bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle
Authors: Dodge Greg J , Anderson Alyssa J , He Yi , Liu Weijing , Viner Rosa , Imperiali Barbara
Published: February 2024

Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge detergent-free methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from the Salmonella enterica (LT2) O-antigen biosynthesis. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for dimerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying other classes of small membrane proteins embedded in liponanoparticles beyond PGTs.
Metabolomics identifies and validates serum androstenedione as novel biomarker for diagnosing primary angle closure glaucoma and predicting the visual field progression
Authors: Li Shengjie , Ren Jun , Jiang Zhendong , Qiu Yichao , Shao Mingxi , Li Yingzhu , Wu Jianing , Song Yunxiao , Sun Xinghuai , Gao Shunxiang , Cao Wenjun
Published: February 2024

Background:

Primary angle closure glaucoma (PACG) is the leading cause of irreversible blindness in Asia, and no reliable, effective diagnostic, and predictive biomarkers are used in clinical routines. A growing body of evidence shows metabolic alterations in patients with glaucoma. We aimed to develop and validate potential metabolite biomarkers to diagnose and predict the visual field progression of PACG.

Methods:

Here, we used a five-phase (discovery phase, validation phase 1, validation phase 2, supplementary phase, and cohort phase) multicenter (EENT hospital, Shanghai Xuhui Central Hospital), cross-sectional, prospective cohort study designed to perform widely targeted metabolomics and chemiluminescence immunoassay to determine candidate biomarkers. Five machine learning (random forest, support vector machine, lasso, K-nearest neighbor, and GaussianNaive Bayes [NB]) approaches were used to identify an optimal algorithm. The discrimination ability was evaluated using the area under the receiver operating characteristic curve (AUC). Calibration was assessed by Hosmer-Lemeshow tests and calibration plots.

Results:

Studied serum samples were collected from 616 participants, and 1464 metabolites were identified. Machine learning algorithm determines that androstenedione exhibited excellent discrimination and acceptable calibration in discriminating PACG across the discovery phase (discovery set 1, AUCs=1.0 [95% CI, 1.00–1.00]; discovery set 2, AUCs = 0.85 [95% CI, 0.80–0.90]) and validation phases (internal validation, AUCs = 0.86 [95% CI, 0.81–0.91]; external validation, AUCs = 0.87 [95% CI, 0.80–0.95]). Androstenedione also exhibited a higher AUC (0.92–0.98) to discriminate the severity of PACG. In the supplemental phase, serum androstenedione levels were consistent with those in aqueous humor (r=0.82, p=0.038) and significantly (p=0.021) decreased after treatment. Further, cohort phase demonstrates that higher baseline androstenedione levels (hazard ratio = 2.71 [95% CI: 1.199–6.104], p=0.017) were associated with faster visual field progression.

Conclusions:

Our study identifies serum androstenedione as a potential biomarker for diagnosing PACG and indicating visual field progression.

Funding:

This work was supported by Youth Medical Talents – Clinical Laboratory Practitioner Program (2022-65), the National Natural Science Foundation of China (82302582), Shanghai Municipal Health Commission Project (20224Y0317), and Higher Education Industry-Academic-Research Innovation Fund of China (2023JQ006).
Neural attentional filters and behavioural outcome follow independent individual trajectories over the adult life span
Authors: Tune Sarah , Obleser Jonas
Published: February 2024

Preserved communication abilities promote healthy aging. To this end, the age-typical loss of sensory acuity might in part be compensated for by an individual’s preserved attentional neural filtering. Is such a compensatory brain–behaviour link longitudinally stable? Can it predict individual change in listening behaviour? We here show that individual listening behaviour and neural filtering ability follow largely independent developmental trajectories modelling electroencephalographic and behavioural data of N = 105 aging individuals (39–82 yrs). First, despite the expected decline in hearing- threshold–derived sensory acuity, listening-task performance proved stable over 2 years. Second, neural filtering and behaviour were correlated only within each separate measurement timepoint (T1, T2). Longitudinally, however, our results raise caution on attention-guided neural filtering metrics as predictors of individual trajectories in listening behaviour: Neither neural filtering at T1 nor its two-year change could predict individual two-year behavioural change, under a combination of modelling strategies.
Strategies for Education and Literacy in the Preservation and Transmission of Jiujiang Folk Songs in Jiangxi Province
Authors: Huang Hui , Thotham Awirut
Published: February 2024

Jiujiang Folk Songs, from Jiujiang County in Jiangxi Province, is a traditional Chinese folk genre with unique musical styles and themes focusing on daily life, labor, love, and historical narratives. Beginning with an introduction that highlights the cultural significance of these songs, the study’s objective is to propose strategies for education and literacy in the preservation and transmission of Jiujiang folk songs in Jiangxi Province. Focusing on Jiujiang County, known for its rich cultural heritage, the research involves key informants with deep roots in the region and extensive experience in performing and teaching Jiujiang folk songs. Through qualitative data analysis, including live performance observations and structured interviews, the study identifies key challenges such as an aging population of practitioners, language barriers, and a lack of modern promotion. Drawing from these findings, the research suggests strategies at multiple levels, including legislative protection, cultural promotion, and school involvement, to bridge these gaps and ensure the continued preservation and transmission of Jiujiang folk songs. This study contributes to the broader discourse on the preservation of traditional cultural heritage in the face of modernization and serves as a model for safeguarding similar treasures worldwide.
Literacy Transmission of Guqin Culture at the Wangji School in Henan Province, China
Authors: Zhu Xiaobei , Sornyai Phiphat
Published: February 2024

