bluuebunny/crossref_metadata_2025 huggingface dataset:
moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud
Authors: Choi Joung Min , Park Chaelin , Chae Heejoon
Published: February 2024

Single-cell omics sequencing has rapidly advanced, enabling the quantification of diverse omics profiles at a single-cell resolution. To facilitate comprehensive biological insights, such as cellular differentiation trajectories, precise annotation of cell subtypes is essential. Conventional methods involve clustering cells and manually assigning subtypes based on canonical markers, a labor-intensive and expert-dependent process. Hence, an automated computational prediction framework is crucial. While several classification frameworks for predicting cell subtypes from single-cell RNA sequencing datasets exist, these methods solely rely on single-omics data, offering insights at a single molecular level. They often miss inter-omic correlations and a holistic understanding of cellular processes. To address this, the integration of multi-omics datasets from individual cells is essential for accurate subtype annotation. This article introduces moSCminer, a novel framework for classifying cell subtypes that harnesses the power of single-cell multi-omics sequencing datasets through an attention-based neural network operating at the omics level. By integrating three distinct omics datasets—gene expression, DNA methylation, and DNA accessibility—while accounting for their biological relationships, moSCminer excels at learning the relative significance of each omics feature. It then transforms this knowledge into a novel representation for cell subtype classification. Comparative evaluations against standard machine learning-based classifiers demonstrate moSCminer’s superior performance, consistently achieving the highest average performance on real datasets. The efficacy of multi-omics integration is further corroborated through an in-depth analysis of the omics-level attention module, which identifies potential markers for cell subtype annotation. To enhance accessibility and scalability, moSCminer is accessible as a user-friendly web-based platform seamlessly connected to a cloud system, publicly accessible at http://203.252.206.118:5568. Notably, this study marks the pioneering integration of three single-cell multi-omics datasets for cell subtype identification.
A evolução genética do gênero sorghum e a importância do cereal para a economia mundial e a promoção da segurança alimentar a nível global: uma revisão integrativa
Authors: Do Nascimento Antônio Daniel Lima , De Oliveira Bianca Porfírio Monteiro , De França José Geraldo Eugênio , Siqueira Tânia da Silva , Andrade Mateus Ferreira , Tabosa José Nildo
Published: February 2024

O gênero Sorghum agrupa espécies vegetais com diferentes aptidões produtivas, que são visualizadas pelo porte da planta, tamanho e formato da panícula, rendimento de folha/caule e qualidade dos grãos. As primeiras espécies de sorgo surgiram por meio da seleção natural e de trocas gênicas por autofecundação, que anos depois, resultaram na formação do Sorghum bicolor ssp. bicolor, sendo a primeira espécie doméstica ancestral de grande importância para o surgimento de variedades geneticamente superiores de relevância econômica e nutricional. Assim, o objetivo da pesquisa é mostrar à evolução genética do gênero Sorghum, dando ênfase à importância do cereal para a economia mundial e para a promoção da segurança alimentar a nível global. As pesquisas foram realizadas a partir de bases de dados acadêmico-científicos como SciELO, Google acadêmico e Portal de teses e dissertações, onde foram empregadas como palavras-chave: Cereal, Evolução genética, Sorghum, Importância econômica e Segurança alimentar, sendo selecionados (as) artigos científicos, revisões integrativas, teses, dissertações, trabalhos de conclusão de curso em Português, Inglês e Espanhol, contendo pelo menos três das cinco palavras-chave usadas para filtrar às buscas. Nesse sentido, verificou-se que entre 1940 e 1960, após a exploração da macho-esterilidade citoplasmática e realização de cruzamentos controlados, originaram-se nos EUA os primeiros híbridos comerciais com características melhoradas, destacando-se o ótimo rendimento de grãos e a tolerância a estresses bióticos e abióticos. Os híbridos dispersaram-se por outros países, sendo amplamente utilizados na alimentação humana, animal e produção de biocombustível, contribuindo significativamente para otimização da economia mundial e ampliação do acesso à alimentação.
Smoke Signals: Unraveling the Link between Cigarette Smoking and Serum Liver Markers
Authors: Barapatre Amit , Yadav Swapnil Hindurao , Vengurlekar Shubhada Girish , Shah Meeta Piyush , Kinage Kalpana Ganesh , Shardhul Jyoti Prashant , Pathare Santosh Shivpal
Published: February 2024

Introduction: Cigarette smoking is a major cause of global mortality and morbidity. It exposes the body to many harmful substances, such as cytotoxic, carcinogenic and free radicals, that can damage various organs. This study aims to investigate the effects of different levels of tobacco exposure on liver tissue, by measuring some serum biochemical markers of liver function.

Materials and Methods: The project conducted at T.N.M.C Mumbai from January to December 2021 involved 60 male participants (18–35 years old), divided into smokers (30) and non-smokers (30). Smokers had varying smoking durations (1-5 years). Excluded participants with diseases affecting liver enzymes. Groups were age-matched for analysis. Smokers defined as those smoking >20 cigarettes daily for >1 month. Collected 5.0 ml venous blood, processed in heparinized tubes, and centrifuged for plasma separation. Enzymes SGOT, SGPT, ALP,                    Total Bilirubin, Direct Bilirubin were measured, and statistical analysis revealed significant differences.

