bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic confusion and market mislabelling of threatened skates: important consequences for their conservation status
Authors: Iglésias Samuel P. , Toulhoat Lucile , Sellos Daniel Y. 
Published: November 2009

Abstract
The iconic European common skate (Dipturus batis) has been described as the first clear case of a fish species brought to the brink of extinction by commercial fishing. Its listing was upgraded to Critically Endangered on the 2006 IUCN Red List of Threatened Species. According to FAO fishery statistics, France is responsible for 60.2% of the 502 tonnes reported as ‘D. batis’ in the 2005 world landings.
Noticeable phenotypic differences within the species and inconsistencies in published data on its sexual maturation required careful re‐examination of its taxonomy. Morphology, genetics, and life history reveal that two distinct species have been erroneously confused since the 1920s under the single scientific name D. batis. Here it is argued that they should be resurrected as two valid species. The common skate D. batis species‐complex is split into two nominal species, the blue skate (provisionally called D. cf. flossada) and the flapper skate (D. cf. intermedia) with maximum lengths of 143.2 cm and 228.8 cm respectively.
This taxonomic confusion puts into question all previously accumulated data based on D. batis. Its endangered status highlights the need for an extensive reassessment of population collapses with accurately identified species. In 2006/2007 an extensive survey (4110 skates, 14.081 tonnes by weight) was conducted in the main French ports of the D. batis species‐complex and relatives (D. oxyrinchus, D. nidarosiensis and Rostroraja alba) that are mixed together in landings under the names ‘D. batis’ and ‘D. oxyrinchus’.
The survey reveals that official fishery statistics mask species‐specific declines, due to the mislabelling of five species under only two landing names. Trends in landings since the 1960s and the life history of these species suggest a dramatic decline and collapse of the spawning stock, preventing the recovery of relict populations.
The risk of extinction of these depleted species may be higher than previously assessed and might be unavoidable without immediate and incisive conservation action. Copyright © 2009 John Wiley & Sons, Ltd.
Relationship of the h‐index, g‐index, and e‐index
Authors: Zhang Chun‐Ting 
Published: December 2009

AbstractOf h‐type indices available now, the g‐index is an important one in that it not only keeps some advantages of the h‐index but also counts citations from highly cited articles. However, the g‐index has a drawback that one has to add fictitious articles with zero citation to calculate this index in some important cases. Based on an alternative definition without introducing fictitious articles, an analytical method has been proposed to calculate the g‐index based approximately on the h‐index and the e‐index. If citations for a scientist are ranked by a power law, it is shown that the g‐index can be calculated accurately by the h‐index, the e‐index, and the power parameter. The relationship of the h‐, g‐, and e‐indices presented here shows that the g‐index contains the citation information from the h‐index, the e‐index, and some papers beyond the h‐core.
Commercializing lignocellulosic bioethanol: technology bottlenecks and possible remedies
Authors: Banerjee Saumita , Mudliar Sandeep , Sen Ramkrishna , Giri Balendu , Satpute Devanand , Chakrabarti Tapan , Pandey R.A. 
Published: December 2009

AbstractWith diminishing oil supplies and growing political instability in oil‐producing nations, the world is facing a major energy threat which needs to be solved by virtue of alternative energy sources. Bioethanol has received considerable attention in the transportation sector because of its utility as an octane booster, fuel additive, and even as neat fuel. Brazil and the USA have been producing ethanol on a large scale from sugarcane and corn, respectively. However, due to their primary utility as food and feed, these crops cannot meet the global demand for ethanol production as an alternative transportation fuel. Lignocellulosic biomass is projected as a virtually eternal raw material for fuel ethanol production. The main bottleneck so far has been the technology concerns, which do not support cost‐effective and competitive production of lignocellulosic bioethanol. This review sheds light on some of the practical approaches that can be adopted to make the production of lignocellulosic bioethanol economically attractive. These include the use of cheaper substrates, cost‐effective pre‐treatment techniques, overproducing and recombinant strains for maximized ethanol tolerance and yields, improved recovery processes, efficient bioprocess integration, economic exploitation of side products, and energy and waste minimization. An integrated and dedicated approach can help in realizing large‐scale commercial production of lignocellulosic bioethanol, and can contribute toward a cleaner and more energy efficient world. Copyright © 2009 Society of Chemical Industry and John Wiley & Sons, Ltd
Why microalgal biofuels won't save the internal combustion machine
Authors: van Beilen Jan B. 
Published: December 2009