This research investigates the literacy transmission of Guqin culture at the Wangji School in Henan Province, China, through the lenses of ethnomusicology and transmission theory. The goal is to gain an understanding of the educational opportunities provided by this institution and its function in preserving and advancing this ancient Chinese musical tradition. Located in Henan, a province known as the “Cradle of Chinese Civilization,” the Wangji School serves as a vital hub for Guqin education, performance, and transmission. Key informants provide perspectives on the diverse backgrounds and pedagogical approaches of Guqin instructors at the school. Using thematic analysis to look at observations and interviews as data shows that there is a focus on copying, expressing oneself, and combining lifestyle elements. The research highlights the school’s commitment to cultural preservation, fostering an inclusive learning environment, and employing online outreach. In conclusion, the Wangji School emerges as a beacon of Guqin culture, bridging tradition and innovation to ensure the continuity and vitality of this cherished musical tradition, offering valuable lessons for the preservation of cultural heritage in contemporary educational settings.
Effect of High-intensity Interval Training Session Timing on Inflammatory Biomarkers in Overweight and Obese Individuals with Different Chronotypes
Authors: Jayavel Ayyappan , Shivasekar Meera , V.M Vinodhini
Published: February 2024

Background: Global attention on obesity prevention emphasizes cost-effective strategies, particularly physical activity. Evaluating chronobiological influences is crucial for effective treatment plans. Noncommunicable disease management requires a nuanced approach to address this pervasive health concern. Objective: This study aims to determine the effect of chronotype-based high-intensity interval training (HIIT) on inflammatory biomarkers among overweight and obese individuals. Methods: This experimental study, involving 58 obese adults, utilized pretest and post-test evaluations. Participants, aged 31.65 ± 9.1 years with a mean BMI of 29.04 ± 4.04, underwent 12 weeks of cycling HIIT (10 sec on/10 sec off) thrice weekly. Pre- and post-training venous blood samples were collected, centrifuged, and stored at -80°C. Outcome measures included metabolic, inflammatory biomarkers, and anthropometric data. Result: The findings of this study demonstrate that there is a significant difference in metabolic variables such as fasting sugar, fasting insulin, 3.7%, 27% (p=0.00), and IL6 5.7% (p=0.00) levels between the chronotype-based exercise session group (CBES) and non chronotype based exercise session group (NCBES). Anthropometric and other inflammatory variables, such as Tumor necrosis factor alpha (TNF -alpha) and high sensitive C-reactive protein (hs CRP), showed no significant differences between groups. Conclusion: The study concluded that chronotype-based HIIT is effective on metabolic markers but not on inflammatory markers in obese individuals.
Statistical learning for maintenance optimization: modeling the hazard function with variable recovery factors
Authors: De Souza Fábio Lucas Costa , Da Silva Allan Jonathan
Published: February 2024

Abstract: This study aims to utilize advanced statistical methods in equipment maintenance within the machining and casting processes of an industrial company, focusing on cost optimization. Employing a methodology that combines literature review, mathematical formulation, and statistical treatment of historical data from preventive and corrective maintenance, the study stands out for the use of maximum likelihood estimation to determine not only the model parameters but also the recovery factor used during preventive maintenance. It also calculates the optimal maintenance time to minimize the total cost. This work not only underscores the importance of a data-driven maintenance approach, balancing reliability and cost to achieve effective optimization but also signals the need for future studies, especially in simulations to further enhance preventive maintenance scheduling, encompassing all aspects of the production process.
A Study on the Health and Nutritional Status of Mawasi Tribal Women in Villages of Chitrakoot Region in Madhya Pradesh, India
Authors: Negi Soumya , Jagre Akhilesh , Negi R.S.
Published: February 2024

The present study is a cross sectional survey in which an attempt was made to understand the socio- demographic profile and assess nutritional status of Mawasi tribal women in Majhgawan block of Satna district in Madhya Pradesh. The sample comprised of 100 females between the age groups of 18-46 which were selected from 100 households for assessment of health and nutritional status. Stratified random sampling method was used for selection of 5 villages. The primary tool in the study was predesigned and pretested interview schedule. Height, weight recording, clinical examination and body type of females were the part of the study. The design of the study is qualitative that include data from 100 in depth interviews with the mothers. To calculate nutrient intake, twenty –four hour dietary recall method was adopted and was compared with the RDA-2020 given by ICMR. Nearly half (51%) females were short stature and thin. 79 % women were suffering from severe to moderate anemia. Daily intake of foods were deficit in vitamin A (75.5%), vitamin C (54.83%), folic acid (70.32%),Vitamin B12(63%), iron (61.43%) and calcium (47.67%) nutrients. The mean weight of the female was 42.72 Kg. The vast majority (92%) of females had weight less than the weight of the reference women (55Kg). The mean body mass index was 19.39. Only one-third (32%) females were normal( BMI 20.0-25.0).More than half (51%)of the study women suffered from chronic energy deficiency (BMI<18.5). 98 % women were found anemic according to the cut-off (HB<12.0g/dl) proposed by WHO. The overall nutritional status of the tribal females was poor and their nutrient intake was also insufficient showing high percentage deficit in calories, proteins, fats, iron, zinc, calcium and vitamins A, B and C intake. Nutritional anemia, Vit-A and vit-C, VitaminB12 deficiencies were common problems in Mawasi women.
Occurrence of Potentially Pathogenic Bacteria in Commercially Sold Seafood from Misamis Occidental, Philippines
Authors: Dumaloan-Canini Nelfa , Cadelinia Emily E. , Olarte-Bala Jessie Jane
Published: February 2024

