bluuebunny/crossref_metadata_2025 huggingface dataset:
Requiem for a Growth Machine
Authors: Whittemore Andrew H.
Published: November 2011

In the last quarter century, the city of Los Angeles has suffered a chronic housing shortage due to exclusive zoning policies tied to the rise of antigrowth advocates over developers as the prime determinants of land use policy. This article considers the history of two major land use reforms affecting the city of Los Angeles in the 1980s: the General Plan Zoning Code Consistency Program (GPZCP) and Proposition U. These reforms represented the decline of the growth machine in 1980s Los Angeles and demonstrate the viability of an antigrowth regime in a large, non-suburban jurisdiction. This shift has not necessarily led to more democratic planning in Los Angeles. The GPZCP and Proposition U instead represented the empowerment of new antigrowth elites at the expense of old capital-driven elites. This has been to the detriment of hopeful homeowners and renters seeking economic and social opportunities in the city of Los Angeles.
A new dependence parameter approach to improve the design of cluster randomized trials with binary outcomes
Authors: Crespi Catherine M , Wong Weng Kee , Wu Sheng
Published: November 2011

Background and Purpose Power and sample size calculations for cluster randomized trials require prediction of the degree of correlation that will be realized among outcomes of participants in the same cluster. This correlation is typically quantified as the intraclass correlation coefficient (ICC), defined as the Pearson correlation between two members of the same cluster or proportion of the total variance attributable to variance between clusters. It is widely known but perhaps not fully appreciated that for binary outcomes, the ICC is a function of outcome prevalence. Hence, the ICC and the outcome prevalence are intrinsically related, making the ICC poorly generalizable across study conditions and between studies with different outcome prevalences.

Methods We use a simple parametrization of the ICC that aims to isolate that part of the ICC that measures dependence among responses within a cluster from the outcome prevalence. We incorporate this parametrization into sample size calculations for cluster randomized trials and compare our method to the traditional approach using the ICC.

Results Our dependence parameter, R, may be less influenced by outcome prevalence and has an intuitive meaning that facilitates interpretation. Estimates of R from previous studies can be obtained using simple statistics. Comparison of methods showed that the traditional ICC approach to sample size determination tends to overpower studies under many scenarios, calling for more clusters than truly required.

Limitations The methods are developed for equal-sized clusters, whereas cluster size may vary in practice.

Conclusions The dependence parameter R is an alternative measure of dependence among binary outcomes in cluster randomized trials that has a number of advantages over the ICC.
Some methodological points to consider when performing systematic reviews in comparative effectiveness research
Authors: Berlin Jesse A , Cepeda M Soledad
Published: November 2011

Background The purpose of comparative effectiveness research (CER) is to assist consumers, clinicians, purchasers, and policy makers to make informed decisions that will improve health care at both the individual and population levels. There is an ongoing discussion as to what types of evidence are appropriate to inform CER and how best to interpret various forms of evidence.

Purpose The purpose of this article is primarily to highlight several interesting methodological issues in the conduct of CER reviews.

Methods We describe several key challenges related to randomized trials, with a particular focus on noninferiority studies, which include active comparators used to assess ‘assay sensitivity’ (defined below), and on the use of randomized studies to perform indirect comparisons between therapies. We touch briefly on the use of observational studies in CER, particularly because of the importance of observational studies in assessing infrequently occurring harms.

Results We argue that studies that may be perceived as unsuitable to address some CER questions may well be appropriate to address others. As an example, noninferiority studies (assuming they include an appropriate comparator at an appropriate dose), are sometimes discounted or excluded from consideration because of concerns that the sponsor’s incentive is to conduct a study that is biased toward showing no difference between the treatment groups. If the purpose of a systematic review of CER is to show superiority with respect to a purported benefit, including studies that may be biased toward equality of treatments would tend to underestimate the proposed benefit, that is, the bias works against the sponsor.

Limitations This is not a comprehensive review of all methodological issues related to CER, and we recognize that there may be dissenting opinions regarding some of the points we raise.

Conclusions In considering the use of systematic reviews, we believe it is sound advice to perform the head-to-head comparison when possible, in the relevant populations, using endpoints relevant to patients, caregivers, physicians, or payers. These endpoints should include patient-reported outcomes (e.g., symptoms), when relevant. Indirect comparisons and mixed treatment meta-analyses may be useful for simultaneously comparing multiple treatments, provided the assumptions underlying such analyses are plausible.
Transparency in the presentation of trial results may not increase patients’ trust in medical researchers
Authors: Mancini Julien , Genre Dominique , Dalenc Florence , Maylevin Françoise , Martin Anne-Laure , Viens Patrice , Julian-Reynier Claire
Published: November 2011

Background One of the expected benefits of sharing trial results with participants is that it may enhance trust in medical researchers (TMRs).

Purpose In a prospective study on a sample of clinical trial participants, we investigated the effect on the participants’ TMRs of providing final trial results to participants via the Internet.

Methods Participants in the FNCLCC-PACS04 trial (ClinicalTrials.gov Identifier: NCT00054587) were surveyed on average 6 years after enrollment, when the trial results were available. In the current study, they were randomized to receive (experimental group) or not to receive (control group) a letter informing them that the results of the trial could be consulted on a specific website. TMRs was measured before randomization and 6 months later using mailed self-administered questionnaires.