Results: In the study, age comparison between smokers and non-smokers showed no significant difference (p = 0.71). However, smokers exhibited significantly higher mean serum concentrations of SGOT and SGPT compared to non-smokers (p = 0.002 and p < 0.0001, respectively). Smokers also had elevated levels of ALP and total bilirubin with mean differences of 16.3 IU/L and 0.392 mg/dl, supported by 95% confidence intervals (6.72, 26.18) and (0.28, 0.504) and p values of 0.003 and 0.0004, respectively. No significant difference was observed in direct bilirubin levels (mean difference: 0.084 mg/dl, 95% CI: 0.065, 0.103, p = 0.191)

Conclusion: In summary, the study suggests a correlation between smoking and elevated serum levels of liver enzymes and damage markers, indicating a potential adverse impact on liver function and increased susceptibility to liver diseases.
The Effects of Earning Management and Environmental, Social, Governance (ESG) on Tax Avoidance with Leverage as A Moderating Variable
Authors: Sadjiarto Arja , Ringoman Jonathan Alvin , Angela Leoni
Published: February 2024

The aim of this study is to determine effect of earning management and ESG on tax avoidance (TA) using leverage as a moderating variable. The underlying theories are stakeholder theory and agency theory. Samples of this study are 29 emitent listed on the IDX for the period 2018 - 2022. Earning management is measured using discretionary accrual with the Modified Jones Model method. ESG is measured by ESG score obtained from Refinitiv data. This research uses multiple linear regression by utilizing the Stata program. It is found that earning management does not have an effect on tax avoidance. ESG has an effect on tax avoidance. Leverage does not moderate the effect of earning management and ESG on tax avoidance.
Complex Concentrated Alloy Catalyst of AlCrFeCoNi for Heterogeneous degradation of Rhodamine B
Authors: Sembiring Kiky Corneliasari , Fahrezi Irgi Ahmad , Muhdarina Muhdarina , Afandi Ahmad
Published: February 2024

The Fe-based catalysts have attracted good attention due to their earth abundance and low toxicity with good Fenton-like performance. However, the narrow pH working range and iron-containing sludge produced during the reaction drove the necessary of developing a potential catalyst in the corresponding application. High entropy alloy that now expands to complex concentrated alloy (CCA) represents a new class of material owing to a broader range of functional and structural properties. A new application of CCA as a catalyst for catalytic degradation of azo dyes has already been a scientific research hotspot. AlCrFeCoNi CCA powder has been successfully synthesized by mechanical alloying (MA) method using a vertical planetary ball mill. Based on the characterization, the catalyst possessed a spherical morphology with a particle size range of 3.5-12.6 mm. The catalyst exhibited photo-Fenton performance up to 85.3% which would be a promising Fenton-like catalyst for wastewater treatment. Copyright © 2024 by Authors, Published by BCREC Publishing Group. This is an open access article under the CC BY-SA License (https://creativecommons.org/licenses/by-sa/4.0).
Hexagonal TiO2/SiO2 Porous Microplates for Methylene Blue Photodegradation
Authors: Ulfa Maria , Anggreani Cindy Nur , Mulyani Bakti , Sholeha Novia Amalia
Published: February 2024

Hexagonal TiO2/SiO2 Porous Microplates have been successfully synthesized by incorporation of Ti precursors into SiO2 synthesized from Si precursors in a gelatin-CTAB mixture via the hydrothermal method. The prepared samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), EDX, nitrogen adsorption-desorption and Fourier transform infrared spectroscopy (FTIR). The sample has a surface area of 735 m2/g, pore volume of 0.67 cc/g, and pore diameter of 3.2 nm, according to the results of the characterization of hexagonal TiO2/SiO2 porous microplates. The transformation of SiO2 microspheres into hexagonal TiO2/SiO2 porous microplates is revealed by a microparticle size increase of 84% and the transition of Si−O bonds into Ti−O and Si−O as measured by FTIR. The photocatalytic activity of hexagonal TiO2/SiO2 porous microplates resulted in 81.15% photodegradation of methylene blue under UV light irradiation within 60 min, which was 21 % better than SiO2. Copyright © 2024 by Authors, Published by BCREC Publishing Group. This is an open access article under the CC BY-SA License (https://creativecommons.org/licenses/by-sa/4.0).
A Study to Improve the Stress Management Policy for Firefighters
Authors: Kim HyoungAh , Han Jaeho , Hwang Sungyu , Jang Jaehyeok , Kang Dongmin
Published: February 2024

The National Fire Agency in Korea has implemented various stress management programs for firefighters. However, few studies have focused on the actual effectiveness of these programs. This study thus aimed to explore problems in the psychological counseling system for firefighters, focusing on the case of Jeju Island, and to prepare an efficient operation plan for the system. Survey results indicate that counselors’ lack of understanding of firefighting results in low satisfaction with counseling services, and that firefighters with short service periods require counselors who understand the firefighting profession more than other groups do. In order to overcome these limitations, it is proposed that a counselor’s education program be introduced and that retired firefighters be hired for the psychological counseling program.
Comparative Study on Domestic and International Criteria of Evacuation Route Designs for Improved Evacuation Safety in a Logistics Facility
Authors: Seo Donggoo , Kim Bongchan , Kim Hansaem , Yeom Taejun
Published: February 2024