Seafood is a nutritious food that is an enviable component of a healthy diet. Nevertheless, there are health risks associated with the consumption of seafood.

This study aimed to investigate the occurrence of potentially pathogenic Vibrio spp., Staphylococcus aureus, and Salmonella spp. in 200 seafood samples purchased from several retail outlets in Ozamiz City, Philippines. Different samples analyzed using standard microbiological techniques were clam, shrimp, squid, and fish (anchovy and oil sardines). The Vibrio species identified and isolated were V. parahaemolyticus (47%), V. cholerae (16%) and V. alginolyticus (9%). Thirty percent (30%) of the samples analyzed were positive for S. aureus and 9% of the samples were contaminated with Salmonella sp. The total aerobic plate count mean log10 cfu/g of clams, shrimps, head/gills, intestine of fish (oil sardine, anchovy), and squids were considered as medium to high risk of transmitting pathogenic bacteria. Moreover, the clams and head/gills of oil sardines were considered to be at medium to high risk of transmitting pathogenic V. parahaemolyticus. The findings revealed that seafood samples analyzed microbiologically were loaded with potentially pathogenic bacteria. This result is of public health concern because these organisms are documented as causes of food-borne diseases.
An indirect adaptive pole‐placement control for MIMO discrete‐time stochastic systems
Authors: Yu Wen‐Shyong
Published: April 2005

In this paper, an indirect adaptive pole‐placement control scheme for multi‐input multi‐output (MIMO) discrete‐time stochastic systems is developed. This control scheme combines a recursive least squares (RLS) estimation algorithm with pole‐placement control design to produce a control law with self‐tuning capability. A parametric model with a priori prediction outputs is adopted for modelling the controlled system. Then, a RLS estimation algorithm which applies the a posteriori prediction errors is employed to identify the parameters of the model. It is shown that the implementation of the estimation algorithm including a time‐varying inverse logarithm step size mechanism has an almost sure convergence. Further, an equivalent stochastic closed‐loop system is used here for constructing near supermartingales, allowing that the proposed control scheme facilitates the establishment of the adaptive pole‐placement control and prevents the closed‐loop control system from occurring unstable pole‐zero cancellation. An analysis is provided that this control scheme guarantees parameter estimation convergence and system stability in the mean squares sense almost surely. Simulation studies are also presented to validate the theoretical findings. Copyright © 2005 John Wiley & Sons, Ltd.
Toward localizing genes underlying cerebral asymmetry and mental health
Authors: Smalley Susan L. , Loo Sandra K. , Yang May H. , Cantor Rita M.
Published: April 2005

Genome investigations of autism, attention deficit hyperactivity disorder (ADHD), and dyslexia suggest possible genetic overlap. Atypical cerebral asymmetry (ACA), the absence of the left hemisphere dominance for language, may be a shared phenotype due to genes located in regions of overlap. A binomal test is used to evaluate whether linked regions overlap more than expected by chance for 15 genome‐wide scans in autism, ADHD, and dyslexia. Significant evidence of linkage overlap (P = 10−7) is seen for autism, ADHD, and dyslexia for seven chromosomal regions (2p11–12, 5p13, 7q22–33, 9q33–34, 13q22, 16p13, and 17p11–q11). Linkage analysis of ACA and molecular markers for 270 sibling pairs with ADHD is conducted using the Haseman–Elston statistic. Linkage analysis supports ACA as a shared phenotype with risk genes located on 9q33–34 or 16p13 (P < 0.004). Further support stems from the overlap of these regions in schizophrenia, bipolar illness, specific language impairment (SLI), and handedness, all traits associated with ACA. Autism, ADHD, and dyslexia share regions of linkage overlap and ACA may be a shared phenotype for such genes similar to HLA in autoimmune disease. Because ACA is associated with certain aspects of creativity, such risk genes may also be enhancer genes for creativity. © 2005 Wiley‐Liss, Inc.
Vesicular glutamate transporter‐1 colocalizes with endogenous opioid peptides in axon terminals of the rat locus coeruleus
Authors: Barr Jeffrey , Van Bockstaele Elisabeth J.
Published: April 2005