Results The response rate was 93% ( N = 107). TMRs remained unchanged in the control group (mean effect size = −0.06, 95% confidence interval (CI): −0.28 to 0.17, p = 0.617) but decreased in the experimental group (−0.30, 95% CI: −0.53 to −0.06, p = 0.015). However, the difference between the two effect sizes was not statistically significant ( p = 0.144).

Limitations The results obtained here on the disclosure of final trial results to breast cancer patients via the Internet cannot be generalized to all situations involving the disclosure of phase III randomized controlled trial results.

Conclusions Transparency is an ethical research requirement, but it may not enhance participants’ TMRs.
Simultaneous powering of forearm pronation and key pinch in tetraplegia using a single muscle-tendon unit
Authors: Fridén J. , Reinholdt C. , Gohritz A. , Peace W. J. , Ward S. R. , Lieber R. L.
Published: November 2011

This study clinically assessed the concept that both thumb flexion and forearm pronation can be restored by brachioradialis (BR)-to-flexor pollicis longus (FPL) tendon transfer if the BR is passed dorsal to the radius. Six patients [two women and four men, mean age 32.3 years (SD 4.9, range 23–56)] underwent BR-to-FPL transfer dorsal to the radius and through the interosseous membrane (IOM). Lateral key pinch strength and pronation range of motion (ROM) were measured 1 year after surgery. A group of six patients [two women and four men, mean age 31.2 years (SD 5.0, range 19–52)] who underwent traditional palmar BR-to-FPL was included for comparison. Postoperative active pronation was significantly greater in the dorsal transfer group compared to the palmar group [149 (SD 6) and 75 (SD 3), respectively] and pinch strength was similar in the two groups [1.28 (SD 0.16) kg and 1.20 (SD0.21) kg, respectively]. We conclude that it is feasible to reconstruct lateral key pinch and forearm pronation simultaneously using only the BR motor.
‘I am not at risk – typical tourists are’! Social comparison of risk in tourists
Authors: Larsen Svein , Brun Wibecke
Published: November 2011

Aim: The presented research aims to study the relationship between judgements of risks to oneself as a tourist as compared to risks to ‘typical tourists’, ‘average tourists’ and ‘typical tourist from your home country’.

Methods: Altogether, 1,892 tourists visiting Norway (summer 2010) filled in a questionnaire on aspects of being a tourist. Respondents were randomly assigned to one of four groups. Group 1 was asked about risk to themselves; Group 2 was asked to indicate their thoughts about ‘risk to typical tourists’; Group 3 indicated risks for ‘average tourists’; and Group 4 was asked about risks for typical tourists from their home country.

Results: Results show that all risks were judged to be low, but significantly higher risks were attributed to the typical and average tourist than to ‘self’.

Conclusions: The results are interpreted in terms of social cognitive processes such as the ‘optimistic bias’.
Nutritional and health benefits as the determinants of food choice in Polish consumers
Authors: Rejman Krystyna , Kasperska Aleksandra
Published: November 2011

Aims: The aim of the study was to find out how nutritional value, health benefits of foods and relevant information on food labels affect consumers’ dietary choices and shopping behaviour.

Methods: Data were collected using a questionnaire on a sample of 200 adult consumers, inhabitants of Poland’s capital city. The majority were young, well-educated and almost equally divided into four income groups.

Results: The study showed that only 12% of the consumers never took into consideration the health impact of purchased foods, while 42% were deeply aware of it. This behaviour was the only one significantly influenced by consumer income, while the others were determined by education level and gender. Consumers revealed that food labels had a rather low influence on purchase decisions. Half of them always looked for obligatory information such as brand, producer, expiry date or price, and only 2% of the sample never looked. In contrast, only 3%–6% always checked the list of ingredients, nutrition facts, and nutritional or health claims, while one third of the group did not. Consumers looking for this information were interested mostly in energy value, total fat content and presence of artificial additives. The smallest attention was paid to saturated fat and trans-fatty acid content. This behaviour was in line with the finding that understanding the impact on health of these fat components was generally low. Health claims perception differed depending on the type of claim: the highest regarded was lowering cholesterol level, followed by ‘natural product’ and boosting immunity. However only one third of the group declared that health claims influenced their purchase decision and the same proportion negated the impact. The perception of labelling schemes (e.g. GDA, My choice) was even lower, so this information had very limited influence on food choice.

Conclusions: Nutritional and healthy values of foods were found to be rather weak determinants of purchase decision and food choice. Consumers should have better knowledge of food–nutrition–health linkages and different labelling formats, otherwise nutritional marketing tools are not useful for them in making healthy, informed food choices.
Relationship between cooking habits and skills and Mediterranean diet in a sample of Portuguese adolescents
Authors: da Rocha Leal Fernanda Maria , de Oliveira Bruno Miguel Paz Mendes , Pereira Sara Simões Rodrigues
Published: November 2011

Aims: To assess the cooking habits and skills of adolescents and its relation to Mediterranean diet adherence.