This study aims to critically analyze the classification system used in domestic logistics facilities and assess local and international standards for designing evacuation routes. The goal is to identify safety issues in the evacuation processes of logistics facilities and suggest improvements for future logistics facility planning. This involved reviewing classification systems and evacuation route design standards for domestic and international logistics facilities, as well as analyzing building standards in the United States, the United Kingdom, and Japan. The results indicated the necessity for a differentiated assessment based on the risk levels, which were determined by the travel distance limit standard for evacuation routes and the separation distance to the direct exit. Furthermore, a review of enhancements was deemed essential due to the absence of standards for measuring walking distances and providing announcements about the final evacuation exit point. Specifically, in the context of mid-rise building design, there is a recognized need to refine standards such as in area restrictions and domestic guidelines, where sufficient supporting evidence is currently lacking.
Cold-Resistance Characteristics and Adequacy of Low-Temperature Test Standards of Carbon Monoxide Alarms
Authors: Jung Jongjin
Published: February 2024

In this study, we considered domestic and international standards to experimentally evaluate and analyze the cold-resistance characteristics of carbon monoxide alarms and assess the suitability of low-temperature test standards. The analyzed standards include the technical standards for type approval and product inspection of gas leak detectors, specifically KS C 6596, Britain's BS EN 50291-1, and Japan's JIA E 001-07. We found that the technical standards specify a temperature of –20 °C for 1 h; those for KS C 6596 are –10 °C for 2 h; those for Britain’s BS EN 50291-1 are –10 °C for 6 h; and those for Japan’s JIA E 001-07 follow suit. We inferred that the low-temperature test of the technical standards for type approval and product inspection of gas leak detectors required the highest cold resistance. Furthermore, we experimented on samples from two domestic manufacturers, employing the low-temperature test standards deduced from the standard analysis to examine their characteristics. All test samples operated normally when subjected to a temperature of –20 °C for 1 to 4 h, and similarly maintained normal operation at –10 °C for 6 and 24 h. These findings indicate that the carbon monoxide alarms certified in Korea have a high cold resistance. Additionally, this study entailed a review of the low-temperature test standards for carbon monoxide alarms by analyzing the temperature conditions of apartment verandas, where these alarms are predominantly installed. Based on the results, the cold resistance tended to be high using the low-temperature test standards for carbon monoxide alarms. The findings of this research can serve as a valuable reference for future revisions of low-temperature test standards.
Crossroads Traffic Data Analysis Using Drone-Based Deep Learning
Authors: Lee TaeWon , Park SaeJun , Oh JaeChul , Kang Dae-Hung
Published: February 2024

This study proposes a method for monitoring traffic conditions via the collection of road traffic data using drones and deep learning-based analysis. Utilizing the YOLOv8 object detection model, we analyzed traffic videos captured at 45 and 90 degrees at intersections, which revealed differences in object detection capabilities based on the shooting angle. To address issues related to occluded areas during object tracking, we optimized the shooting angles, and achieved a final model with an average of 96.9% and 93.7% path and vehicle type recognition rate, respectively. This validates the effective utilization of drone-based traffic data collection and deep learning analysis in road traffic management. Further research is necessary for the development and application of more sophisticated traffic information systems in the future.
Correlates of body mass evolution in primates
Authors: Soligo Christophe
Published: January 2006

Body mass is undoubtedly central to the overall adaptive profile of any organism. Despite this, very little is known of what forces drive evolutionary changes in body mass and, consequently, shape patterns of body mass distribution exhibited by animal radiations. The search for factors that may influence evolutionary processes in general frequently focuses on environmental parameters such as climate change or interspecific competition. With respect to body mass, there is also the suggestion that evolutionary lineages may follow an inherent trend toward increased body mass, known as Cope's rule. The present paper investigates whether overall directional trends of body mass change, or correlations between patterns of body mass evolution and environmental factors have influenced the evolution of body mass in plesiadapiforms and primates. Analyses of the global fossil record of plesiadapiforms and primates suggest that the former did indeed follow an overall trend toward increased body mass compatible with the predictions of Cope's rule. In contrast, neither primates as a whole, nor a number of individual primate radiations (Adapiformes, Omomyiformes, and Anthropoidea), show any indication of overall directional patterns of body mass change. No correlations of primate body mass change with either the latitudinal distribution of fossil species, or with estimates of global temperature trends, were found. There is evidence, however, that direct competition between omomyiforms and adapiforms (the two main primate radiations known from the Paleogene) influenced processes of body mass evolution in omomyiforms. Am J Phys Anthropol, 2006. © 2006 Wiley‐Liss, Inc.
Connexin43 levels are increased in mouse neural crest cells exposed to homocysteine
Authors: Boot Marit J. , Gittenberger‐de Groot Adriana C. , Poelmann Robert E. , Gourdie Robert G.
Published: January 2006

BACKGROUND

Elevated homocysteine levels during embryonic development can result in neural tube and cardiovascular defects. The mechanisms that underlie the toxic effect of homocysteine are largely unknown.

METHODS

We cultured mouse neural tube explants to study the effects of homocysteine on the migratory behavior of neural crest cells and on the levels of the gap junction protein Connexin43 (Cx43) and the actin‐ and Cx43‐interacting protein ZO‐1.

RESULTS

Homocysteine exposure resulted in a significantly augmented maximal migration distance (MMD). The level of Cx43 immunolabeling was 2 times higher in the cytoplasm and cell protrusions of neural crest cells in homocysteine‐treated cultures than in control cultures. Furthermore, colocalization of Cx43 and ZO‐1 was increased in neural crest cell protrusions by this treatment.