We have previously shown that a subset of axon terminals in the locus coeruleus (LC) containing methionine5‐enkephalin (ENK) forms type I (asymmetric‐type) synaptic specializations that are characteristic of excitatory‐type transmitters. In addition, we previously provided ultrastructural evidence showing that ENK is colocalized with glutamate using a combination of pre‐ and postembedding immunohistochemistry. To examine cellular substrates for interactions between glutamate and other endogenous opioid peptides in the LC, we examined the localization of the vesicular glutamate transporter 1 (VGLUT1), a transporter protein involved in the accumulation of the transmitter glutamate into synaptic vesicles, with either ENK or preprodynorphin (ppDYN). Dual‐immunofluorescence and electron microscopy showed prominent coexistence of VGLUT1 and ENK in varicose processes of the LC, confirming our previous report using postembedding immunolabeling for glutamate. Likewise, VGLUT1 and ppDYN were identified in common varicose processes in the LC using confocal fluorescence microscopy. Immunoelectron microscopy using gold‐silver labeling for VGLUT1 and peroxidase labeling for ppDYN established that this endogenous opioid peptide also colocalizes with glutamate transporters. The majority of these formed asymmetric‐type synapses. Taken together, these results demonstrate that excitatory LC afferents are enriched with endogenous opioid peptides and are positioned to modulate LC neuronal activity dually. © 2005 Wiley‐Liss, Inc.
Embryonic cerebrospinal fluid regulates neuroepithelial survival, proliferation, and neurogenesis in chick embryos
Authors: Gato Ángel , Moro J.A. , Alonso M.I. , Bueno D. , De La Mano A. , Martín C.
Published: April 2005

Early in development, the behavior of neuroepithelial cells is controlled by several factors, which act in a developmentally regulated manner. Diffusible factors are secreted locally by the neuroepithelium itself, although other nearby structures may also be involved. Evidence suggests a physiological role for the cerebrospinal fluid in the development of the brain. Here, using organotypic cultures of chick embryo neuroepithelial explants from the mesencephalon, we show that the neuroepithelium in vitro is not able to self‐induce cell survival, replication, and neurogenesis. We also show that the embryonic cerebrospinal fluid (E‐CSF) promotes neuroepithelial stem cell survival and induces proliferation and neurogenesis in mesencephalic explants. These data strongly suggest that E‐CSF is involved in the regulation of neuroepithelial cells behavior, supporting the hypothesis that this fluid plays a key role during the early development of the central nervous system. © 2005 Wiley‐Liss, Inc.
Arterial embolization using poly‐N‐acetyl glucosamine gel in a rat kidney model
Authors: Kang Qian K. , An Yuehuei H. , Moreira Patricia L. , Demcheva Marina V. , Vournakis John N.
Published: April 2005

Aqueous solutions of poly‐N‐acetyl glucosamine (p‐GlcNAc) exhibit a liquid‐gel transition at physiological pH and temperature. This feature inspired the authors to conduct a study to evaluate the macro‐ and histological changes of rat kidneys after embolization using either p‐GlcNAc gel injection into the renal artery or ligation of the renal artery. The procedures were performed in 46 rats through open abdominal surgeries. Animals were sacrificed at 3 days and at 1, 3, 5, and 8 weeks postoperatively. The results of both macro‐observation and histological study showed that p‐GlcNAc gels were effective in causing necrosis and subsequent fibrosis in all embolized kidneys. The data indicate that p‐GlcNAc gel may have promise as an effective agent for therapeutic embolization. © 2005 Wiley‐Liss, Inc.
Community networks: Community capital or merely an affordable Internet access tool?
Authors: Kwon Nahyun
Published: April 2005

In this study a perceived gap between the ideal and the reality of a community network (CN) is examined. Most proponents of CNs state that building a better physical community is their major service goal. However, there has been a concern that citizens might use the service simply as a means to connect to the Internet rather than as a means to connect to their communities. Using a survey research method (n = 213), users' perceptions of community aspects of CN service and the influence of such perceptions on their use were investigated. User demographics and alternative service accessibility were also examined as predictors of use. The present study found that the respondents were using the service mainly for general Internet features. More than two thirds of the respondents were not aware of the community content aspect of the service. Approximately 20% of respondents were identified as those whose perceptions of the community aspects actually affected their use of the service. They were both aware of community contents and using an additional Internet service provider. Findings suggest that the providers did not fully communicate the community aspects of the service with the users, while the user perception of community aspects is a key to further promotion of the service.
Testing user interaction with a prototype visualization‐based information retrieval system
Authors: Koshman Sherry
Published: April 2005

The VIBE (Visual Information Browsing Environment) prototype system, which was developed at Molde College in Norway in conjunction with researchers at the University of Pittsburgh, allows users to evaluate documents from a retrieved set that is graphically represented as geometric icons within one screen display. While the formal modeling behind VIBE and other information visualization retrieval systems is well known, user interaction with the system is not. This investigation tested the designer assumption that VIBE is a tool for a smart (expert) user and asked: What are the effects of the different levels of user expertise upon VIBE usability? Three user groups including novices, online searching experts, and VIBE system experts totaling 31 participants were tested over two sessions with VIBE. Participants selected appropriate features to complete tasks, but did not always solve the tasks correctly. Task timings improved over repeated use with VIBE and the nontypical visually oriented tasks were resolved more successfully than others. Statistically significant differences were not found among all parameters examined between novices and online experts. The VIBE system experts provided the predicted baseline for this study and the VIBE designer assumption was shown to be correct. The study's results point toward further exploration of cognitive preattentive processing, which may help to understand better the novice/expert paradigm when testing a visualized interface design for information retrieval.
Growth characteristics of Arthrospira platensis cultured inside a new close‐coil photobioreactor incorporating a mandrel to control culture temperature
Authors: Carlozzi Pietro , Pinzani Edoardo
Published: April 2005

