bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and molecular detection of methylotrophic bacteria occurring in the human mouth
Authors: Anesti Vasiliki , McDonald Ian R. , Ramaswamy Meghna , Wade William G. , Kelly Donovan P. , Wood Ann P.
Published: July 2005

Diverse methylotrophic bacteria were isolated from the tongue, and supra‐ and subgingival plaque in the mouths of volunteers and patients with periodontitis. One‐carbon compounds such as dimethylsulfide in the mouth are likely to be used as growth substrates for these organisms. Methylotrophic strains of Bacillus, Brevibacterium casei, Hyphomicrobium sulfonivorans, Methylobacterium, Micrococcus luteus and Variovorax paradoxus were characterized physiologically and by their 16S rRNA gene sequences. The type strain of B. casei was shown to be methylotrophic. Enzymes of methylotrophic metabolism were characterized in some strains, and activities consistent with growth using known pathways of C1‐compound metabolism demonstrated. Genomic DNA from 18 tongue and dental plaque samples from nine volunteers was amplified by the polymerase chain reaction using primers for the 16S rRNA gene of Methylobacterium and the mxaF gene of methanol dehydrogenase. MxaF was detected in all nine volunteers, and Methylobacterium was detected in seven. Methylotrophic activity is thus a feature of the oral bacterial community.
Assessing children's appraisals of security in the family system: the development of the Security in the Family System (SIFS) scales
Authors: Forman Evan M. , Davies Patrick T.
Published: July 2005

Background:  Although delineating the processes by which children appraise the family as a source of security from their collective experiences in the family subsystem has assumed center stage in many conceptualizations of child development, the dearth of measures of child adaptation in the family system has hindered empirical advances. Therefore, this study introduced and tested the psychometric properties of the Security in the Family System (SIFS) scales, a new measure designed to assess children's appraisals of security in their family as a whole.

Methods:  The SIFS was administered to 853 10–15‐year‐old schoolchildren and readministered to a smaller subsample two weeks later. Additional data was gathered from children, caregivers and teachers using a variety of instruments tapping family instability, cohesion, and conflict; parenting warmth and psychological control; child externalizing and internalizing symptoms; parent–child and interparental insecurity; and children's reactions to conflict simulations.

Results:  Consistent with models of emotional security in the family, exploratory and confirmatory factor analyses yielded three reliable (i.e., good internal consistency, test–retest reliability) dimensions of family security: Preoccupation, Security, and Disengagement. Concurrent and prospective associations between the SIFS scales and measures of family functioning, children's psychological problems, and insecurity in specific family relationships supported the validity of the SIFS. Support for the discriminant validity of the SIFS was evidenced by its specific patterns of relations with children's psychological problems and ability to predict psychological problems after controlling for insecurity in specific family subsystems.

Conclusions:  Results indicate that the SIFS is a psychometrically sound tool capable of advancing family process models, and that family security is a viable construct whose factors parallel already‐identified patterns of children's security in other family relationships.
The facility and transfer points location problem
Authors: Berman Oded , Drezner Zvi , Wesolowsky George O.
Published: July 2005

In this paper, we investigate the location of a facility and several transfer points to serve as collector points for customers who need the services of the facility. For example, demand for emergency services is generated at a set of demand points that need the services of a central facility (such as a hospital). Patients are transferred to a helicopter pad (transfer point) at normal speed, and from there they are transferred to the facility at increased speed. The model involves the location of multiple transfer points and one facility. Locating one transfer point when the set of demand points and the location of the facility are known was investigated in Berman et al. (2004a). Location of several transfer points when the location of the facility is given is investigated in Berman et al. (2004b). In this paper, we propose heuristic approaches for the solution of this problem and report computational experiments on a test set of 40 problems.
P–T–fluid evolution in the Mahalapye Complex, Limpopo high‐grade terrane, eastern Botswana
Authors: HISADA K. , PERCHUK L. L. , GERYA T. V. , VAN REENEN D. D. , PAYA B. K.
Published: July 2005

Metapelites, migmatites and granites from the c. 2 Ga Mahalapye Complex have been studied for determining the P–T–fluid influence on mineral assemblages and local equilibrium compositions in the rocks from the extreme southwestern part of the Central Zone of the Limpopo high‐grade terrane in Botswana. It was found that fluid infiltration played a leading role in the formation of the rocks. This conclusion is based on both well‐developed textures inferred to record metasomatic reactions, such as Bt ⇒ And + Qtz + (K2O) and Bt ± Qtz ⇒ Sil + Kfs + Ms ± Pl, and zonation of Ms | Bt + Qtz | And + Qtz and Grt | Crd | Pl | Kfs + Qtz reflecting a perfect mobility (Korzhinskii terminology) of some chemical components. The conclusion is also supported by the results of a fluid inclusion study. CO2 and H2O ( = 0.6) are the major components of the fluid. The fluid has been trapped synchronously along the retrograde P–T path. The P–T path was derived using mineral thermobarometry and a combination of mineral thermometry and fluid inclusion density data. The Mahalapye Complex experienced low‐pressure granulite facies metamorphism with a retrograde evolution from 770 °C and 5.5 kbar to 560 °C and 2 kbar, presumably at c. 2 Ga.
Determining a Maximum‐Tolerated Schedule of a Cytotoxic Agent
Authors: Braun Thomas M. , Yuan Zheng , Thall Peter F.
Published: July 2005