CONCLUSION

Increased Cx43 levels were previously shown to result in abnormal embryonic development. Our data raises the hypothesis that the embryotoxic effects of homocysteine may be mediated in part by its effects on Cx43 expression level and gap junction function in neural crest cells. Birth Defects Research (Part A), 2005. © 2005 Wiley‐Liss, Inc.
Synthesis and Testing of Mechanism‐Based Protein‐Profiling Probes for Retaining Endo‐glycosidases
Authors: Williams Spencer J. , Hekmat Omid , Withers Stephen G.
Published: January 2006

New functional proteomics methods are required for targeting and identification of subsets of a proteome in an activity‐based fashion. Glycosidases play critical roles in biology, yet a robust method for functional analysis of their activities and identities in biological proteomes is still lacking. An aryl 2‐deoxy‐2‐fluoro xylobioside inactivator was conjugated through cleavable and noncleavable linker arms to a biotin tag, thereby yielding two new active‐site‐directed reagents for activity‐based profiling of retaining β‐glycanases in complex proteomes. Crucially, these tagged reagents possess high specificity for their target enzymes with kinetic parameters similar to those of the untagged reagent. Western blotting showed that these reagents bind and covalently label active retaining β‐glycanases both in pure enzyme samples and in the secreted proteome of the soil bacterium Cellulomonas fimi. Such reagents therefore show great promise for future activity‐based targeting of glycanases.
Reverse Prenyltransferase in the Biosynthesis of Fumigaclavine C in Aspergillus fumigatus: Gene Expression, Purification, and Characterization of Fumigaclavine C Synthase FGAPT1
Authors: Unsöld Inge A. , Li Shu‐Ming
Published: January 2006

A putative prenyltransferase gene—fgaPT1—has been identified in the biosynthetic gene cluster of fumigaclavines in Aspergillus fumigatus AF293. The gene was cloned and overexpressed in Escherichia coli, and the His6‐fusion FgaPT1 was purified to near homogeneity and characterized biochemically. The enzyme was found to convert fumigaclavine A into fumigaclavine C by attaching a dimethylallyl moiety to C‐2 of the indole nucleus in a “reverse” manner, that is, by connection of C‐3 of the dimethylallyl moiety to an aromatic nucleus. FgaPT1 is a soluble, dimeric protein with a subunit size of 50 kDa. Km(app) values for fumigaclavine A and dimethylallyl diphosphate were determined to be 6 and 13 μM, respectively, while the turnover number was 0.8 s−1. Metal ions such as Mg2+ and Ca2+ are not essential for the enzymatic activity. FgaPT1 showed relatively strict substrate specificity towards fumigaclavine A, with only dimethylallyl diphosphate being accepted as a donor under our conditions. FgaPT1 is the first reverse prenyltransferase from fungi to have been purified and characterized in homogenous form after heterologous overproduction. Surprisingly, it shows very low sequence similarity to the recently identified prenyltransferase LtxC from cyanobacteria, which also catalyzes the reverse prenylation of an indole nucleus.
Cover Picture: Regioselective Carbon–Carbon Bond Formation in Proteins with Palladium Catalysis; New Protein Chemistry by Organometallic Chemistry (ChemBioChem 1/2006)
Authors: Kodama Koichiro , Fukuzawa Seketsu , Nakayama Hiroshi , Kigawa Takanori , Sakamoto Kensaku , Yabuki Takashi , Matsuda Natsuko , Shirouzu Mikako , Takio Koji , Tachibana Kazuo , Yokoyama Shigeyuki
Published: January 2006

The cover picture shows how the carbon–carbon bond formation in a protein has been achieved by a combined approach of organic synthesis and genetic engineering. Palladium‐catalyzed reactions have been used in the synthesis of a wide variety of organic molecules. Among them, the Mizoroki–Heck reaction allows alkenylation of an aryl iodide to be performed under mild conditions. In the article by S. Fukuzawa, K. Tachibana, S. Yokoyama, et al. on p. 134 ff, it is demonstrated how fragile biomolecules like proteins can be substrates for palladium‐catalyzed reactions.
Predictive Dynamic Model of Air Separation by Pressure Swing Adsorption
Authors: Sadeghzadeh Ahari J. , Pakseresht S. , Mahdyarfar M. , Shokri S. , Zamani Y. , Nakhaei pour A. , Naderi F.
Published: January 2006

A general dynamic model is developed for separation of air over a carbon molecular sieve and a zeolite adsorbent for production of nitrogen and oxygen. The proposed model is validated using experimental data from working laboratory scale N2–PSA and laboratory scale O2–PSA systems. Simulations studies are performed to investigate the effect of changing various process variables, such as the duration of PSA steps, bed length and feed inlet velocity.
Separation of tert‐Butyl Alcohol‐Water Mixtures by a Heterogeneous Azeotropic Batch Distillation Process
Authors: Huiyuan W. , Songlin X.
Published: January 2006