The aim of this study was to investigate Arthrospira growth inside a new CCP incorporating a mandrel for culture temperature control. Some hydrodynamic aspects and photobioreactor performances were investigated as well. The bioreactor incorporated A. platensis grown under batch and semicontinuous conditions. Two systems were used to recycle Arthrospira cultures: a peristaltic pump and an airlift system. When the pump recycled the culture, we achieved a very high Dean number (De = 3,950), which decreased a great deal when the pump was replaced with the airlift system. During outdoor Arthrospira batch growth, a cell concentration of 16.4 g (DW)l−1 was reached after 9 days. However, the maximum chlorophyll content of the biomass (2.0% of DW) was achieved on the fifth and sixth days. The highest daily biomass output rate was obtained using the airlift system, when the CCP was operated under a semicontinuous regime: the gross output rate was 2.85 ± 0.37 g (DW) l−1 d−1 and the net was 2.32 ± 0.11 g (DW) l−1 d−1. The advantages of the airlift system may be due to the low concentration of oxygen built up inside Arthrospira culture and the lack of cell damage due to the pump system. Thus, oxygen and pump stress may have been avoided. © 2005 Wiley Periodicals, Inc.
Immobilized N‐alkylated polyethylenimine avidly kills bacteria by rupturing cell membranes with no resistance developed
Authors: Milović Nebojša M. , Wang Jun , Lewis Kim , Klibanov Alexander M.
Published: April 2005

Several critical mechanistic and phenomenological aspects of the microbicidal surface coatings based on immobilized hydrophobic polycations, previously developed by us, are addressed. Using Escherichia coli (Gram‐negative) and Staphylococcus aureus (Gram‐positive) bacteria, remarkable bactericidal action (up to a 109‐fold reduction in live bacteria count in the surface‐exposed solution and a 100% inactivation of the surface‐adhered bacteria) of an amino‐glass slide covalently derivatized with N‐hexyl,methyl‐polyethylenimine (PEI) is found to be due to rupturing bacterial cell membranes by the polymeric chains. The bacteria fail to develop noticeable resistance to this lethal action over the course of many successive generations. Finally, the immobilized N‐alkyl‐PEI, while deadly to bacteria, is determined to be harmless to mammalian (monkey kidney) cells. © 2005 Wiley Periodicals, Inc.
Fed‐batch culture of a metabolically engineered Escherichia coli strain designed for high‐level succinate production and yield under aerobic conditions
Authors: Lin Henry , Bennett George N. , San Ka‐Yiu
Published: April 2005

An aerobic succinate production system developed by Lin et al. (Metab Eng, in press) is capable of achieving the maximum theoretical succinate yield of 1.0 mol/mol glucose for aerobic conditions. It also exhibits high succinate productivity. This succinate production system is a mutant E. coli strain with five pathways inactivated: ΔsdhAB, Δ(ackA‐pta), ΔpoxB, ΔiclR, and ΔptsG. The mutant strain also overexpresses Sorghum vulgare pepc. This mutant strain is designated HL27659k(pKK313). Fed‐batch reactor experiments were performed for the strain HL27659k(pKK313) under aerobic conditions to determine and demonstrate its capacity for high‐level succinate production. Results showed that it could produce 58.3 g/l of succinate in 59 h under complete aerobic conditions. Throughout the entire fermentation the average succinate yield was 0.94 ± 0.07 mol/mol glucose, the average productivity was 1.08 ± 0.06 g/l‐h, and the average specific productivity was 89.77 ± 3.40 mg/g‐h. Strain HL27659k (pKK313) is, thus, capable of large‐scale succinate production under aerobic conditions. The results also showed that the aerobic succinate production system using the designed strain HL27659k(pKK313) is more practical than conventional anaerobic succinate production systems. It has remarkable potential for industrial‐scale succinate production and process optimization. © 2005 Wiley Periodicals, Inc.
Quantitative determination of alkylated quaternary amines and their n‐hydroxylated metabolites in an enzyme incubation matrix by liquid chromatography electrospray ionization mass spectrometry
Authors: Holmes Victoria E. , Shaw P. Nicholas , Ortori Catharine A. , Barrett David A.
Published: April 2005