Summary Most phase I clinical trials are designed to determine a maximum‐tolerated dose (MTD) for one initial administration or treatment course of a cytotoxic experimental agent. Toxicity usually is defined as the indicator of whether one or more particular adverse events occur within a short time period from the start of therapy. However, physicians often administer an agent to the patient repeatedly and monitor long‐term toxicity due to cumulative effects. We propose a new method for such settings. It is based on the time to toxicity rather than a binary outcome, and the goal is to determine a maximum‐tolerated schedule (MTS) rather than a conventional MTD. The model and method account for a patient's entire sequence of administrations, with the overall hazard of toxicity modeled as the sum of a sequence of hazards, each associated with one administration. Data monitoring and decision making are done continuously throughout the trial. We illustrate the method with an allogeneic bone marrow transplantation (BMT) trial to determine how long a recombinant human growth factor can be administered as prophylaxis for acute graft‐versus‐host disease (aGVHD), and we present a simulation study in the context of this trial.
A Bayesian Approach to Jointly Modeling Toxicity and Biomarker Expression in a Phase I/II Dose‐Finding Trial
Authors: Nebiyou Bekele B. , Shen Yu
Published: July 2005

Summary In this article, we propose a Bayesian approach to phase I/II dose‐finding oncology trials by jointly modeling a binary toxicity outcome and a continuous biomarker expression outcome. We apply our method to a clinical trial of a new gene therapy for bladder cancer patients. In this trial, the biomarker expression indicates biological activity of the new therapy. For ethical reasons, the trial is conducted sequentially, with the dose for each successive patient chosen using both toxicity and activity data from patients previously treated in the trial. The modeling framework that we use naturally incorporates correlation between the binary toxicity and continuous activity outcome via a latent Gaussian variable. The dose‐escalation/de‐escalation decision rules are based on the posterior distributions of both toxicity and activity. A flexible state‐space model is used to relate the activity outcome and dose. Extensive simulation studies show that the design reliably chooses the preferred dose using both toxicity and expression outcomes under various clinical scenarios.
Partly Conditional Survival Models for Longitudinal Data
Authors: Zheng Yingye , Heagerty Patrick J.
Published: July 2005

SummaryIt is common in longitudinal studies to collect information on the time until a key clinical event, such as death, and to measure markers of patient health at multiple follow‐up times. One approach to the joint analysis of survival and repeated measures data adopts a time‐varying covariate regression model for the event time hazard. Using this standard approach, the instantaneous risk of death at timetis specified as a possibly semiparametric function of covariate information that has accrued through timet. In this manuscript, we decouple the time scale for modeling the hazard from the time scale for accrual of available longitudinal covariate information. Specifically, we propose a class of models that condition on the covariate information through timesand then specifies the conditional hazard for timest, wheret>s. Our approach parallels the “partly conditional” models proposed byPepe and Couper(1997,Journal of the American Statistical Association92,991–998) for pure repeated measures applications. Estimation is based on the use of estimating equations applied to clusters of data formed through the creation of derived survival times that measure the time from measurement of covariates to the end of follow‐up. Patient follow‐up may be terminated either by the occurrence of the event or by censoring. The proposed methods allow a flexible characterization of the association between a longitudinal covariate process and a survival time, and facilitate the direct prediction of survival probabilities in the time‐varying covariate setting.
The Full EM Algorithm for the MLEs of QTL Effects and Positions and Their Estimated Variances in Multiple‐Interval Mapping
Authors: Chen Zehua
Published: July 2005

SummaryThe advent of complete genetic linkage maps of DNA markers has made systematic studies of mapping quantitative trait loci (QTL) in experimental organisms feasible. The method of multiple‐interval mapping provides an appropriate way for mapping QTL using genetic markers. However, efficient algorithms for the computation involved remain to be developed. In this article, a full EM algorithm for the simultaneous computation of the MLEs of QTL effects and positions is developed. EM‐based formulas are derived for computing the observed Fisher information matrix. The full EM algorithm is compared with an ECM algorithm developed byKao and Zeng(1997,Biometrics53,653–665). The validity of the inverted observed Fisher information matrix as an estimate of the variance matrix of the MLEs is demonstrated by a simulation study.
A General Class of Bayesian Survival Models with Zero and Nonzero Cure Fractions
Authors: Yin Guosheng , Ibrahim Joseph G.
Published: July 2005

SummaryWe propose a new class of survival models which naturally links a family of proper and improper population survival functions. The models resulting in improper survival functions are often referred to as cure rate models. This class of regression models is formulated through the Box–Cox transformation on the population hazard function and a proper density function. By adding an extra transformation parameter into the cure rate model, we are able to generate models with a zero cure rate, thus leading to a proper population survival function. A graphical illustration of the behavior and the influence of the transformation parameter on the regression model is provided. We consider a Bayesian approach which is motivated by the complexity of the model. Prior specification needs to accommodate parameter constraints due to the nonnegativity of the survival function. Moreover, the likelihood function involves a complicated integral on the survival function, which may not have an analytical closed form, and thus makes the implementation of Gibbs sampling more difficult. We propose an efficient Markov chain Monte Carlo computational scheme based on Gaussian quadrature. The proposed method is illustrated with an example involving a melanoma clinical trial.
Semiparametric Analysis of Survival Data with Left Truncation and Dependent Right Censoring
Authors: Jiang Hongyu , Fine Jason P. , Chappell Rick
Published: July 2005

