
Authors: Earnhardt Joanne M. , Thompson Steven D. , Marhevsky Emily A. 
Published: November 2004

AbstractWhen established conservation programs expand and evolve, management practices may become inconsistent with program goals. In the past decade, the American Zoo and Aquarium Association expanded species conservation programs by increasing the number of Species Survival Plans (SSP) and establishing more than 300 new Population Management Plan (PMP) programs. However, limited space in captive breeding facilities forces a competition among SSPs and less intensively managed PMPs. Regional Collection Plans establish priorities and allocate space accordingly by setting target population size for each species; species of high conservation priority (SSPs) are allocated space at the expense of lower priority species (PMPs). Because population size and genetic composition interact to impact population viability, target population size is a significant factor to a population’s prospects for long‐term survival. We examined four population parameters (current population size, target population size, current gene diversity, and mean generation time) for 46 mammalian SSPs and 17 PMPs. Relative to SSPs, PMPs combine smaller current and target population sizes, lower levels of current gene diversity, and shorter mean generation times than SSPs. Thus, the average PMP population can expect to lose gene diversity more rapidly than the average SSP population. PMPs are projected to lose 10% or more of their founding gene diversity, within only 2 years. In contrast, the average SSP population is projected to lose 10% in 40 years. Populations with small current or target population sizes require intensive management to avoid extinction. More intensive genetic management of populations typically designated as PMPs, through recruitment of potential founders and equalization of founder representation, could increase gene diversity and improve viability. Less rigorous population management should be reserved for populations whose long‐term survival is either secure or that can be readily replenished from the wild. Because PMP populations need intense genetic management similar to that currently in effect for SSPs, there should be neither a management‐level distinction between programs nor an arbitrary difference in space allocated to programs. Zoo Biol 20:169–183, 2001. © 2001 Wiley‐Liss, Inc.
Probabilities of spurious connections in gene networks: application to expression time series
Authors: Bickel David R. 
Published: November 2004

Abstract
Motivation: The reconstruction of gene networks from gene-expression microarrays is gaining popularity as methods improve and as more data become available. The reliability of such networks could be judged by the probability that a connection between genes is spurious, resulting from chance fluctuations rather than from a true biological relationship.
Results: Unlike the false discovery rate and positive false discovery rate, the decisive false discovery rate (dFDR) is exactly equal to a conditional probability without assuming independence or the randomness of hypothesis truth values. This property is useful not only in the common application to the detection of differential gene expression, but also in determining the probability of a spurious connection in a reconstructed gene network. Estimators of the dFDR can estimate each of three probabilities: (1) The probability that two genes that appear to be associated with each other lack such association. (2) The probability that a time ordering observed for two associated genes is misleading. (3) The probability that a time ordering observed for two genes is misleading, either because they are not associated or because they are associated without a lag in time. The first probability applies to both static and dynamic gene networks, and the other two only apply to dynamic gene networks.
Availability: Cross-platform software for network reconstruction, probability estimation, and plotting is free from http://www.davidbickel.com in Statomics, a suite of R functions with a Java application.
Contact: bickel@prueba.info
Supplementary information: Color figures are available from http://www.davidbickel.com
Extracellular pressure stimulates colon cancer cell proliferation via a mechanism requiring PKC and tyrosine kinase signals
Authors: Walsh M. F. , Woo R. K.‐Y. , Gomez R. , Basson M. D. 
Published: November 2004