Tert‐butyl alcohol and water form an azeotrope at normal pressure. Simple distillation cannot be used to separate these two components. In this article, a systematic study of the separation of tert‐butyl alcohol–water mixtures with an entrainer by heterogeneous azeotropic batch distillation was performed. Based upon the thermodynamic behavior of the ternary mixtures, cyclohexane was chosen as the entrainer. It formed ternary and binary heterogeneous azeotropes with the original components. The process feasibility analysis was validated by using rigorous simulation with chemical process simulation software – HYSYS Plant 2.2 and DISTIL 4.1. Simulation results were then corroborated in a batch experimental column for the selected entrainer.
Micromixing in Reactive, Deformable Bubble and Droplet Swarms
Authors: Koynov A. A. , Khinast J. G.
Published: January 2006

Detailed, high‐resolution numerical simulations have been performed of the buoyancy‐driven motion of deformable, chemically reacting bubble and droplet swarms. Mass transfer rates and chemical reaction selectivities were determined and a comparison is presented between the results for bubble/droplet swarms and single bubbles. The mixing in the wake of bubbles was characterized as well. It was shown that for mixing‐sensitive reaction networks, the hydrodynamics of the bubble swarm may significantly impact the reaction selectivity. Four special cases are highlighted, i.e., highly exothermic reactions, heterogeneously catalyzed reactions, animal cell cultures and experiments. The most important outcome of this work is that bubble swarms and the impact of the swarm hydrodynamics on reacting systems can be studied in detail. This is the first study of this kind reported in the literature. Its importance is paramount as knowledge of the unique flow dynamics inside bubble swarms is crucial to understanding the mechanisms controlling mass transport and chemical reactions and is a prerequisite for effective process intensification.
Factors influencing inclusion of patients with malignancies in clinical trials
Authors: Tournoux Caroline , Katsahian Sandrine , Chevret Sylvie , Levy Vincent
Published: January 2006

Participation in clinical trials remains low and is a central issue in oncology. The authors identified, through a systematic review, 75 papers published up to August 2004 that report barriers to recruitment of patients in clinical trials. These barriers range from patient preference and concern about information/consent to clinical problems with protocols. Strategies to overcome barriers on the part of patients and clinicians are needed and should be carefully evaluated. Thirty‐three (44%) papers reported factors related to patients as influencing the inclusion of patients, 28 (37%) reported clinician's related factors, and 37 (49%) other factors from either specific groups of patients (30 papers, 40%) and/or other scopes (13 papers, 17%). No differences in prevalence were found between papers dedicated to hematologic malignancies and solid tumors. Factors related to clinicians as influential were more frequently reported before 1995 (70%) than thereafter (25%; P = 0.0009). Reporting specific groups of patients as influential was more frequent in North American articles (50%) than in others (14%, P = 0.008).

Patients' barriers included mostly patient preference (12 papers), concern about information and/or consent (11 papers), worry about uncertainty (7 papers), and/or relationship with medical team (7 papers). Concerning clinicians, incompatibility of protocol with normal practice (nine papers), problems in complying with the protocol (eight papers), and/or consent procedure (eight papers) were the most reported factors. The remaining factors mostly relied on specific groups of patients (30 papers), notably age of patients (18 papers) and/or minority population (11 papers, all from the USA).

Strategies to overcome these barriers are needed and should be carefully evaluated. Cancer 2006. © 2005 American Cancer Society.
Numerical boundary corrector for elliptic equations with rapidly oscillating periodic coefficients
Authors: Versieux H. M. , Sarkis M.
Published: January 2006

We develop a numerical method to solve

where the matrix a(y)=(aij(y)) is symmetric positive definite, whose entries are periodic functions of y with periodic cell Y. More specifically we assume $ a_{ij} \in C^{1, \beta} (\Re^{2}), \quad \beta > 0 $. It is also assumed that there exists positive constants γa and βa such that $ \gamma_{a} ||\xi ||^{2} \le a_{ij} (y) \xi_{i} \xi_{j} \le \beta_{a} ||\xi||^{2} $ for all $ \xi \in \Re^{2} $ and $ y \in {\bar Y} $. The major goal in this paper is to develop a numerical approximation scheme on a mesh size h > ε (or h≫ε) with quasi‐optimal approximation on L2 and broken H1 norms. The new method is based on asymptotic analysis and a careful treatment of the boundary corrector term. This kind of equation has applications in areas such as the study of flow through porous media and composite materials. Copyright © 2005 John Wiley & Sons, Ltd.
Ruthenium‐Catalyzed Propargylation of Aromatic Compounds with Propargylic Alcohols
Authors: Inada Youichi , Yoshikawa Masato , Milton Marilyn Daisy , Nishibayashi Yoshiaki , Uemura Sakae
Published: January 2006

Reactions of propargylic alcohols bearing a terminal alkyne moiety with aromatic compounds in the presence of a catalytic amount of thiolate‐bridged diruthenium complexes give the corresponding propargylated aromatic compounds in high yields with complete selectivity. Intramolecular reactions of propargylic alcohols bearing an aromatic moiety proceed smoothly to afford the cyclized products in high yields with complete selectivity. The stoichiometric reaction of the ruthenium–allenylidene complex [Cp*RuCl(μ2‐SMe)2RuCp*(=C=C=CHPh)]BF4 (Cp* = η5‐C5Me5) with 10 equiv. 2‐methylfuran results in the formation of 2‐methyl‐5‐(1‐phenyl‐2‐propynyl)furan in 34 % yield, indicating that these catalytic reactions proceed via ruthenium–allenylidene intermediates. The reaction is considered to be an electrophilic substitution of aromatic compounds by the ruthenium‐stabilized propargyl cation. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
1H chemical shifts in NMR: Part 23, the effect of dimethyl sulphoxide versus chloroform solvent on 1H chemical shifts
Authors: Abraham Raymond J. , Byrne Jonathan J. , Griffiths Lee , Perez Manuel
Published: January 2006