SummaryStudies of chronic life‐threatening diseases often involve both mortality and morbidity. In observational studies, the data may also be subject to administrative left truncation and right censoring. Because mortality and morbidity may be correlated and mortality may censor morbidity, the Lynden‐Bell estimator for left‐truncated and right‐censored data may be biased for estimating the marginal survival function of the nonterminal event. We propose a semiparametric estimator for this survival function based on a joint model for the two time‐to‐event variables, which utilizes the gamma frailty specification in the region of the observable data. First, we develop a novel estimator for the gamma frailty parameter under left truncation. Using this estimator, we then derive a closed‐form estimator for the marginal distribution of the nonterminal event. The large sample properties of the estimators are established via asymptotic theory. The methodology performs well with moderate sample sizes, both in simulations and in an analysis of data from a diabetes registry.
Control of defects during continuous casting of line pipe (API) quality steels
Authors: Pradhan N. , Banerjee N. , Reddy B. B. , Sahay S. K. , Basu D. S. , Bhor P. K. , Das S. , Bhattyacharya S.
Published: July 2005

Internal and surface quality of line pipe (API) grade steels are very important in addition to the various property requirements such as YS and UTS, YS/UTS ratio, elongation, fatigue strength at zero and sub zero temperature and weldability. Surface cracking is predominant in these steel grades because of the presence of various micro‐alloying (Nb, V, etc.) elements for their precipitation in various forms like nitrides and carbo‐nitrides at the prior austenite grain boundaries during continuous casting and making the solidified steel brittle.

Besides this, internal soundness in terms of ultrasonic non‐destructive testing is another important requirement of line pipe plates. High rejection of plates of these grades was experienced in the initial phase of production in terms of surface defects (cracks and entrapment of non‐metallics) and internal defects (ultrasonic testing) including low yield at slab stage. These led to low yield of the final product. In view of this, development work was undertaken at Bhilai Steel Plant to improve processing technology to achieve higher yield of API grade plates. This paper discusses the reasons of low yield of slabs and plates in the initial stages of production and measures taken in continuous casting parameters to improve the same including the acceptability of final plates.
Kinetic parameters for the process of sulfatization roasting and leaching of copper–lead matte
Authors: Minić Dušan , Štrbac Nada , Mihajlović Ivan , Petković Desimir , Živković Živan
Published: July 2005

In this paper the results of the copper–lead matte investigations are presented. The investigated copper–lead matte is an intermediate product of lead production in TREPCA‐Zvecan. In the first part of the paper the characterization of the starting material is presented, consisting of chemical composition analysis, scanning electron microscopy and the X‐ray diffractometry. Using the results of the above analysis optimal conditions for sulfatization roasting and leaching of roasted copper–lead matte in water were determined. In this manner, the optimal roasting temperature was determined to be 600°C, during a time period of 150 min, providing 57% of CuSO4. Optimal conditions for leaching of obtained roasted material are: leaching temperature 125°C, time period 30 min and liquid‐to‐solid ratio of 5:1. Copper utilization during leaching under these conditions is near 95.3%. In the second part of the paper kinetics parameters are presented, describing the process of sulfatization roasting of the mattes at a temperature interval of 450–650°C and leaching in water.
Sunscreen use and sun protection practices in students and personnel of Celal Bayar University
Authors: Ermertcan Aylin Türel , Öztürkcan Serap , Dinç Gönül , Yurtman Deniz , Pala Tümer , Şahin Mustafa Turhan
Published: July 2005

Background/Purpose: The steady increase in the incidence of melanoma, non‐melanoma cutaneous neoplasia and preneoplastic disorders has contributed to the demand for more effective protection from the sun. In this study, we aimed to determine the prevalence of sunscreen use and other sun protection behaviors in a large sample of students and personnel of Celal Bayar University, Manisa, Turkey.

Methods: The study group included 1018 participants of whom 607 work in the Celal Bayar University Hospital and 411 are students from the Medical Faculty and School for Health Professionals. All participants completed a questionnaire composed of 45 items about sun protection and other health behaviors, such as sports activity, use of cigarettes, alcohol and seat‐belts. Sun protection factor (SPF) of sunscreen, avoiding sun exposure during peak hours, wearing clothing, a hat and sunglasses were studied.

Results: Of the 1018, 403 participants were male and 615 were female. While avoiding sun exposure during peak hours was the most popular preventive behavior for men (42.5%), wearing sunglasses was the most popular one for women (50.7%). Avoiding exposure was the second preventive behavior for women (42.1%). Use of sunscreen with SPF 15+ was the second popular protective measure for men (19.4%) and the third one for women (39.2%). There were no significant relationships between sun protection behaviors and obesity, use of cigarettes and alcohol. We also investigated behavioral changes with sunburn experience in the participants who had sunburn history. Among these behavioral changes, increased use of sunscreen and decreased sun exposure during peak hours with sunburn experience were significant.