Abstract.  Pressure in colonic tumours may increase during constipation, obstruction or peri‐operatively. Pressure enhances colonocyte adhesion by a c‐Src‐ and actin‐cytoskeleton‐dependent PKC‐independent pathway. We hypothesized that pressure activates mitogenic signals.Methods.  Malignant colonocytes on a collagen I matrix were subjected to 15 mmHg pressure. ERK, p38, c‐Src and Akt phosphorylation and PKCα redistribution were assessed by western blot after 30 min and PKC activation by ELISA. Cells were counted after 24 h and after inhibition of each signal, tyrosine phosphorylation or actin depolymerization.Results.  Pressure time‐dependently increased SW620 and HCT‐116 cell counts on collagen or fibronectin (P < 0.01). Pressure increased the SW620 S‐phase fraction from 28 ± 1 to 47 ± 1% (P = 0.0002). Pressure activated p38, ERK, and c‐Src (P < 0.05 each) but not Akt/PKB. Pressure decreased cytosolic PKC activity, and translocated PKCα to a membrane fraction. Blockade of p38, ERK, c‐Src or PI‐3‐K or actin depolymerization did not inhibit pressure‐stimulated proliferation. However, global tyrosine kinase blockade (genistein) and PKC blockade (calphostin C) negated pressure‐induced proliferation.Conclusions.  Extracellular pressure stimulates cell proliferation and activates several signals. However, the mitogenic effect of pressure requires only tyrosine kinase and PKCα activation. Pressure may modulate colon cancer growth and implantation by two distinct pathways, one stimulating proliferation and the other promoting adhesion.
Stressors, burnout and social support: nurses in acute mental health settings
Authors: Jenkins Richard , Elliott Peter 
Published: November 2004

Aims.  This paper reports a study which aims (1) to investigate and compare levels of stressors and burnout of qualified and unqualified nursing staff in acute mental health settings; (2) to examine the relationships between stressors and burnout and (3) to assess the impact of social support on burnout and stressor–burnout relationships.Background.  Several studies have noted that the work of mental health nurses can be highly stressful, but relatively few have focused specifically on staff working in acute inpatient settings. Although many of the pressures faced by this group are similar to those in other nursing specialities, a number of demands relate specifically to mental health settings, including the often intense nature of nurse–patient interaction and dealing with difficult and challenging patient behaviours on a regular basis.Methods.  A convenience sample of 93 nursing staff from 11 acute adult mental health wards completed the Mental Health Professionals Stress Scale, Maslach Burnout Inventory and House and Wells Social Support Scale.Results.  Lack of adequate staffing was the main stressor reported by qualified staff, while dealing with physically threatening, difficult or demanding patients was the most stressful aspect for unqualified staff. Qualified nurses reported significantly higher workload stress than unqualified staff. Approximately half of all nursing staff showed signs of high burnout in terms of emotional exhaustion. A variety of stressors were positively correlated with emotional exhaustion and depersonalization. Higher levels of support from co‐workers were related to lower levels of emotional exhaustion. Higher stressor scores were associated with higher levels of depersonalization for staff reporting high levels of social support, but not for those reporting low levels of support (a reverse buffering effect).Conclusions.  Qualified and unqualified nursing staff differed in terms of the prominence given to individual stressors in their work environment. The findings were consistent with the notion of burnout developing in response to job‐related stressors. While staff support groups may be useful in alleviating feelings of burnout, the reverse buffering effect suggests that they should be structured in a way that minimizes negative communication and encourages staff to discuss their concerns in a constructive way.
Effects of absorbent incontinence pads on pressure management mattresses
Authors: Fader Mandy , Bain Duncan , Cottenden Alan 
Published: November 2004

Aim.  The aim of this paper is to report a study to determine the effects of absorbent pads on the pressure‐relieving properties of ‘standard’ and pressure management mattresses.Background.  Pressure ulcers and incontinence often co‐exist. There is a strong association between poor mobility and continence problems and patients using pressure management products are therefore also likely to be using absorbent pads.Methods.  An instrumented articulated anthropometric phantom with simulated soft body ‘tissues’ in the gluteal and sacral areas was used as the ‘subject’. The phantom was raised and lowered on to three mattresses (standard foam, visco‐elastic foam and surface‐cut foam) in three states: naked, wearing a dry pad (Tena Super, SCA Hygiene AB) and wearing a wet pad. The pressure mapping device Xsensor was used to record the distribution of pressure over the sacral and ischial areas of the phantom. Peak pressure was used as the primary outcome variable and 10 repeats were made on each mattress under each condition.Results.  There were substantial and significant differences for all three mattresses in recorded peak pressures between the naked buttocks and the buttocks wearing a dry pad. There were no significant differences between measurements made using the dry vs. wet pad. Peak pressures frequently occurred over areas of pad folds. Additional testing showed that pads that were ‘smoothed’ by hand had significantly lower peak pressures than ‘unsmoothed’ pads.Conclusions.  Absorbent pads have a substantial adverse effect on the pressure redistribution properties of mattresses. Pad folds appear to contribute to this effect, which can be ameliorated slightly by smoothing. Absorbent pad manufacturers should consider engineering pads that minimize disruption to pressure management. Further examination of continence and pressure management products is necessary to establish optimum combinations for nursing care.
Multicomponent individualized smoking cessation intervention for patients with lung disease
Authors: Jonsdottir Helga , Jonsdottir Rosa , Geirsdottir Thora , Sveinsdottir K. Sigridur , Sigurdardottir Thorunn 
Published: November 2004