A simple, rapid and sensitive reversed‐phase liquid chromatography method coupled to electrospray ionization mass spectrometry has been developed for studying the in vitro metabolism of the long‐chain quaternary ammonium compounds dodecyltrimethylamine, tetradecyltrimethylamine and hexadecyltrimethylamine. Samples were prepared from the biological matrix by a simple protein precipitation stage. The separation was performed using a BDS Hypersil C8 3 µm particle size (100 × 3 mm i.d.) column with a fast gradient separation (60% B to 100% B) using a mobile phase of 10 mm aqueous ammonium acetate (pH 4.0, with 0.06% triethylamine; (A)–acetonitrile (B) at 0.7 mL min−1. To minimize contamination of the MS source a switching value was used to divert the solvent front to waste. Decylammonium bromide was used as the internal standard and analytes were identified and quantified by positive ion electrospray selected ion monitoring of their intact molecular cations. The assay had a limit of quantitation of 0.25 µm (6.25 pmol on column) and was linear over the range 0.25–100 µm assay concentration for this series of long‐chain quaternary amines. The precision of intra‐ and inter‐day assays was better than 19% and the accuracy was between 93 and 109%. The method was used to assess the in vitro metabolism of the quaternary amines by wild‐type cytochrome P450 enzyme CYP4A1 and mutants in an artifical membrane system. Copyright © 2005 John Wiley & Sons, Ltd.
The effects of ligand chain length, salt concentration and temperature on the adsorption of bovine serum albumin onto polypropyleneglycol–Sepharose
Authors: Dias‐Cabral A. C. , Ferreira A. S. , Phillips J. , Queiroz J. A. , Pinto N. G.
Published: April 2005

The interaction thermodynamics associated with bovine serum albumin adsorption on polypropylene glycol (n = 3)–Sepharose CL‐6B and polypropylene glycol (n = 7)–Sepharose CL‐6B, using ammonium sulfate as the modulator was studied. Analysis of data under linear conditions was accomplished with the stoichiometric displacement retention model, preferential interaction approach and van't Hoff plots applied to HIC systems. Preferential interaction analysis indicated a strong entropic driving force under linear conditions, due to the release of a large amount of solvent on adsorption. In contrast, flow microcalorimetry under overloaded conditions showed that the adsorption of bovine serum albumin may be entropically or enthalpically driven. It is postulated that adsorption in the nonlinear region is influenced by the degree of water release, protein–protein interactions on the surface, reorientation of ligand, and conformational changes in the protein. Copyright © 2005 John Wiley & sons, Ltd.
Nucleocytoplasmic Glycosylation: O‐Linked β‐N‐Acetylglucosamine
Authors: Zachara N. E. , Cheung W. D. , Hart G. W.
Published: April 2005

For Abstract see ChemInform Abstract in Full Text.
Coherent Control for Spectroscopy and Manipulation of Biological Dynamics
Authors: Wohlleben Wendel , Buckup Tiago , Herek Jennifer L. , Motzkus Marcus
Published: April 2005

Motivated originally by the goal of steering a photoreaction into desired product channels, the concept of coherent control is to adapt the spectral and temporal characteristics of the excitation light to the inherent molecular resonances and dynamics, such that these can be selectively addressed and manipulated. In the last decade, the ultrafast dynamics of many atomic and molecular quantum systems in the gas and condensed phase have been controlled successfully. Motivations in chemistry are now 1) to perform spectroscopy by coherent control, which requires a deeper understanding of control mechanisms, 2) to treat more complex, biological photoreactions, and 3) the pragmatic use of coherent control techniques, for example, for pulse compression or enhanced contrast in multiphoton microscopy. As examples for 1) and 2) we review here the combined effort and interplay of conventional spectroscopy and coherent control experiments, applied to the energy flow in the light‐harvesting complex LH2 from bacterial photosynthesis. Closed‐loop control experiments allowed the characteristic coupling frequency of internal conversion in the carotenoid in LH2 to be extracted. Open‐loop three‐pulse control experiments, on the other hand, could directly observe an anticipated Raman‐excited carotenoid ground state. As a variant of difference spectroscopy, coherent control has thus served to gain complementary spectroscopic knowledge about the energy flow in carotenoids by comparing natural to manipulated dynamics. Finally, we propose future coherent control experiments on the electronic state structure of carotenoids and discuss prospects of coherent control for other biological chromophores.
Theoretical Study of Inversion and Topomerization Processes of Substituted Cyclohexanes: The Relevance of the Energy 3D Hypersurface
Authors: Fernández‐Alonso María del Carmen , Cañada Javier , Jiménez‐Barbero Jesús , Cuevas Gabriel
Published: April 2005

Although the potential energy surface of highly symmetric cyclohexane has been extensively reviewed, no attention has been paid to the study of the effect of substitution of a methylene group by a heteroatom. The substitution may cause changes in molecular symmetry as well as the dipole moment, and the unshared electron pairs associated with the heteroatom may also introduce changes in molecular reactivity. However, these phenomena are not yet completely understood. To address these issues, a rigorous description of the inversion–topomerization process of methylcyclohexane and a revision of the conformational potential energy of oxane and thiane are presented. Moreover, the usefulness of providing a three‐dimensional representation of these processes is discussed. In the case of methylcyclohexane, calculations show that three transition states are associated with inversion and four more with topomerization. In contrast, for oxane and thiane, only two transition states are involved with inversion and two with topomerization.