Conclusion: Our study demonstrated that the risk of sun exposure is largely unrecognized in Manisa, Turkey, and we have very incomplete information about protective measures. An efficient policy of education on the effective use of sun protection methods should be developed to prevent skin cancer.
Gene expression profiles of TNF‐α, TACE, furin, IL‐1β and matrilysin in UVA‐ and UVB‐irradiated HaCat cells
Authors: Skiba Beata , Neill Bronwyn , Piva Terrence J.
Published: July 2005

Background/Purpose: It is known that solar ultraviolet (UV) irradiation exerts multiple effects on mammalian skin tissues, one of which is the induction of local and systemic immunosuppression as well as inflammation. Tumor necrosis factor‐α (TNF‐α) and other cytokines are suggested to play a role in these responses. Quantitative real‐time polymerase chain reaction (TaqMan RTPCR) was used to elucidate the effect of UVA and UVB irradiation on the expression of genes coding for TNF‐α, IL‐1β, IL‐10, FasL, matrilysin, TACE and furin in HaCaT cells over a 48 h period (IL‐1β, interleukin‐1β; FasL, Fas ligand).

Methods: Cultured HaCaT cells were either sham irradiated (control) or exposed to UVA (2000 and 8000 J/m2) or UVB (200 and 2000 J/m2) radiation. RNA was extracted from cells at 0, 4, 8, 12, 16, 24, 48 h post‐irradiation and reverse transcribed to generate cDNA for subsequent real‐time PCR amplification.

Results: Significant increases in the mRNA levels for all genes tested were detected in both UVA‐ and UVB‐irradiated HaCaT cells compared with control (sham‐irradiated) cells. TNF‐α mRNA levels were immediately up‐regulated (0 h) after irradiation, with maximal induction at 8 h post 2000 J/m2 UVA and 200 J/m2 UVB irradiation, at 4 h post 8000 J UVA irradiation and at 48 h post 2000 J/m2 UVB irradiation. No correlation was observed between TNF‐α, TACE and furin mRNA induction in the different irradiated cohorts.

Conclusion: Results suggest that time‐distinct gene induction of TNF‐α, furin, IL‐1β and matrilysin may be involved in UV‐induced cellular responses, but not for TACE. In general, mRNA induction was dose dependent at some time points post‐irradiation, but not throughout the whole time course tested. Our results show that quantitative real‐time PCR is a useful tool in the analysis of quantitative changes of mRNA levels in cultured HaCaT cells after UV exposure.
Research utilization among dental hygienists in Sweden – a national survey
Authors: Öhrn K , Olsson C , Wallin L
Published: July 2005

Over the last decade evidence‐based practice has become increasingly important in health care as an approach to improve patient outcomes. It is vital that dental hygienists, like other health professionals, use research findings to inform clinical practice. The objective of the present study was to investigate the extent of research utilization among dental hygienists in Sweden and to investigate the relationship between level of education and factors related to research utilization. A random sample of 261 dental hygienists in Sweden, 113 with 1 year and 148 with 2‐year education, responded to a postal questionnaire covering various aspects of research utilization, i.e. their attitudes towards research, availability and support for the implementation of research findings, use of research in daily practice, their activity in seeking new research findings and their participation in a range of research‐related activities. Dental hygienists with 2‐year education had a more positive attitude towards research, used research to a greater extent and were more active in seeking new research findings than dental hygienists with 1‐year education. Overall, relatively few dental hygienists reported that they implemented research findings in practice; the most frequently reported activity concerned reading research articles in professional journals. The conclusions are that the length of dental hygiene education is a key factor influencing the application of research findings to practice. One‐year education appears to be inadequate to achieve evidence‐based practice. Moreover, not even two years of formal education guarantees necessary competence in research for evidence‐based dental hygiene practice.
Swedish dental hygienists’ preferences for workplace improvement and continuing professional development
Authors: Petrén V , Levin G , Chohan T , Preber H , Candell A , Bergström J
Published: July 2005

The present study examined factors for workplace improvement and continuing professional development (CPD) for Swedish dental hygienists. Seventy‐one per cent of 577 randomly selected members of Sweden's Dental Hygienist Association responded to a questionnaire. The chi‐square test, Spearman's rank correlation, and multiple stepwise logistic regression modelling were used in the statistical analysis. The results showed that dental hygienists having more than 10 sick days annually and with a strong commitment to their work increased the preference for workplace improvements, such as peer recognition of dental hygienists’ professional qualifications, clinical process quality, and time for reading research articles and participating in projects. In addition, dental hygienists in the 41–52 age group were associated with workplace improvements. This is in contrast to the factors that decreased preferences for workplace improvements: clear work roles, a 1‐year training programme, a male clinic manager, and working in the private sector. Practicing dental hygiene in the public sector and lifestyle factors were the most influential determinants for a strong interest in CPD.