Aims.  This paper reports a study examining the process and outcomes of a long‐term, multicomponent smoking cessation intervention for patients with lung disease initiated while hospitalized and provided over 1‐year postdischarge.Background.  Successful smoking cessation interventions are of primary importance for people with lung disease. Initiation of such an intervention in hospital settings is particularly important as patients may be especially motivated to quit as a result of strong perceptions of vulnerability while hospitalized for a smoking‐related disease. Tailoring the intervention to each person's needs is a promising approach to practice.Methods.  All patients who smoked and were admitted to a pulmonary unit over 2 years were invited to participate in this quasi‐experimental study (n = 85), and 69 continued beyond the first month. The intervention was shaped by the TransTheoretical Model and used nicotine replacement therapy, along with individual and group counselling and support grounded in the nurse–patient relationship. The intervention was provided during hospitalization and by telephone after discharge at 1 week, and 1, 3, 6 and 12 months.Results.  At 12‐months postdischarge, 39% of the patients reported continuous abstinence from smoking from the time they joined the programme and 52% were not smoking at that time. No relationship was found between abstinence and the number of quit attempts, readiness to quit, nicotine dependency and length of hospital stay. Readiness to quit had increased and nicotine dependency decreased significantly by the end of the programme. No gender differences were found for the main variables.Conclusions.  Comprehensive, individualized smoking cessation interventions for hospitalized patients having lung disease, with a 1‐year follow‐up, was successful. Abstinence was high in comparison with other studies. This may in part be explained by significantly enhanced motivation to quit during the smoking cessation programme.
Signaling requirements and role of salicylic acid in HRT‐ and rrt‐mediated resistance to turnip crinkle virus in Arabidopsis
Authors: Chandra‐Shekara A.C. , Navarre DuRoy , Kachroo Aardra , Kang Hong‐Gu , Klessig Daniel , Kachroo Pradeep 
Published: November 2004

SummaryInoculation of turnip crinkle virus (TCV) on the resistant Arabidopsis ecotype Di‐17 elicits a hypersensitive response (HR), which is accompanied by increased expression of pathogenesis‐related (PR) genes. Previous genetic analyses revealed that the HR to TCV is conferred by HRT, which encodes a coiled‐coil (CC), nucleotide‐binding site (NBS) and leucine‐rich repeat (LRR) class resistance (R) protein. In contrast to the HR, resistance to TCV requires both HRT and a recessive allele at a second locus designated rrt. Here, we demonstrate that unlike most CC‐NBS‐LRR R genes, HRT/rrt‐mediated resistance is dependent on EDS1 and independent of NDR1. Resistance is also independent of RAR1 and SGT1. HRT/rrt‐mediated resistance is compromised in plants with reduced salicylic acid (SA) content as a consequence of mutations eds5, pad4, or sid2. By contrast, HR is not affected by mutations in eds1, eds5, pad4, sid2, ndr1, rar1, or sgt1b. Resistance to TCV is restored in both SA‐deficient Di‐17 plants expressing the nahG transgene and mutants containing the eds1, eds5, or sid2 mutations by exogenous application of SA or the SA analog benzo(1,2,3)thiadiazole‐7‐carbothioic acid (BTH). In contrast, SA/BTH treatment failed to enhance resistance in HRT pad4, Col‐0, or hrt homozygous progeny of a cross between Di‐17 and Col‐0. Thus, HRT and PAD4 are required for SA‐induced resistance. Exogenously supplied SA or high endogenous levels of SA, due to the ssi2 mutation, overcame the suppressive effects of RRT and enhanced resistance to TCV, provided the HRT allele was present. High levels of SA upregulate HRT expression via a PAD4‐dependent pathway. As Col‐0 transgenic lines expressing high levels of HRT were resistant to TCV, but lines expressing moderate to low levels of HRT were not, we conclude that SA enhances resistance in the RRT background by upregulating HRT expression. These data suggest that the HRT‐TCV interaction is unable to generate sufficient amounts of SA required for a stable resistance phenotype, and the presence of rrt possibly corrects this deficiency.
Engineering of ubiquinone biosynthesis using the yeast coq2 gene confers oxidative stress tolerance in transgenic tobacco
Authors: Ohara Kazuaki , Kokado Yoshimasa , Yamamoto Hirobumi , Sato Fumihiko , Yazaki Kazufumi 
Published: November 2004