Two fundamental conclusions can be drawn from this study. The first is that the inversion process occurs through elementary stages that we have denoted “conformational elemental stages”, which is an analogous term to that used for reaction mechanism description (minima–transition state–minima) where several elemental steps take place. The second conclusion is that two independent processes, inversion and topomerization, are connected by some common conformers. The inversion process controls the ring interchange, while topomerization allows exchange between skewed boats.
Single‐Molecule Quantum‐Dot Fluorescence Resonance Energy Transfer
Authors: Hohng Sungchul , Ha Taekjip
Published: April 2005

Colloidal semiconductor quantum dots are promising for single‐molecule biological imaging due to their outstanding brightness and photostability. As a proof of concept for single‐molecule fluorescence resonance energy transfer (FRET) applications, we measured FRET between a single quantum dot and a single organic fluorophore Cy5. DNA Holliday junction dynamics measured with the quantum dot/Cy5 pair are identical to those obtained with the conventional Cy3/Cy5 pair, that is, conformational changes of individual molecules can be observed by using the quantum dot as the donor.
Thermomechanics of the shape memory effect in polymers for biomedical applications
Authors: Gall Ken , Yakacki Christopher M. , Liu Yiping , Shandas Robin , Willett Nick , Anseth Kristi S.
Published: April 2005

We examine the shape memory effect in polymer networks intended for biomedical, and specifically cardiovascular, applications. The polymers were synthesized by photopolymerization from a tert‐butyl acrylate monomer with a diethyleneglycol diacrylate crosslinker. Three‐point flexural tests were used to systematically investigate the thermomechanics of shape storage (predeformation) and shape recovery. The glass transition temperature, Tg, of the polymers was determined to be approximately 65°C. The polymers show 100% strain recovery, at low and high predeformation temperatures, up to maximum strains of ∼80%. The polymers show a sigmoidal free strain recovery response as a function of increasing temperature at a constant heating rate. Free strain recovery was determined to depend on the temperature during predeformation; lower predeformation temperatures (T < Tg) decreased the temperature required for free strain recovery. Constrained stress recovery shows a complex evolution as a function of temperature and also depends on the temperature during predeformation. Stress recovery after low‐temperature predeformation (T < Tg) shows a peak in the generated recovery stress, whereas stress recovery after high‐temperature predeformation (T > Tg) is sigmoidal. The isothermal free strain recovery rate was found to increase with increasing temperature or decreasing predeformation temperature. The thermomechanical results are discussed in light of potential biomedical applications, and a prototype device is presented. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res 73A: 339–348, 2005
Properties of titanium–silver alloys for dental application
Authors: Oh Keun‐Taek , Shim Hyung‐Min , Kim Kyoung‐Nam
Published: April 2005

The purpose of this study was to develop titanium–silver alloys with biocompatibility, high corrosion resistance, and low ion‐release rate, and to evaluate the electrochemical properties of titanium–silver alloys in artificial saliva. Titanium–silver alloys with silver contents ranging from 0 to 4.5 at % in steps of 0.5 at % were designed. The alloys were arc melted, homogenized at 950°C for 72 h, hot rolled to 2 mm in thickness, and finally solution heat treated at 950°C for 1 h and quenched in water. Chemical compositions, phases, hardnesses, electrochemical properties, and the cytotoxicity of the alloys were investigated. The purity of titanium–silver alloys was maintained above 99.9%, because few impurities were introduced through their manufacture. In the case of alloys containing silver in the range 2.0–4.0 at %, the formation of an acicular α phase was observed inside the β phase. The acicular phase got thinner with increasing amounts of silver. This means that silver is a β‐phase stabilizing element in titanium–silver alloys. The hardness value tended to rise with increasing silver content and increased largely over 3.5 at %, and the increase of the hardness value versus pure titanium was about 33%. It is believed that the substantial increases in hardness was due to the effects of solid solution strengthening and of α–β phase transition. Moreover, titanium–silver alloys had higher corrosion resistances than pure titanium. These results mean that silver additions to titanium can improve alloy corrosion resistance. Passive current densities in the potentiodynamic polarization curves were dependent on the chemical compositions of the titanium–silver alloys. However, they did not show a linear relationship with respect to silver contents. Titanium–silver alloys did not show pitting corrosion in artificial saliva. It is believed that silver addition to titanium strengthened the passive film due to titanium dissolution induced by the different electromotive forces of titanium and silver. In the agar overlay test, the cytotoxicity of the titanium–silver alloys and of titanium were none or mild. In summary, titanium–silver alloys had higher mechanical properties and corrosion resistance than titanium, and toxicities that were similar to titanium. Therefore, it is recommended that titanium–silver alloys be adopted cautiously by the biomedical and dental fields. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater
Molecular dynamics simulation of clustered DNA damage sites containing 8‐oxoguanine and abasic site
Authors: Fujimoto Hirofumi , Pinak Miroslav , Nemoto Toshiyuki , O'Neill Peter , Kume Etsuo , Saito Kimiaki , Maekawa Hideaki
Published: April 2005

Clustered DNA damage sites induced by ionizing radiation have been suggested to have serious consequences to organisms, such as cancer, due to their reduced probability to be repaired by the enzymatic repair machinery of the cell. Although experimental results have revealed that clustered DNA damage sites effectively retard the efficient function of repair enzymes, it remains unclear as to what particular factors influence this retardation. In this study, approaches based on molecular dynamics (MD) simulation have been applied to examine conformational changes and energetic properties of DNA molecules containing clustered damage sites consisting of two lesioned sites, namely 7,8‐dihydro‐8‐oxoguanine (8‐oxoG) and apurinic/apyrimidinic (AP) site, located within a few base pairs of each other. After 1 ns of MD simulation, one of the six DNA molecules containing a clustered damage site develops specific characteristic features: sharp bending at the lesioned site and weakening or complete loss of electrostatic interaction energy between 8‐oxoG and bases located on the complementary strand. From these results it is suggested that these changes would make it difficult for the repair enzyme to bind to the lesions within the clustered damage site and thereby result in a reduction of its repair capacity. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 788–798, 2005
Carbon boronyls: Species with higher viable possibility than boron carbonyls at the density functional theory
Authors: Li Si‐Dian , Miao Chang‐Qing , Guo Jin‐Chang , Ren Guang‐Ming
Published: April 2005