Methods: Adolescents ( N = 390) from the seventh, eighth and ninth grades in a school from a semi-urban region in northern Portugal were asked to fill in a questionnaire. The questionnaire assessed self-reported cooking habits and skills, for example enjoying and knowing how to cook and wanting to cook and learn more. Answers were taken on a scale from 0 to 5, 0 being ‘no’ and 5 being ‘very much’. Learning sources, cooking frequency, and confidence in cooking ten particular foods were also assessed using the following answers: ‘no, never’, ‘yes, with help from family/friends’, ‘yes, all by myself’. Adherence to Mediterranean diet was evaluated using the KIDMED index.

Results: Adolescents who said that they cooked, did so usually between one and four times a month (56.2%). A high proportion of respondents had never cooked vegetables (57%), fish (51%) and soup (49%). Girls were more likely to have cooked foods listed in the questionnaire ( p ≤ .002). Adolescents who did not know how to cook (8.7%) stated that the main reasons were that they had someone to cook for them (47%) and had no interest (35%). Those who knew how to cook mainly stated that they had learnt from their family (87.9%) and by themselves (7.9%). Most of our sample wanted ‘to learn how to cook better’ ( M = 3.8, SD = 1.5), preferably with family/friends (82%) or by taking culinary courses (10%). The KIDMED index was poor for 7.2% of the sample, average for 50.8% and good for 42.1%. Adolescents with higher KIDMED scores were younger ( p = .025), knew how to cook better ( p < .001), cooked more often ( p < .001), enjoyed cooking ( p < .001), would like to cook more frequently ( p < .001), and would like to learn how to cook better ( p < .001).

Conclusion: Almost one in every ten adolescents did not know how to cook. Vegetables, fish and soup were found to be foods that nearly half of the adolescents had never cooked. Female adolescents were more involved in cooking than males. Better cooking habits and skills were positively related with adolescents’ adherence to the Mediterranean diet, which reinforces the idea that teaching cooking skills may have a positive impact in future food choice.
Forty days of free school meals as a tool for introducing market-based healthy school meal systems in 35 Danish schools
Authors: Brinck N , Hansen M Weinreich , Kristensen N Heine
Published: November 2011

Aims: When approaching school meal systems, different concepts can guide the design of the food preparation and serving activities. This paper presents a government-planned intervention concept of 40 days of free school meals. The argument behind this intervention was to kick-start the implementation of healthy school meal systems in Danish schools. This paper argues that the initiative (in reality) invited the establishment of a service system concept, which dominated the initiative and led to a lack of involvement of important key players needed in health promotion.

Methods: The method used for data collection was semi-structured, qualitative interviews.

Results: The main results from a systematic examination of the 35 participating schools show that the systems were mainly organized with external suppliers, and only a few of the 35 schools succeeded in establishing a user-paid school meal system afterwards.

Conclusions: The established meal systems contained a lack of embedding factors, which is pointed to as one of the main challenges to a user-financed school meal system. The experiences of these 35 participating schools show that a period of free school meals is not a sustainable tool for achieving the goal of establishing new, healthy and user-paid school meals.
First See, Then Nod
Authors: Wennekers Annemarie M. , Holland Rob W. , Wigboldus Daniël H. J. , Knippenberg Ad van
Published: November 2011

Head nodding and shaking are bodily signals of approval and disapproval, respectively. Previous research has shown that these movements can be used to shape attitudes by means of evaluative conditioning. In the present experiment, the authors studied the conditions under which evaluative conditioning with head movements can alter social attitudes. Specifically, the authors investigated whether the evaluative conditioning effect depends on the order in which the target stimulus and the head movement are presented. The results showed that repeated coupling of head nodding with out-group names reduced negative implicit associations with this out-group only when the head nodding movement followed the target name. No effects were found when the movement preceded the name in the conditioning procedure. The authors conclude that embodied evaluative conditioning effects are constrained to a sequence of the target stimulus and head movement that corresponds to the natural temporal script in which the stimulus precedes the evaluative embodied reaction.
Radiolabeled antibodies directed at CD45 for conditioning prior to allogeneic transplantation in acute myeloid leukemia and myelodysplastic syndrome
Authors: Orozco Johnnie J. , Zeller Jill , Pagel John M.
Published: November 2011

While allogeneic hematopoietic cell transplantation (HCT) may offer the best chance of cure for patients suffering from aggressive hematological malignancies such as acute myeloid leukemia, acute lymphoblastic leukemia, and myelodysplastic syndrome, successful outcomes for the subgroup of patients with high-risk disease remain disappointing and lag behind those of lower-risk patients. Because relatively high rates of relapse are an important contributor to these poor outcomes, efforts have explored approaches to increase the cytotoxic effects of treatment. Relapse rates have been shown to improve with the addition of increased doses of total body irradiation (TBI) and/or the introduction of additional chemotherapy to a HCT conditioning regimen. However, the increase in TBI dose and/or additional chemotherapy has also been associated with a significant increase in life-threatening toxicities, resulting in no change in overall survival. Radioimmunotherapy (RIT) has been employed as an adjunct to HCT where targeted delivery of radiation may allow for further escalation of therapy to reduce relapse with minimal toxicity. In this review we describe these efforts, including the benefits of escalating the dose of radiation to sites of hematologic disease prior to HCT, the various cellular targets for antibody-mediated delivery of radiation, as well as the rationale for incorporation of various radionuclides such as alpha emitters and beta emitters into the preparative regimen prior to HCT. Lastly, newer novel approaches such as pretargeted RIT (PRIT) are described as a method to further increase delivery of targeted radiation to hematological tissues while sparing noninvolved organs.
Anthracycline dose intensification in young adults with acute myeloid leukemia
Authors: Padron Eric , Fernandez Hugo
Published: November 2011