The 1H chemical shifts of 124 compounds containing a variety of functional groups have been recorded in CDCl3 and DMSO‐d6 (henceforth DMSO) solvents. The 1H solvent shift Δδ = δ(DMSO) − δ(CDCl3) varies from −0.3 to +4.6 ppm. This solvent shift can be accurately predicted (rms error 0.05 ppm) using the charge model of α, β, γ and long‐range contributions. The labile protons of alcohols, acids, amines and amides give both, the largest solvent shifts and the largest errors. The contributions for the various groups are tabulated and it is shown that for H.C.C.X γ‐effects (X = OH, NH, O, NH.CO) there is a dihedral angle dependence of the γ‐effect. The group contributions are discussed in terms of the possible solvent–solute interactions. For protic hydrogens, hydrogen bonding is the dominant interaction, but for the remaining protons solvent anisotropy and electric field effects appear to be the major factors. Copyright © 2006 John Wiley & Sons, Ltd.
Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins
Authors: Mihalek I. , Reš I. , Lichtarge O.
Published: January 2006

It has been noted that slowly evolving protein residues have two properties: (a) they tend to cluster in the native fold, and (b) they delineate functional surfaces—parts of the surface through which the protein interacts with other proteins or small ligands. Herein, we demonstrate that the two are coupled sufficiently strongly that one effect, when observed, statistically implies the other. Detection of both can be accomplished in multiple sequence alignment related methods by the careful selection of relevant sequences. For the demonstration, we use two sets of protein families: a small set of diverse proteins with diverse functional surfaces, and a large set of homodimerizing enzymes. A practical outcome of our considerations is a simple prescriptive rule for the selection of homologous sequences for the comparative analysis of proteins: in order to optimize the detection of (potentially unknown) functional surfaces, it is sufficient to select sequences in such a way that the residues observed at any level of evolutionary divergence, as implied by the alignment, cluster on the folded protein. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Accuracy of the activation energy calculated from a thermoluminescence glow‐peak using a method that uses three points on the peak
Authors: Ogundare F. O. , Chithambo M. L.
Published: January 2006

This paper shows that the limitations of the general‐order and peak‐shape methods of kinetic analysis in cases where the retrapping probability greatly exceeds the recombination probability may be avoided if the analysis method proposed by Rasheedy [6–8] is applied. Analysis of computer simulated glow‐curves using the general‐order, peak‐shape, and Rasheedy's protocol showed that Rasheedy's method gave the best agreement between calculated and default values. The accuracy of the method improved for data selected well below 10% of the peak maximum in the initial‐rise region of a glow‐peak. The observed improvement has been attributed to the fact that in the initial‐rise region, the quasiequilibrium condition is better satisfied than at the higher temperature end of the glow‐peak. In general, we find that when the retrapping probability increases, the analysis for kinetic parameters is better carried out on data selected well below 10% of maximum peak intensity. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modeling dioxygen binding to the non‐heme iron‐containing enzymes
Authors: Nemukhin A. V. , Grigorenko B. L. , Topol I. A. , Burt S. K.
Published: January 2006

The structures and properties of the complexes formed upon binding the oxygen molecule to the iron sites in non‐heme 2‐oxoglutarate‐dependent enzymes are characterized by QM(CASSCF)/MM and density functional theory (DFT) calculations. Molecular models for the calculations are constructed following the crystal structure of hypoxia‐inducible factor asparaginyl hydroxylase (FIH‐1). DFT calculations for the 37‐atomic cluster have been carried out at the B3LYP(LANL2DZdp) level. The flexible effective fragment potential method is used as a combined quantum mechanical–molecular mechanical (QM/MM) technique to characterize the fragment of the enzymatic system, including 1,758 atoms in the MM part and 27 atoms in the QM part. In these calculations, the CASSCF(LANL2DZdp) approach is applied in the QM subsystem, and AMBER force field parameters are used in the MM subsystem. With both approaches, equilibrium geometry configurations have been located for different spin states of the system. In DFT calculations, the order of the states is as follows: septet, triplet (+7.7 kcal/mol), quintet (+10.7 kcal/mol). Geometry configurations correspond to the end‐on structures with no evidences of electron transfer from Fe(II) to molecular oxygen. In contrast, QM(CASSCF)/MM calculations predict the quintet state as the lowest one, while the septet structure has slightly (<2 kcal/mol) higher energy, and the triplet state is considerably more energetic. In QM/MM calculations, in both quintet and septet states, the electronic configurations show considerable electron charge transfer from iron to oxygen, and the oxidation state of iron in the metal binding site can be characterized as Fe(III). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Sequential genome‐wide association studies for monitoring adverse events in the clinical evaluation of new drugs
Authors: Kelly Patrick , Stallard Nigel , Zhou Yinghui , Whitehead John , Bowman Clive
Published: January 2006

Pharmacovigilance, the monitoring of adverse events (AEs), is an integral part in the clinical evaluation of a new drug. Until recently, attempts to relate the incidence of AEs to putative causes have been restricted to the evaluation of simple demographic and environmental factors. The advent of large‐scale genotyping, however, provides an opportunity to look for associations between AEs and genetic markers, such as single nucleotides polymorphisms (SNPs). It is envisaged that a very large number of SNPs, possibly over 500 000, will be used in pharmacovigilance in an attempt to identify any genetic difference between patients who have experienced an AE and those who have not.