Density functional theory investigations indicate that carbon boronyls (CBO)n (n = 3–7) are considerably more stable in thermodynamics than their boron carbonyl isomers (BCO)n and exhibit aromaticity throughout the whole series. The extra stabilities of (CBO)n originate from their frontier π molecular orbitals delocalized over the Dnh Cn central rings which are absent in (BCO)n. It is expected that experimental characterization of these (CBO)n species may open a new branch of chemistry on carbon boronyls. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 799–802, 2005
Decomposition and long‐lasting downregulation of extracellular matrix in perineuronal nets induced by focal cerebral ischemia in rats
Authors: Hobohm Carsten , Günther Albrecht , Grosche Jens , Roßner Steffen , Schneider Dietmar , Brückner Gert
Published: April 2005

The upregulation of extracellular matrix components, especially chondroitin sulfate proteoglycans, after brain injury and stroke is known to accompany the glial reaction, forming repellent scars that hinder axonal growth and the reorganization of the injured neuronal networks. The extracellular matrix associated with perineuronal nets (PNs) in the primarily injured and remote regions has not yet been systematically analyzed. We use the model of permanent middle cerebral artery occlusion (MCAO) to investigate the acute and long‐lasting consequences of ischemia for PNs, related to the damage of neurons and reactions of glial cells, in spontaneously hypertensive rats. Extracellular matrix components associated with PNs around cortical interneurons and neurons in thalamic nuclei were characterized 1, 7, 14, and 35 days after MCAO, using Wisteria floribunda agglutinin (WFA) staining and immunocytochemistry. The degradation of PNs in the infarct core was initiated by loss of WFA‐binding matrix components, indicating the cleavage of glycosaminoglycan chains of chondroitin sulfate proteoglycans. Immunostaining showed the subsequent removal of proteoglycan core proteins within the extending microglia/macrophage invasion zone lasting for 2 weeks after MCAO. In the cortical periinfarct region, delineated by an astrocytic scar against the infarct core, the number of WFA‐stained and proteoglycan core protein‐immunoreactive PNs was permanently reduced. In the homolateral ventroposterior thalamus, the delayed decrease in perineuronal matrix was related to the distribution pattern of activated microglia and massive neuronal degeneration. It can be concluded from these results that complementary to the known upregulation of matrix components in the glial scar, deficits in the expression of the neuron‐associated extracellular matrix develop in the periinfarct and remote regions. These deficits may contribute to the long‐lasting functional impairments after stroke. © 2005 Wiley‐Liss, Inc.
A correlated method for quantifying mixed and dispersed carbon nanotubes: analysis of the Raman band intensities and evidence of wavenumber shift
Authors: Athalin Han , Lefrant Serge
Published: April 2005

We present an experimental investigation of a correlated quantitative analytical method based on advanced Raman spectroscopy. This method was developed for the intensity weight distribution analysis of mixed and dispersed carbon nanotube (CNT) mixtures. For Raman spectroscopy, mixtures of single‐walled CNTs (SWNTs) and multi‐walled CNTs (MWNTs) were prepared and dispersed on a coverslip. Mixtures were made in the range from 1 to 100 mg (wt%) of SWNTs in 100 to 1 mg (wt%) of MWNTs. The ratios of the relative intensities of the Raman bands corresponding to pure SWNTs and pure MWNTs were used for the construction of calibration curves used for quantitative analysis. The relative intensity of the deconvoluted spectral bands shows a characteristic feature at 1350 and 1592 cm−1 which was found to be proportional to the relative amounts of SWNTs and MWNTs in the mixtures. A correlation between the atomic force microscopy images and the tangential mode Raman intensity ratio was used without the need for other analytical techniques. With this feature, it is possible to quantify the different components in the mixed, dispersed or unknown bulk of the CNTs investigated. Copyright © 2005 John Wiley & Sons, Ltd.
Raman spectroscopic identification of single yeast cells
Authors: Rösch Petra , Harz Michaela , Schmitt Michael , Popp Jürgen
Published: April 2005

Eukaryotes (such as yeasts) and prokaryotes (such as bacteria) differ in size, molecular complexity, etc. By definition, eukaryotic cells store their DNA in a separate internal compartment, the so‐called nucleus. Owing to this molecular compartmentalization, the identification of yeast cells by vibrational spectroscopy at a single‐cell level is challenging. This contribution reports on first results of micro‐Raman analysis together with a hierarchical cluster analysis allowing for an online identification method for yeast cells at a single‐cell level. For the classification analysis, an average spectrum from 10 different measuring points within a single yeast cell was used to overcome the heterogeneity of the yeast cells. Copyright © 2005 John Wiley & Sons, Ltd.