The initial treatment for acute myeloid leukemia (AML) has remained largely unchanged for nearly 40 years. Our growing understanding of the molecular pathology of AML has resulted in improved measures to risk stratify patients by recurrent cytogenetic and molecular abnormalities without marked advancement in its initial treatment. The most common regimen consists of a 3-day course of an anthracycline and a 7-day infusion of cytarabine. This regimen has been employed across the globe in various iterations for many years with modest improvements in results yet this remains the first choice for the treatment of younger adults with AML. Despite this, the chemotherapeutic agents in this regimen are only now being fully understood. Recent evidence has suggested that dose intensification of anthracycline in young adults has a significant survival benefit. In this paper we review the evidence behind the use of anthracyclines in the initial induction of AML in younger adults focusing on the choice and dose of this long used drug combination.
Voice Over the Internet Protocol as a Medium for Delivering Reading Intervention
Authors: Wright Craig , Conlon Elizabeth G. , Wright Michalle
Published: November 2011

Voice Over the Internet Protocol (VoIP) holds promise as a platform by which services can be delivered to students in rural and remote regions who have reading difficulties. VoIP is an Internet-based protocol that allows two or more individuals to videoconference from remote locations. This study used a single-case research design to investigate whether VoIP would produce significant gains in reading ability in BM, a 10-year-old with long-standing word-level reading problems. BM was provided with a theoretically motivated reading intervention 4 times weekly. The intervention was delivered remotely using the Apple iChat software. Substantial growth in regular- and nonword reading covaried with onset and removal of treatment. Treatment gains were maintained at 10-week follow-up. Meaningful gains were also seen in text-reading accuracy and reading comprehension. VoIP-based instruction represents an important avenue for future research and is a teaching method that holds much promise for rural and remote students.
Enucleation of human erythroblasts involves non-muscle myosin IIB
Authors: Ubukawa Kumi , Guo Yong-Mei , Takahashi Masayuki , Hirokawa Makoto , Michishita Yoshihiro , Nara Miho , Tagawa Hiroyuki , Takahashi Naoto , Komatsuda Atsushi , Nunomura Wataru , Takakuwa Yuichi , Sawada Kenichi
Published: November 2011

Mammalian erythroblasts undergo enucleation, a process thought to be similar to cytokinesis. Although an assemblage of actin, non-muscle myosin II, and several other proteins is crucial for proper cytokinesis, the role of non-muscle myosin II in enucleation remains unclear. In this study, we investigated the effect of various cell-division inhibitors on cytokinesis and enucleation. For this purpose, we used human colony-forming unit-erythroid (CFU-E) and mature erythroblasts generated from purified CD34+ cells as target cells for cytokinesis and enucleation assay, respectively. Here we show that the inhibition of myosin by blebbistatin, an inhibitor of non-muscle myosin II ATPase, blocks both cell division and enucleation, which suggests that non-muscle myosin II plays an essential role not only in cytokinesis but also in enucleation. When the function of non-muscle myosin heavy chain (NMHC) IIA or IIB was inhibited by an exogenous expression of myosin rod fragment, myosin IIA or IIB, each rod fragment blocked the proliferation of CFU-E but only the rod fragment for IIB inhibited the enucleation of mature erythroblasts. These data indicate that NMHC IIB among the isoforms is involved in the enucleation of human erythroblasts.
Myosin II activity dependent and independent vinculin recruitment to the sites of E-cadherin-mediated cell-cell adhesion
Authors: Sumida Grant M , Tomita Tyler M , Shih Wenting , Yamada Soichiro
Published: November 2011

Background

Maintaining proper adhesion between neighboring cells depends on the ability of cells to mechanically respond to tension at cell-cell junctions through the actin cytoskeleton. Thus, identifying the molecules involved in responding to cell tension would provide insight into the maintenance, regulation, and breakdown of cell-cell junctions during various biological processes. Vinculin, an actin-binding protein that associates with the cadherin complex, is recruited to cell-cell contacts under increased tension in a myosin II-dependent manner. However, the precise role of vinculin at force-bearing cell-cell junctions and how myosin II activity alters the recruitment of vinculin at quiescent cell-cell contacts have not been demonstrated.

Results

We generated vinculin knockdown cells using shRNA specific to vinculin and MDCK epithelial cells. These vinculin-deficient MDCK cells form smaller cell clusters in a suspension than wild-type cells. In wound healing assays, GFP-vinculin accumulated at cell-cell junctions along the wound edge while vinculin-deficient cells displayed a slower wound closure rate compared to vinculin-expressing cells. In the presence of blebbistatin (myosin II inhibitor), vinculin localization at quiescent cell-cell contacts was unaffected while in the presence of jasplakinolide (F-actin stabilizer), vinculin recruitment increased in mature MDCK cell monolayers.