SummaryUbiquinone (UQ), an electron carrier in the respiratory chain ranging from bacteria to humans, shows antioxidative activity in vitro, but its physiological role in vivo is not yet clarified in plants. UQ biosynthesis was modified by overexpressing the yeast gene coq2, which encodes p‐hydroxybenzoate:polyprenyltransferase, to increase the accumulation of UQ‐6 in yeast and UQ‐10 in tobacco. The yeast and tobacco transgenic lines showed about a three‐ and six‐fold increase in UQ, respectively. COQ2 polypeptide, the localization of which was forcibly altered to the endoplasmic reticulum, had the same or a greater effect as mitochondria‐localized COQ2 on the increase in UQ in both the yeast and tobacco transformants, indicating that the UQ intermediate is transported from the endoplasmic reticulum to the mitochondria. Plants with a high UQ level are more resistant to oxidative stresses caused by methyl viologen or high salinity. This is attributable to the greater radical scavenging ability of the transgenic lines when compared with the wild type.
The Pseudomonas syringae type III effector AvrRpt2 promotes virulence independently of RIN4, a predicted virulence target in Arabidopsis thaliana
Authors: Lim Melisa T.S. , Kunkel Barbara N. 
Published: November 2004

SummaryAvrRpt2, an effector protein from Pseudomonas syringae pv. tomato (Pst), behaves as an avirulence factor that activates resistance in Arabidopsis thaliana lines expressing the resistance gene RPS2. AvrRpt2 can also enhance pathogen fitness by promoting the ability of the bacteria to grow and to cause disease on susceptible lines of A. thaliana that lack functional RPS2. The activation of RPS2 is coupled to the AvrRpt2‐induced disappearance of the A. thaliana RIN4 protein. However, the significance of this RIN4 elimination to AvrRpt2 virulence function is unresolved. To clarify our understanding of the contribution of RIN4 disappearance to AvrRpt2 virulence function, we generated new avrRpt2 alleles by random mutagenesis. We show that the ability of six novel AvrRpt2 mutants to induce RIN4 disappearance correlated well with their avirulence activities but not with their virulence activities. Moreover, the virulence activity of wild‐type AvrRpt2 was detectable in an A. thaliana line lacking RIN4. Collectively, these results indicate that the virulence activity of AvrRpt2 in A. thaliana is likely to rely on the modification of host susceptibility factors other than, or in addition to, RIN4.
DNA array analyses of Arabidopsis thaliana lacking a vacuolar Na+/H+ antiporter: impact of AtNHX1 on gene expression
Authors: Sottosanto Jordan B. , Gelli Angie , Blumwald Eduardo 
Published: November 2004

SummaryAtNHX1, a vacuolar cation/proton antiporter of Arabidopsis, plays an important role in salt tolerance, ion homeostasis and development. We used the T‐DNA insertional mutant of AtNHX1 (nhx1 plants) and Affymetrix ATH1 DNA arrays to assess differences in transcriptional profiles and further characterize the roles of a vacuolar cation/proton antiporter. Mature, soil‐grown plants were used in this study to approximate typical physiological growing conditions. A comparison of plants grown in the absence of salt stress yielded many transcripts that were affected by the absence of the AtNHX1 vacuolar antiporter. Furthermore, changes in gene expression due to a non‐lethal salt stress (100 mm NaCl) in the nhx1 plants were significantly different from the changes seen in wild‐type plants. The nhx1 transcriptome was differentially affected when the plants were grown in the absence or presence of salt. In conclusion, in addition to the known role(s) of AtNHX1 on ion homeostasis, the vacuolar cation/proton antiporter plays a significant role in intracellular vesicular trafficking, protein targeting, and other cellular processes.