We propose a sequential genome‐wide association test for analysing AEs as they arise, allowing evidence‐based decision‐making at the earliest opportunity. This gives us the capability of quickly establishing whether there is a group of patients at high‐risk of an AE based upon their DNA. Our method provides a valid test which takes account of linkage disequilibrium and allows for the sequential nature of the procedure. The method is more powerful than using a correction, such as Šidák, that assumes that the tests are independent. Copyright © 2006 John Wiley & Sons, Ltd.
An evaluation of the WAsP model at a coastal mountainous site in Norway
Authors: Berge Erik , Nyhammer Finn , Tallhaug Lars , Jacobsen Øystein
Published: January 2006

The prediction errors of WAsP are analysed by use of five 50 m measuring masts and the differences in the RIX‐values in a mountainous site of wind energy development at the Norwegian coast. The RIX‐values range from 13% to 18% thus the terrain is quite complex. High correlation (0.96) is found between the prediction error of WAsP and the differences in the RIX‐values. The inclusion of a coastal background station contributes strongly to this correlation. Predictions errors of 10%–15% are found based on the background coastal site. One should therefore be careful in applying background meteorological stations to wind resource assessment at the coastal mountains. Adjustments of the wind speed predictions based on the present findings are recommended. For the measuring stations within the wind farm area only a rather high correlation (0.76) between prediction errors and differences in the RIX‐values are also encountered. Prediction errors are in the range 0%–6%, which is considered quite low taking the complexity of the terrain into account. Copyright © 2006 John Wiley & Sons, Ltd.
Effect of enriched rotifers on growth, survival, and composition of larval Atlantic cod (Gadus morhua)
Authors: Park Heum Gi , Puvanendran Velmurugu , Kellett Anne , Parrish Christopher C. , Brown Joseph A.
Published: January 2006

Recently, the nutritional requirements of marine finfish larvae have received considerable attention, and studies have shown that docosahexaenoic acid (DHA) affects the growth and survival of marine finfish larvae. We investigated the effects of different rotifer diets containing variable amounts of DHA on the growth and survival of larval Atlantic cod (Gadus morhua L.). Four different commercial rotifer enrichment formulations were used: spray-dried whole cells composed of Crypthecodinium sp. (ED1), spray-dried whole cells of Schizochytrium sp. (ED2), an oil emulsion (ED3) and ED1, and dried Chlorella at a 7:3 ratio by weight (ED4). The resultant rotifers contained a similar concentration of DHA (1.1–1.6% DW), but the level of DHA differed in proportion to EPA for each enrichment, and was designated ER1–4. Twelve 30-l aquaria were used with three replicates per treatment. Larvae were fed with rotifers from 3 to 43 days post-hatch (dph) at 4000 prey l−1. At the end of the experiment, no significant differences were found in body length and dry weight between the larvae reared on ER1 and ER2. However, larvae reared on ER3 were significantly smaller (both in length and weight) than larvae reared on ER1 and ER2. Larval survival on the ER2 treatment at 43 dph was significantly higher than on the other three treatments. Our results showed a positive effect of rotifer DHA proportions on growth and survival of cod larvae, and demonstrated that Atlantic cod larvae require a high ratio of dietary DHA to EPA.
Genetic impact of gadoid culture on wild fish populations: predictions, lessons from salmonids, and possibilities for minimizing adverse effects
Authors: Bekkevold Dorte , Hansen Michael M. , Nielsen Einar E.
Published: January 2006

Little is known about the effects of ranched gadoids escaping into wild populations, and plans for substantial up-scaling of gadoid mariculture raise concerns about detrimental effects on local gene pools. Genetic studies from salmonid populations subjected to intentional or unintentional releases of hatchery-produced fish suggest that wild gene pools are affected by introgression, but that the genetic impact can be minor relative to expectations from the often substantial numbers of released hatchery fish. However, even if resilience to introgression is a general trend, wild population fitness is still predicted to be jeopardized by releases. In this paper, we review theoretical genetic effects of escapes of cultivated individuals and the empirical evidence for introgression effects, which are based mainly on salmonid studies. Based on knowledge of gadoid population structure and life history traits, we make predictions for effects of gadoid mariculture on wild populations and discuss approaches for monitoring and minimizing introgression effects.
Ab Initio multireference configuration-interaction study of hydrogen molecule activation by Cs-promoted Pt clusters
Authors: Benitez J. I. , Castillo S. , Poulain E. , Bertin V.
Published: January 2006