Conclusion

These results demonstrate that vinculin plays an active role at adherens junctions under increased tension at cell-cell contacts where vinculin recruitment occurs in a myosin II activity-dependent manner, whereas vinculin recruitment to the quiescent cell-cell junctions depends on F-actin stabilization.
Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation
Authors: Schröder Jasmin , Maus Irena , Trost Eva , Tauch Andreas
Published: November 2011

Background

Corynebacterium variabile is part of the complex microflora on the surface of smear-ripened cheeses and contributes to the development of flavor and textural properties during cheese ripening. Still little is known about the metabolic processes and microbial interactions during the production of smear-ripened cheeses. Therefore, the gene repertoire contributing to the lifestyle of the cheese isolate C. variabile DSM 44702 was deduced from the complete genome sequence to get a better understanding of this industrial process.

Results

The chromosome of C. variabile DSM 44702 is composed of 3, 433, 007 bp and contains 3, 071 protein-coding regions. A comparative analysis of this gene repertoire with that of other corynebacteria detected 1, 534 predicted genes to be specific for the cheese isolate. These genes might contribute to distinct metabolic capabilities of C. variabile, as several of them are associated with metabolic functions in cheese habitats by playing roles in the utilization of alternative carbon and sulphur sources, in amino acid metabolism, and fatty acid degradation. Relevant C. variabile genes confer the capability to catabolize gluconate, lactate, propionate, taurine, and gamma-aminobutyric acid and to utilize external caseins. In addition, C. variabile is equipped with several siderophore biosynthesis gene clusters for iron acquisition and an exceptional repertoire of AraC-regulated iron uptake systems. Moreover, C. variabile can produce acetoin, butanediol, and methanethiol, which are important flavor compounds in smear-ripened cheeses.

Conclusions

The genome sequence of C. variabile provides detailed insights into the distinct metabolic features of this bacterium, implying a strong adaption to the iron-depleted cheese surface habitat. By combining in silico data obtained from the genome annotation with previous experimental knowledge, occasional observations on genes that are involved in the complex metabolic capacity of C. variabile were integrated into a global view on the lifestyle of this species.
Hakai reduces cell-substratum adhesion and increases epithelial cell invasion
Authors: Rodríguez-Rigueiro Teresa , Valladares-Ayerbes Manuel , Haz-Conde Mar , Aparicio Luis A , Figueroa Angélica
Published: November 2011

Background

The dynamic regulation of cell-cell adhesions is crucial for developmental processes, including tissue formation, differentiation and motility. Adherens junctions are important components of the junctional complex between cells and are necessary for maintaining cell homeostasis and normal tissue architecture. E-cadherin is the prototype and best-characterized protein member of adherens junctions in mammalian epithelial cells. Regarded as a tumour suppressor, E-cadherin loss is associated with poor prognosis in carcinoma. The E3 ubiquitin-ligase Hakai was the first reported posttranslational regulator of the E-cadherin complex. Hakai specifically targetted E-cadherin for internalization and degradation and thereby lowered epithelial cell-cell contact. Hakai was also implicated in controlling proliferation, and promoted cancer-related gene expression by increasing the binding of RNA-binding protein PSF to RNAs encoding oncogenic proteins. We sought to investigate the possible implication of Hakai in cell-substratum adhesions and invasion in epithelial cells.

Methods

Parental MDCK cells and MDCK cells stably overexpressing Hakai were used to analyse cell-substratum adhesion and invasion capabilities. Western blot and immunofluoresecence analyses were performed to assess the roles of Paxillin, FAK and Vinculin in cell-substratum adhesion. The role of the proteasome in controlling cell-substratum adhesion was studied using two proteasome inhibitors, lactacystin and MG132. To study the molecular mechanisms controlling Paxillin expression, MDCK cells expressing E-cadherin shRNA in a tetracycline-inducible manner was employed.

Results

Here, we present evidence that implicate Hakai in reducing cell-substratum adhesion and increasing epithelial cell invasion, two hallmark features of cancer progression and metastasis. Paxillin, an important protein component of the cell-matrix adhesion, was completely absent from focal adhesions and focal contacts in Hakai-overexpressing MDCK cells. The expression of Paxillin was found to be regulated by a proteasome-independent mechanism, possibly due to the decreased abundance of E-cadherin.

Conclusions

Taken together, these results suggest that Hakai may be involved in two hallmark aspects of tumour progression, the lowering cell-substratum adhesion and the enhancement of cell invasion.
New biotechnological perspectives of a NADH oxidase variant from Thermus thermophilus HB27 as NAD+-recycling enzyme
Authors: Rocha-Martín Javier , Vega Daniel , Bolivar Juan M , Godoy Cesar A , Hidalgo Aurelio , Berenguer José , Guisán José M , López-Gallego Fernando
Published: November 2011

Background

The number of biotransformations that use nicotinamide recycling systems is exponentially growing. For this reason one of the current challenges in biocatalysis is to develop and optimize more simple and efficient cofactor recycling systems. One promising approach to regenerate NAD+ pools is the use of NADH-oxidases that reduce oxygen to hydrogen peroxide while oxidizing NADH to NAD+. This class of enzymes may be applied to asymmetric reduction of prochiral substrates in order to obtain enantiopure compounds.