Conclusion:  Workplaces should observe people that are obviously committed to their work, those with many sick days, and those in a specific age group, as they indicate different preferences for workplace improvements. CPD seems to be a lower priority than workplace improvements for Swedish dental hygienists.
Independent dental hygiene practice worldwide: a report of two meetings
Authors: Gatermann‐Strobel B , Perno Goldie M
Published: July 2005

Objectives:  Following a meeting at the EUROPERIO in Berlin in 2003, a forum on Independent Practice of Dental Hygienists was held at the International Symposium on Dental Hygiene (ISDH) in Madrid July, 2004. The forum was organized and moderated by Beate Gatermann, President of the German Dental Hygiene Association. The participants were asked to address the following issues: population of country/state; population of dentists; population of state recognized dental hygienists (Canada/USA etc.); number of hygienists with ‘Diploma’ (Europe); duration of dental hygiene education; cost of education (2/3 year base approximately); when and how independent practice began in the country and who must be consulted or approve the application for an independent office (e.g. Health Department); what services are allowed? Can dental hygienists administer local anaesthesia in the dental office, and if so, must a dentist be present? Can dental hygienists purchase the necessary medication for the injection? Does the dental hygienist require additional education to provide local anaesthesia? How are the patients charged? Does the country offer a service fee list? Do insurance companies pay claims of the dental hygienist? What is the approximate average fee per hour charged (€/$)? Do dentists refer patients to you? If so, do they need a letter of referral? Are dental hygienists allowed to take radiographs in independent dental hygiene offices?
Exit, Voice, and Suffering: Do Couples Adapt to Changing Employment Patterns?
Authors: Gershuny Jonathan , Bittman Michael , Brice John
Published: July 2005

What is the long‐term effect of the emerging predominance of the dual‐earner family? This study uses data from 3 national household panel surveys—the British Household Panel Survey (N= 16,044), the German Socioeconomic Panel (N= 14,164), and the U.S. Panel Study of Income Dynamics (N = 7,423)—which provide, for the first time, clear and direct longitudinal evidence of change in the balance of domestic labor within couples: evidence that women make large adjustments in their domestic work time immediately upon entering full‐time paid work and that men exhibit a less obvious pattern of lagged adaptation, showing larger increases in domestic work in successive years.
“Everything's There Except Money”: How Money Shapes Decisions to Marry Among Cohabitors
Authors: Smock Pamela J. , Manning Wendy D. , Porter Meredith
Published: July 2005

Cohabitation is now the modal path to marriage in the United States. Drawing on data from 115 in‐depth interviews with cohabitors from the working and lower middle classes, this paper explores how economics shape marital decision making. We find that cohabitors typically perceive financial issues as important for marriage, and we delineate several key themes. Whereas some social scientists speculate that cohabitors must think that marriage will change their lives in order to motivate marriage, our findings suggest that cohabitors believe marriage should occur once something has already changed—in this case, their financial status. Our results also imply that political and scientific discourse on financial problems as deterrents to marriage should be broadened beyond a focus on poor unmarried parents.
Incarceration and the Formation and Stability of Marital Unions
Authors: Lopoo Leonard M. , Western Bruce
Published: July 2005

Rising imprisonment rates and declining marriage rates among low‐education African Americans motivate an analysis of the effects of incarceration on marriage. An event history analysis of 2,041 unmarried men from the National Longitudinal Survey of Youth suggests that men are unlikely to marry in the years they serve in prison. A separate analysis of 2,762 married men shows that incarceration during marriage significantly increases the risk of divorce or separation. We simulate aggregate marriage rates using estimates from the National Longitudinal Survey of Youth and find that the prevalence of marriage would change little if incarceration rates were reduced.
Social Support, Traumatic Events, and Depressive Symptoms Among African Americans
Authors: Lincoln Karen D , Chatters Linda M , Taylor Robert Joseph
Published: July 2005

Structural equation modeling was used to examine the relationships among stress, social support, negative interaction, and mental health in a sample of African American men and women between ages 18 and 54 (N= 591) from the National Comorbidity Study. The study findings indicated that social support decreased the number of depressive symptoms, did not mitigate the effects of stress, and was reduced in response to financial strain. Financial strain and traumatic events were associated with increased negative interaction with relatives and depressive symptoms. The findings verify that stressful and traumatic events have direct influences on levels of depressive symptoms and affect the quality of social interactions and suggest how social interaction processes contribute to mental health.
PRESSURE BINDING OF RESTRUCTURED BEEF STEAKS AND CUBES
Authors: FAROUK M.M. , ZHANG S.X.
Published: July 2005

The effect of pressure (1380, 4137 and 6895 kPa) and meat homogenate (0, 2.5, 5 and 10%) on raw and cooked attributes of restructured beef steaks and frozen free‐flow cubes was determined. There was no interaction between pressure and homogenate on the attributes measured. The pressure and homogenate did not affect the color of the raw restructured steaks or the yield or extensibility of the cooked steaks. The bind strength of restructured steaks increased with increasing pressure (P < 0.08) and homogenate content (P < 0.001). The compressive strength and breakability of cooked restructured cubes increased with increased pressure (P < 0.07). The breakability decreased with the increase in the amount of homogenate used during restructuring (P < 0.001). It is concluded that the restructuring of beef may be achieved using pressure alone without binders, and that the use of meat homogenate tended to increase bind strength in restructured beef using pressure.
EFFECT OF MUSCLE‐FIBER/FIBER‐BUNDLE ALIGNMENT ON PHYSICAL AND SENSORY PROPERTIES OF RESTRUCTURED BEEF STEAKS
Authors: FAROUK M.M. , ZHANG S.X. , CUMMINGS T.
Published: July 2005