The adsorption of the H2 molecule on CsnPt(5−n) bcc (111) clusters for Cs∕Pt rates of 20%, 40%, and 80% is studied using ab initio multiconfigurational self-consistent field plus multireference configuration-interaction variational and perturbative calculations. The H2 interaction with the clusters is studied in ground and excited states with geometry optimization, where the hydrogen adsorption takes place by a Pt atom. These calculations are compared with those of H2 adsorption on Pt4. The most stable configurations of CsPt4 and Cs2Pt3 clusters (Cs∕Pt rates of 20% and 40%) are a doublet and a closed-shell singlet, respectively. Both clusters capture and activate the hydrogen molecule and their behaviors resemble Pt4. The H2 capture distances are, respectively, similar and smaller than Pt4 capture distances, while the H–H bond dissociation distances are similar and bigger than those of Pt4; however, none of them presents activation barriers. The most stable Cs4Pt cluster (Cs∕Pt rate of 80%) is also a closed-shell singlet; it also captures and activates the hydrogen molecule and shows a different behavior as compared with CsPt4, Cs2Pt3, and Pt4 clusters. The capture distance is quite smaller and is obtained after surmounting an activation barrier. For all clusters studied here, no hydrogen absorption was observed, only the adsorption of H2.
Al–H bond formation in hydrated aluminum oxide cluster anions
Authors: Das Ujjal , Raghavachari Krishnan
Published: January 2006

Quantum chemical calculations have been performed to investigate the interaction of a water molecule with gas phase aluminum oxide cluster anions. While oxygen-rich clusters (AlxOy−,xy) generate metal hydrides. These hydride species are, in many cases, 30–35kcal∕mol more stable than their hydroxide counterparts. Our observations on such competing reaction pathways may be useful to understand the catalytic role of alumina nanoparticles in many chemical reactions.
Enhanced translational diffusion of rubrene in sucrose benzoate
Authors: Rajesh Rajian Justin , Huang Wei , Richert Ranko , Quitevis Edward L.
Published: January 2006

The translational diffusion of rubrene in the fragile molecular glass former, sucrose benzoate (SB) (fragility index m≈94), has been studied from Tg+6K to Tg+71K(Tg=337K) by using the technique of holographic fluorescence recovery after photobleaching. In the temperature range of the measurements, the translational relaxation functions were observed to decay exponentially, indicating that Fick’s law of diffusion governs the translational motion of rubrene in sucrose benzoate. The value of the translational diffusion coefficient DT obtained from the 1∕e time of the translational relaxation function varied from 5.3×10−15cm2s−1 at 343 K to 5.0×10−9cm2s−1 at 408 K. The temperature dependence of DT for diffusion of rubrene in SB is compared with that of the viscosity and the dielectric relaxation time τD of SB. The temperature dependence of DT is weaker than that of T∕η for T<1.2Tg but tracks the reciprocal of the dielectric relaxation time 1∕τD for 1.05Tg<T<1.21Tg. The translational diffusion coefficient at Tg is enhanced by a factor of ≈2.5×102 over the value predicted by the Stokes-Einstein equation. The decoupling of probe diffusion from the viscosity is characterized by a scaling law, DT∼η−ξ, with ξ=0.729.
Planar optical waveguide in potassium titanyl arsenate formed by oxygen ion implantation at low doses
Authors: Jiang Yi , Wang Ke-Ming , Wang Xue-Lin , Jia Chuan-Lei , Wang Lei , Jiao Yang , Lu Qing-Ming , Ma Hong-Ji , Nie Rui , Shen Ding-Yu
Published: January 2006

Monomode, nonleaky planar optical waveguides have been fabricated in x-cut biaxial crystal potassium titanyl arsenate (KTiOAsO4 or KTA) by 3.0 MeV O+ ion implantation at doses from 5×1012 to 1×1014ions∕cm2 at room temperature. The waveguide properties were characterized by the method of prism coupling at 633 nm. Positive changes of both nx and ny refractive indices (corresponding TE and TM polarized light separately) occur in the waveguide region. The propagation loss of the waveguide formed at a dose of 5×1013ions∕cm2 was reduced to 0.66dB∕cm after annealing at 230 °C for 30 minutes. Continuous and homogeneous magnified field pattern of the propagation light in the annealed waveguide was collected and studied by end-coupling method.
Multifunctionalization of organosilanes on submicron-sized island-type electrodes for the selective detection of metal ions
Authors: Kim Younghun , Choi Inhee , Kang Sung Koo , Lee Jeongjin , Yi Jongheop
Published: January 2006

A submicron-sized metal ion detector with two electrodes was fabricated by atomic force microscopy lithography. Two detection zones were functionalized with thiol (SH) and amine (NH2) groups, which have a high affinity for mercury and copper, respectively. Conductance with metal adsorption was measured by the forced contact of the tip (mobile electrode) with the gold-deposited center (fixed electrode) at a constant repulsive force (38nN). In Cu2+∕Hg2+ binary solutions, one electrode (thiol group) showed a high affinity for mercury, and the other for copper. This two-electrode system immobilized with different functional groups was used in the selective adsorption and detection of target materials.
Influence of dehydrated nanotubed titanic acid on polymer light-emitting diodes with phosphorescent dye
Authors: Qian L. , Zhang T. , Wang Y. S. , Xu X. R. , Jin Z. S. , Du Z. L.
Published: January 2006

In this letter, we demonstrate that hole injection and transport in polymer light-emitting diodes with phosphorescent dye Ir(ppy)3 can be significantly enhanced by doping p-type conductive dehydrated nanotubed titanic acid into poly(vinylcarbazole) (PVK) films at 2wt.%. At the same time, both energy transfer and exciton recombination efficiency are improved because of the open and straight conformation of the PVK molecule in the nanocomposite. The performance of these devices was greatly improved, showing higher luminance, enhanced efficiency, and a lower turn-on voltage.