Results

The NADH-oxidase (NOX) presented here is a flavoenzyme which needs exogenous FAD or FMN to reach its maximum velocity. Interestingly, this enzyme is 6-fold hyperactivated by incubation at high temperatures (80°C) under limiting concentrations of flavin cofactor, a change that remains stable even at low temperatures (37°C). The hyperactivated form presented a high specific activity (37.5 U/mg) at low temperatures despite isolation from a thermophile source. Immobilization of NOX onto agarose activated with glyoxyl groups yielded the most stable enzyme preparation (6-fold more stable than the hyperactivated soluble enzyme). The immobilized derivative was able to be reactivated under physiological conditions after inactivation by high solvent concentrations. The inactivation/reactivation cycle could be repeated at least three times, recovering full NOX activity in all cases after the reactivation step. This immobilized catalyst is presented as a recycling partner for a thermophile alcohol dehydrogenase in order to perform the kinetic resolution secondary alcohols.

Conclusion

We have designed, developed and characterized a heterogeneous and robust biocatalyst which has been used as recycling partner in the kinetic resolution of rac-1-phenylethanol. The high stability along with its capability to be reactivated makes this biocatalyst highly re-useable for cofactor recycling in redox biotransformations.
Protein trafficking, ergosterol biosynthesis and membrane physics impact recombinant protein secretion in Pichia pastoris
Authors: Baumann Kristin , Adelantado Núria , Lang Christine , Mattanovich Diethard , Ferrer Pau
Published: November 2011

Background

The increasing availability of 'omics' databases provide important platforms for yeast engineering strategies since they offer a lot of information on the physiology of the cells under diverse growth conditions, including environmental stresses. Notably, only a few of these approaches have considered a performance under recombinant protein production conditions. Recently, we have identified a beneficial effect of low oxygen availability on the expression of a human Fab fragment in Pichia pastoris. Transcriptional analysis and data mining allowed for the selection of potential targets for strain improvement. A first selection of these candidates has been evaluated as recombinant protein secretion enhancers.

Results

Based on previous transcriptomics analyses, we selected 8 genes for co-expression in the P. pastoris strain already secreting a recombinant Fab fragment. Notably, WSC4 (which is involved in trafficking through the ER) has been identified as a novel potential target gene for strain improvement, with up to a 1.2-fold increase of product yield in shake flask cultures. A further transcriptomics-based strategy to modify the yeast secretion system was focused on the ergosterol pathway, an aerobic process strongly affected by oxygen depletion. By specifically partially inhibiting ergosterol synthesis with the antifungal agent fluconazole (inhibiting Erg11p), we tried to mimic the hypoxic conditions, in which the cellular ergosterol content was significantly decreased. This strategy led to an improved Fab yield (2-fold) without impairing cellular growth. Since ergosterol shortage provokes alterations in the plasma membrane composition, an important role of this cellular structure in protein secretion is suggested. This hypothesis was additionally supported by the fact that the addition of non-ionic surfactants also enhanced Fab secretion.

Conclusions

The current study presents a systems biotechnology-based strategy for the engineering of the industrially important yeast P. pastoris combining the use of host specific DNA microarray technologies and physiological studies under well defined environmental conditions. Such studies allowed for the identification of novel targets related with protein trafficking and ergosterol biosynthesis for improved recombinant protein production. Nevertheless, further studies will be required to elucidate the precise mechanisms whereby membrane biogenesis and composition impact on protein secretion in P. pastoris.
Mesenchymal stem cells as carriers and amplifiers in CRAd delivery to tumors
Authors: Xia Xi , Ji Teng , Chen Pingbo , Li Xiao , Fang Yong , Gao Qinglei , Liao Shujie , You Lanying , Xu Hongbin , Ma Quanfu , Wu Peng , Hu Wencheng , Wu Mingfu , Cao Li , Li Kezhen , Weng Yanjie , Han Zhiqiang , Wei Junchen , Liu Ronghua , Wang Shixuan , Xu Gang , Wang Daowen , Zhou Jianfeng , Ma Ding
Published: November 2011

Background

Mesenchymal stem cells (MSCs) have been considered to be the attractive vehicles for delivering therapeutic agents toward various tumor diseases. This study was to explore the distribution pattern, kinetic delivery of adenovirus, and therapeutic efficacy of the MSC loading of E1A mutant conditionally replicative adenovirus Adv-Stat3(-) which selectively replicated and expressed high levels of anti-sense Stat3 complementary DNA in breast cancer and melanoma cells.

Methods

We assessed the release ability of conditionally replicative adenovirus (CRAd) from MSC using crystal violet staining, TCID50 assay, and quantitative PCR. In vitro killing competence of MSCs carrying Adv-Stat3(-) toward breast cancer and melanoma was performed using co-culture system of transwell plates. We examined tumor tropism of MSC by Prussian blue staining and immunofluorescence. In vivo killing competence of MSCs carrying Adv-Stat3(-) toward breast tumor was analyzed by comparison of tumor volumes and survival periods.

Results

Adv-Stat3(-) amplified in MSCs and were released 4 days after infection. MSCs carrying Adv-Stat3(-) caused viral amplification, depletion of Stat3 and its downstream proteins, and led to significant apoptosis in breast cancer and melanoma cell lines. In vivo experiments confirmed the preferential localization of MSCs in the tumor periphery 24 hours after tail vein injection, and this localization was mainly detected in the tumor parenchyma after 72 hours. Intravenous injection of MSCs carrying Adv-Stat3(-) suppressed the Stat3 pathway, down-regulated Ki67 expression, and recruited CD11b-positive cells in the local tumor, inhibiting tumor growth and increasing the survival of tumor-bearing mice.