Cold‐set restructured beef steaks (10 mm thick) were manufactured with meat fibers aligned parallel (PR), perpendicular (PP) or an equal mixture of PR and PP (MX) in relation to the cut‐steak surface. Fiber alignment had no effect (P > 0.05) on the color of raw or the bind strength of both raw and cooked steaks. Raw PR steaks had higher drip loss (P < 0.01) and visual appeal (P < 0.001) than PP or MX steaks; however, cooked PR had higher yield (P < 0.01) and lower (P < 0.04) visual appeal than PP or MX steaks. In‐house panelists found the overall acceptability (P < 0.01), appearance (P < 0.01), texture (P < 0.02) and tenderness (P < 0.002) of cooked PP and MX to be more acceptable than that of PR steaks and ranked the eating quality of the PR steaks significantly lower (P < 0.04) than the others.
Impact of Mineral Fouling on Hydraulic Behavior of Permeable Reactive Barriers
Authors: Li Lin , Benson Craig H. , Lawson Elizabeth M.
Published: July 2005

This paper describes reactive transport simulations conducted to assess the impact of mineral fouling on the hydraulic behavior of continuous‐wall permeable reactive barriers (PRBs) employing granular zero‐valent iron (ZVI) in carbonate‐rich alluvial aquifers. The reactive transport model included a geochemical algorithm for simulating corrosion and mineral precipitation reactions that have been observed in ZVI PRBs. Results of simulations show that porosity and hydraulic conductivity of the ZVI decrease over time and that flows are redistributed throughout the PRB in response to fouling of the pore space. Under typical conditions, only subtle changes occur within the first 10 years (i.e., duration of the current field experience record with PRBs), and the most significant changes do not occur until the PRB has operated for at least 30 years. However, changes can occur sooner (or later) if the rate at which mineral‐forming ions are delivered to the PRB is higher (or lower) than that expected under typical conditions (i.e., due to higher/lower flow rate or inflowing ground water that has higher/lower ionic strength). When the PRB is more permeable than the aquifer, the median Darcy flux in the PRB does not change appreciably over time because the aquifer controls the rate of flow through the PRB. However, seepage velocities in the PRB increase, and residence times decrease, due to porosity reductions caused by accumulation of minerals in the pore space. When fouling becomes extensive, bypassing and reductions in flow rate in the PRB occur.
Arsenic in Glacial Aquifers: Sources and Geochemical Controls
Authors: Kelly Walton R. , Holm Thomas R. , Wilson Steven D. , Roadcap George S.
Published: July 2005

A total of 176 wells in sand‐and‐gravel glacial aquifers in central Illinois were sampled for arsenic (As) and other chemical parameters. The results were combined with archived and published data from several hundred well samples to determine potential sources of As and the potential geochemical controls on its solubility and mobility. There was considerable spatial variability in the As concentrations. High concentrations were confined to areas smaller than 1 km in diameter. Arsenic and well depth were uncorrelated. Arsenic solubility appeared to be controlled by oxidation‐reduction (redox) conditions, especially the presence of organic matter. Geochemical conditions in the aquifers are typically reducing, but only in the most reducing water does As accumulate in solution. In wells in which total organic carbon (TOC) was below 2 mg/L and sulfate (SO42−) was present, As concentrations were low or below the detection limit (0.5 μg/L). Arsenic concentrations >10 μg/L were almost always found in wells where TOC was >2 mg/L and SO42− was absent or at low concentrations, indicating post–SO42−reducing conditions. Iron (Fe) is common in the aquifer sediments, and Fe oxide reduction appears to be occurring throughout the aquifers. Arsenic is likely released from the solid phase as Fe oxide is reduced.
Estimating Aquifer Transmissivity from Specific Capacity Using MATLAB
Authors: McLin Stephen G.
Published: July 2005

Historically, specific capacity information has been used to calculate aquifer transmissivity when pumping test data are unavailable. This paper presents a simple computer program written in the MATLAB programming language that estimates transmissivity from specific capacity data while correcting for aquifer partial penetration and well efficiency. The program graphically plots transmissivity as a function of these factors so that the user can visually estimate their relative importance in a particular application. The program is compatible with any computer operating system running MATLAB, including Windows, Macintosh OS, Linux, and Unix. Two simple examples illustrate program usage.
FKF1 F-Box Protein Mediates Cyclic Degradation of a Repressor of
CONSTANS
in
Arabidopsis
Authors: Imaizumi Takato , Schultz Thomas F. , Harmon Frank G. , Ho Lindsey A. , Kay Steve A.
Published: July 2005

The temporal control of CONSTANS (CO) expression and activity is a key mechanism in photoperiodic flowering in
Arabidopsis
. FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) protein regulates
CO
transcription, although the molecular mechanism is unknown. We demonstrate here that FKF1 controls the stability of a Dof transcription factor, CYCLING DOF FACTOR 1 (CDF1). FKF1 physically interacts with CDF1, and CDF1 protein is more stable in
fkf1
mutants. Plants with elevated levels of CDF1 flower late and have reduced expression of
CO. CDF1
and
CO
are expressed in the same tissues, and CDF1 binds to the
CO
promoter. Thus, FKF1 controls daily
CO
expression in part by degrading CDF1, a repressor of
CO
transcription.
Skeleton of
Euplectella
sp.: Structural Hierarchy from the Nanoscale to the Macroscale
Authors: Aizenberg Joanna , Weaver James C. , Thanawala Monica S. , Sundar Vikram C. , Morse Daniel E. , Fratzl Peter
Published: July 2005