Conclusions

These results indicate that MSCs migrate to the tumor site in a time-dependent manner and could be an effective platform for the targeted delivery of CRAd and the amplification of tumor killing effects.
Banach operator pairs and common fixed points in modular function spaces
Authors: Hussain N , Khamsi MA , Latif A
Published: November 2011

In this article, we introduce the concept of a Banach operator pair in the setting of modular function spaces. We prove some common fixed point results for such type of operators satisfying a more general condition of nonexpansiveness. We also establish a version of the well-known De Marr's theorem for an arbitrary family of symmetric Banach operator pairs in modular function spaces without Δ2-condition.

MSC(2000)

primary 06F30; 47H09; secondary 46B20; 47E10; 47H10.
Effects of 28 days of resistance exercise while consuming commercially available pre- and post-workout supplements, NO-Shotgun® and NO-Synthesize® on body composition, muscle strength and mass, markers of protein synthesis, and clinical safety markers in males
Authors: Spillane Mike , Schwarz Neil , Leddy Sarah , Correa Tracie , Minter Melodie , Longoria Victoria , Willoughby Darryn S
Published: November 2011

Purpose

The effects of 28 days of heavy resistance training while ingesting the pre- and post-workout supplements, NO-Shotgun® and NO-Synthesize® were determined on body composition, muscle strength and mass, markers of protein synthesis, and clinical safety markers.

Methods

Nineteen non-resistance-trained males participated in a resistance training program 4 times/week for 28 days while either ingesting 27 g/day of carbohydrate (CARB) or NO-Shotgun® 30 min pre-exercise and 27 g/day of carbohydrate or NO- Synthesize® 30 min post-exercise (NOSS). Data were analyzed with separate 2 × 2 ANOVA (p < 0.05).

Results

Total body mass was increased in both groups (p = 0.001), but not different between groups. Fat mass was unchanged with CARB, but NOSS decreased fat mass (p = 0.026). Both groups increased fat-free mass (p = 0.001); however, the increases were greater with NOSS (p = 0.023). NOSS underwent greater increases in upper-body (p = 0.023) and lower-body (p = 0.035) strength than CARB. Myofibrillar protein significantly increased in both groups (p = 0.041), with NOSS being greater than CARB (p = 0.049). All of the MHC isoforms were significantly increased in both groups; however, NOSS was greater than CARB for MHC 1 (p = 0.013) and MHC 2A (p = 0.046). All of the myogenic regulatory factors were significantly increased in both groups; however, NOSS was greater than CARB for Myo-D (p = 0.038) and MRF-4 (p = 0.001). For the whole blood and serum clinical chemistry markers, all variables remained within normal clinical ranges.

Conclusions

Heavy resistance training for 28 days, with NO-Shotgun® and NO-Synthesize® ingested before and after exercise, respectively, significantly improved body composition and increased muscle mass and performance without abnormally impacting any of the clinical chemistry markers.
Strong nuclear EGFR expression in colorectal carcinomas is associated with cyclin-D1 but not with gene EGFR amplification
Authors: Dekanić Andrea , Dobrila Dintinjan Renata , Budisavljević Ivana , Pećanić Sanja , Žuvić Butorac Marta , Jonjić Nives
Published: November 2011

Background

Prognostic and predictive significance of epidermal growth factor receptor (EGFR) in colorectal carcinomas (CRCs) is still controversial. The aim of the present study was to explore and correlate membrane and nuclear EGFR and cyclin-D1 protein expression with EGFR gene status of tumor cells.

Methods

Immunohistochemical and FISH analysis was performed on 135 archival formalin fixed and paraffin embedded CRCs.

Results

Strong membrane and strong nuclear EGFR staining was detected in 16% and 57% of cases, respectively, and strong cyclin-D1 expression in 57% samples. Gene EGFR amplification was identified in 5.9% and polysomy in 7.4% of cases, while 87% showed no EGFR gene changes. A statistically significant difference was only found between tumor grade and expression of membrane EGFR, while nuclear EGFR and cyclin-D1 expression was not associated with the clinicopathologic characteristics analyzed. Tumor cells displaying gene amplification and strong protein membrane EGFR expression overlapped, while EGFR gene status showed no correlation with nuclear EGFR and cyclin-D1. There was no association between membrane EGFR and cyclin-D1, whereas nuclear EGFR expression was strongly related to cyclin-D1 expression.

Conclusions

Study results revealed heterogeneity among CRCs, which could have a predictive value by identifying biologically and probably clinically different subsets of tumors with the possibly diverse response to anti-EGFR therapies.
Planning analysis for locally advanced lung cancer: dosimetric and efficiency comparisons between intensity-modulated radiotherapy (IMRT), single-arc/partial-arc volumetric modulated arc therapy (SA/PA-VMAT)
Authors: Jiang Xiaoqin , Li Tao , Liu Yongmei , Zhou Lin , Xu Yong , Zhou Xiaojuan , Gong Youling
Published: November 2011

Purpose

To analyze the differences between the intensity-modulated radiotherapy (IMRT), single/partial-arc volumetric modulated arc therapy (SA/PA-VMAT) techniques in treatment planning for locally advanced lung cancer.

Materials and methods

12 patients were retrospectively studied. In each patient's case, several parameters were analyzed based on the dose-volume histograms (DVH) of the IMRT, SA/PA-VMAT plans respectively. Also, each plan was delivered to a phantom for time comparison.

Results

The SA-VMAT plans showed the superior target dose coverage, although the minimum/mean/maximum doses to the target were similar. For the total and contralateral lungs, the higher V5/10, lower V20/30 and mean lung dose (MLD) were observed in the SA/PA-VMAT plans (p < 0.05, respectively). The PA-VMAT technique improves the dose sparing (V20, V30 and MLD) of the controlateral lung more notably, comparing to those parameters of the IMRT and SA-VMAT plans respectively. The delivered monitor units (MUs) and treatment times were reduced significantly with VMAT plans, especially PA-VMAT plans (for MUs: mean 458.3 vs. 439.2 vs. 435.7 MUs, p < 0.05 and for treatment time: mean 13.7 vs. 10.6 vs. 6.4 minutes, p < 0.01).

Conclusions

The SA-VMAT technique achieves highly conformal dose distribution to the target. Comparing to the IMRT plans, the higher V5/10, lower V20/30 and MLD were observed in the total and contralateral lungs in the VMAT plans, especially in the PA-VMAT plans. The SA/PA-VMAT plans also reduced treatment time with more efficient dose delivering. But the clinical benefit of the VMAT technique for locally advanced lung cancer needs further investigations.
The plasticity of TGF-βsignaling
Authors: Cellière Geraldine , Fengos Georgios , Hervé Marianne , Iber Dagmar
Published: November 2011

Background

The family of TGF-βligands is large and its members are involved in many different signaling processes. These signaling processes strongly differ in type with TGF-βligands eliciting both sustained or transient responses. Members of the TGF-βfamily can also act as morphogen and cellular responses would then be expected to provide a direct read-out of the extracellular ligand concentration. A number of different models have been proposed to reconcile these different behaviours. We were interested to define the set of minimal modifications that are required to change the type of signal processing in the TGF-βsignaling network.

Results

To define the key aspects for signaling plasticity we focused on the core of the TGF-βsignaling network. With the help of a parameter screen we identified ranges of kinetic parameters and protein concentrations that give rise to transient, sustained, or oscillatory responses to constant stimuli, as well as those parameter ranges that enable a proportional response to time-varying ligand concentrations (as expected in the read-out of morphogens). A combination of a strong negative feedback and fast shuttling to the nucleus biases signaling to a transient rather than a sustained response, while oscillations were obtained if ligand binding to the receptor is weak and the turn-over of the I-Smad is fast. A proportional read-out required inefficient receptor activation in addition to a low affinity of receptor-ligand binding. We find that targeted modification of single parameters suffices to alter the response type. The intensity of a constant signal (i.e. the ligand concentration), on the other hand, affected only the strength but not the type of the response.

Conclusions

The architecture of the TGF-βpathway enables the observed signaling plasticity. The observed range of signaling outputs to TGF-βligand in different cell types and under different conditions can be explained with differences in cellular protein concentrations and with changes in effective rate constants due to cross-talk with other signaling pathways. It will be interesting to uncover the exact cellular differences as well as the details of the cross-talks in future work.
A fast modeling method to solve Maxwell's equations in 1D layered biaxial anisotropic medium
Authors: Davydycheva Sofia , Wang Tsili
Published: November 2011

A fast 1D electromagnetic modeling method has been developed and tested. It allows simulating triaxial responses of induction and propagation resistivity logging tools for both logging-while-drilling and wireline applications. An important new feature of the method is its ability to model resistivity tool responses in 1D biaxial anisotropic medium, whose anisotropy tensor has up to three different principal values. This feature is particularly useful to evaluate fractured formations. A few possible implementations of the method have been suggested. The modeling code has been extensively tested versus three other independent modeling methods. The new method demonstrates a high sensitivity of transverse and cross couplings of triaxial tensor measurement to all three principal values of the conductivity tensor.
Time-reverse imaging with limited S-wave velocity model information
Authors: Steiner Brian , Saenger Erik H. , Schmalholz Stefan M.
Published: November 2011

Time-reverse imaging is a wave propagation algorithm for locating sources. Signals recorded by synchronized receivers are reversed in time and propagated back to the source location by elastic wavefield extrapolation. Elastic wavefield extrapolation requires a P-wave as well as an S-wave velocity model. The velocity models available from standard reflection seismic methods are usually restricted to only P-waves. In this study, we use synthetically produced time signals to investigate the accuracy of seismic source localization by means of time-reverse imaging with the correct P-wave and a perturbed S-wave velocity model. The studies reveal that perturbed S-wave velocity models strongly influence the intensity and position of the focus. Imaging the results with the individual maximum energy density for both body wave types instead of mixed modes allows individual analysis of the two body waves. P-wave energy density images render stable focuses in case of a correct P-wave and incorrect S-wave velocity model. Thus, P-wave energy density seems to be a more suitable imaging condition in case of a high degree of uncertainty in the S-wave velocity model.