Structural materials in nature exhibit remarkable designs with building blocks, often hierarchically arranged from the nanometer to the macroscopic length scales. We report on the structural properties of biosilica observed in the hexactinellid sponge
Euplectella
sp. Consolidated, nanometer-scaled silica spheres are arranged in well-defined microscopic concentric rings glued together by organic matrix to form laminated spicules. The assembly of these spicules into bundles, effected by the laminated silica-based cement, results in the formation of a macroscopic cylindrical square-lattice cagelike structure reinforced by diagonal ridges. The ensuing design overcomes the brittleness of its constituent material, glass, and shows outstanding mechanical rigidity and stability. The mechanical benefits of each of seven identified hierarchical levels and their comparison with common mechanical engineering strategies are discussed.
Resonating Valence-Bond Ground State in a Phenalenyl-Based Neutral Radical Conductor
Authors: Pal S. K. , Itkis M. E. , Tham F. S. , Reed R. W. , Oakley R. T. , Haddon R. C.
Published: July 2005

An organic material composed of neutral free radicals based on the spirobiphenalenyl system exhibits a room temperature conductivity of 0.3 siemens per centimeter and a high-symmetry crystal structure. It displays the temperature-independent Pauli paramagnetism characteristic of a metal with a magnetic susceptibility that implies a density of states at the Fermi level of 15.5 states per electron volt per mole. Extended Hückel calculations indicate that the solid is a three-dimensional organic metal with a band width of ∼0.5 electron volts. However, the compound shows activated conductivity (activation energy, 0.054 electron volts) and an optical energy gap of 0.34 electron volts. We argue that these apparently contradictory properties are best resolved in terms of the resonating valence-bond ground state originally suggested by Pauling, but with the modifications introduced by Anderson.
Functional Identification of Novel Genes Involved in the Glutathione-Independent Gentisate Pathway inCorynebacterium glutamicum
Authors: Shen Xi-Hui , Jiang Cheng-Ying , Huang Yan , Liu Zhi-Pei , Liu Shuang-Jiang
Published: July 2005

Corynebacterium glutamicumused gentisate and 3-hydroxybenzoate as its sole carbon and energy source for growth. By genome-wide data mining, a gene cluster designatedncg12918-ncg12923was proposed to encode putative proteins involved in gentisate/3-hydroxybenzoate pathway. Genes encoding gentisate 1,2-dioxygenase (ncg12920) and fumarylpyruvate hydrolase (ncg12919) were identified by cloning and expression of each gene inEscherichia coli. The gene ofncg12918encoding a hypothetical protein (Ncg12918) was proved to be essential for gentisate-3-hydroxybenzoate assimilation. Mutant strain RES167Δncg12918lost the ability to grow on gentisate or 3-hydroxybenzoate, but this ability could be restored inC. glutamicumupon the complementation with pXMJ19-ncg12918. Cloning and expression of thisncg12918gene inE. colishowed that Ncg12918 is a glutathione-independent maleylpyruvate isomerase. Upstream ofncg12920, the genesncg12921-ncg12923were located, which were essential for gentisate and/or 3-hydroxybenzoate catabolism. The Ncg12921 was able to up-regulate gentisate 1,2-dioxygenase, maleylpyruvate isomerase, and fumarylpyruvate hydrolase activities. The genesncg12922andncg12923were deduced to encode a gentisate transporter protein and a 3-hydroxybenzoate hydroxylase, respectively, and were essential for gentisate or 3-hydroxybenzoate assimilation. Based on the results obtained in this study, a GSH-independent gentisate pathway was proposed, and genes involved in this pathway were identified.
Phylogenetic Diversity and Specificity of Bacteria Closely Associated with
Alexandrium
spp. and Other Phytoplankton
Authors: Jasti Suresh , Sieracki Michael E. , Poulton Nicole J. , Giewat Michael W. , Rooney-Varga Juliette N.
Published: July 2005

While several studies have suggested that bacterium-phytoplankton interactions have the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at the species composition level. The objective of the current study was to determine whether there are specific associations between diverse phytoplankton and the bacteria that co-occur with them. We determined the phylogenetic diversity of bacterial assemblages associated with 10
Alexandrium
strains and representatives of the major taxonomic groups of phytoplankton in the Gulf of Maine. For this analysis we chose xenic phytoplankton cultures that (i) represented a broad taxonomic range, (ii) represented a broad geographic range for
Alexandrium
spp. isolates, (iii) grew under similar cultivation conditions, (iv) had a minimal length of time since the original isolation, and (v) had been isolated from a vegetative phytoplankton cell. 16S rRNA gene fragments of most
Bacteria
were amplified from DNA extracted from cultures and were analyzed by denaturing gradient gel electrophoresis and sequencing. A greater number of bacterial species were shared by different
Alexandrium
cultures, regardless of the geographic origin, than by
Alexandrium
species and nontoxic phytoplankton from the Gulf of Maine. In particular, members of the
Roseobacter
clade showed a higher degree of association with
Alexandrium
than with other bacterial groups, and many sequences matched sequences reported to be associated with other toxic dinoflagellates. These results provide evidence for specificity in bacterium-phytoplankton associations.
Seasonal Variation in Abundance of Total and Pathogenic
Vibrio parahaemolyticus
Bacteria in Oysters along the Southwest Coast of India
Authors: Deepanjali A. , Kumar H. Sanath , Karunasagar I. , Karunasagar I.
Published: July 2005

The seasonal abundance of
Vibrio parahaemolyticus
in oysters from two estuaries along the southwest coast of India was studied by colony hybridization using nonradioactive labeled oligonucleotide probes. The density of total
V. parahaemolyticus
bacteria was determined using a probe binding to the
tlh
(thermolabile hemolysin) gene, and the density of pathogenic
V. parahaemolyticus
bacteria was determined by using a probe binding to the
tdh
(thermostable direct hemolysin) gene. Furthermore, the prevalence of
V. parahaemolyticus
was studied by PCR amplification of the
toxR
,
tdh
, and
trh
genes. PCR was performed directly with oyster homogenates and also following enrichment in alkaline peptone water for 6 and 18 h.
V. parahaemolyticus
was detected in 93.87% of the samples, and the densities ranged from <10 to 10
4
organisms per g. Pathogenic
V. parahaemolyticus
could be detected in 5 of 49 samples (10.2%) by colony hybridization using the
tdh
probe and in 3 of 49 samples (6.1%) by PCR. Isolates from one of the samples belonged to the pandemic serotype O3:K6. Twenty-nine of the 49 samples analyzed (59.3%) were positive as determined by PCR for the presence of the
trh
gene in the enrichment broth media.
trh
-positive
V. parahaemolyticus
was frequently found in oysters from India.
Survey of Motile Microaerophilic Bacterial Morphotypes in the Oxygen Gradient above a Marine Sulfidic Sediment
Authors: Thar Roland , Fenchel Tom
Published: July 2005

Enrichment cultures for free-swimming microaerophilic bacteria were prepared from marine sulfidic sediment samples (Nivå Bay, Denmark). We observed nine different morphotypes; three of these morphotypes represented already-described species, i.e.,
Thiovulum majus
, “
Candidatus
Ovobacter propellens,” and an as-yet-unnamed large vibrioid bacterium. In addition, we observed several morphotypes of spirilla and one vibrioid morphotype. A common feature of all investigated bacteria was that they aggregated chemotactically at the oxic-anoxic interface, whereas preferred oxygen concentration were in the range of 1 to 10 μM. The motile behavior and flagellar dynamics are analyzed in detail with an emphasis on spirilla.
Growth and Population Dynamics of Anaerobic Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in a Continuous-Flow Bioreactor
Authors: Girguis Peter R. , Cozen Aaron E. , DeLong Edward F.
Published: July 2005

The consumption of methane in anoxic marine sediments is a biogeochemical phenomenon mediated by two archaeal groups (ANME-1 and ANME-2) that exist syntrophically with sulfate-reducing bacteria. These anaerobic methanotrophs have yet to be recovered in pure culture, and key aspects of their ecology and physiology remain poorly understood. To characterize the growth and physiology of these anaerobic methanotrophs and the syntrophic sulfate-reducing bacteria, we incubated marine sediments using an anoxic, continuous-flow bioreactor during two experiments at different advective porewater flow rates. We examined the growth kinetics of anaerobic methanotrophs and
Desulfosarcina
-like sulfate-reducing bacteria using quantitative PCR as a proxy for cell counts, and measured methane oxidation rates using membrane-inlet mass spectrometry. Our data show that the specific growth rates of ANME-1 and ANME-2 archaea differed in response to porewater flow rates. ANME-2 methanotrophs had the highest rates in lower-flow regimes (μ
ANME-2
= 0.167 · week
−1
), whereas ANME-1 methanotrophs had the highest rates in higher-flow regimes (μ
ANME-1
= 0.218 · week
−1
). In both incubations,
Desulfosarcina
-like sulfate-reducing bacterial growth rates were approximately 0.3 · week
−1
, and their growth dynamics suggested that sulfate-reducing bacterial growth might be facilitated by, but not dependent upon, an established anaerobic methanotrophic population. ANME-1 growth rates corroborate field observations that ANME-1 archaea flourish in higher-flow regimes. Our growth and methane oxidation rates jointly demonstrate that anaerobic methanotrophs are capable of attaining substantial growth over a range of environmental conditions used in these experiments, including relatively low methane partial pressures.
Enhanced Trehalose Production Improves Growth of
Escherichia coli
under Osmotic Stress
Authors: Purvis J. E. , Yomano L. P. , Ingram L. O.
Published: July 2005

The biosynthesis of trehalose has been previously shown to serve as an important osmoprotectant and stress protectant in
Escherichia coli
. Our results indicate that overproduction of trehalose (integrated
lacI
-P

tac

-
otsBA
) above the level produced by the native regulatory system can be used to increase the growth of
E. coli
in M9-2% glucose medium at 37°C to 41°C and to increase growth at 37°C in the presence of a variety of osmotic-stress agents (hexose sugars, inorganic salts, and pyruvate). Smaller improvements were noted with xylose and some fermentation products (ethanol and pyruvate). Based on these results, overproduction of trehalose may be a useful trait to include in biocatalysts engineered for commodity chemicals.