AbstractProponents of microalgae biofuel technologies often claim that the world demand of liquid fuels, about 5 trillion liters per year, could be supplied by microalgae cultivated on only a few tens of millions of hectares. This perspective reviews this subject and points out that such projections are greatly exaggerated, because (1) the productivities achieved in large‐scale commercial microalgae production systems, operated year‐round, do not surpass those of irrigated tropical crops; (2) cultivating, harvesting and processing microalgae solely for the production of biofuels is simply too expensive using current or prospective technology; and (3) currently available (limited) data suggest that the energy balance of algal biofuels is very poor. Thus, microalgal biofuels are no panacea for depleting oil or global warming, and are unlikely to save the internal combustion machine. Copyright © 2009 Society of Chemical Industry and John Wiley & Sons, Ltd
Organic anion transporters: discovery, pharmacology, regulation and roles in pathophysiology
Authors: VanWert Adam L. , Gionfriddo Michael R. , Sweet Douglas H. 
Published: December 2009

AbstractOur understanding of the mechanisms behind inter‐ and intra‐patient variability in drug response is inadequate. Advances in the cytochrome P450 drug metabolizing enzyme field have been remarkable, but those in the drug transporter field have trailed behind. Currently, however, interest in carrier‐mediated disposition of pharmacotherapeutics is on a substantial uprise. This is exemplified by the 2006 FDA guidance statement directed to the pharmaceutical industry. The guidance recommended that industry ascertain whether novel drug entities interact with transporters. This suggestion likely stems from the observation that several novel cloned transporters contribute significantly to the disposition of various approved drugs. Many drugs bear anionic functional groups, and thus interact with organic anion transporters (OATs). Collectively, these transporters are nearly ubiquitously expressed in barrier epithelia. Moreover, several reports indicate that OATs are subject to diverse forms of regulation, much like drug metabolizing enzymes and receptors. Thus, critical to furthering our understanding of patient‐ and condition‐specific responses to pharmacotherapy is the complete characterization of OAT interactions with drugs and regulatory factors. This review provides the reader with a comprehensive account of the function and substrate profile of cloned OATs. In addition, a major focus of this review is on the regulation of OATs including the impact of transcriptional and epigenetic factors, phosphorylation, hormones and gender. Copyright © 2009 John Wiley & Sons, Ltd.
The role of the calmodulin‐dependent pathway in static magnetic field‐induced mechanotransduction
Authors: Yang Jen‐Chang , Lee Sheng‐Yang , Chen Chi‐An , Lin Che‐Tong , Chen Chang‐Chih , Huang Haw‐Ming 
Published: December 2009

AbstractWhile the effects of static magnetic fields (SMFs) on osteoblastic differentiation are well demonstrated, the mechanotransduction pathways of SMFs are still unclear. The aim of this study was to explore the role of calmodulin in the biophysical effects of SMFs on osteoblastic cells. MG63 cells were exposed to a 0.4 T SMF. The expression of phosphodiesterase RNA in the cytoplasm was tested using real‐time polymerase chain reaction. The differentiation of the cells was assessed by detecting changes in alkaline phosphatase activity. The role of calmodulin antagonist W‐7 was used to evaluate alterations in osteoblastic proliferation and differentiation after the SMF simulations. Our results showed that SMF exposure increased alkaline phosphatase activity and phosphodiesterase 1C gene expression in MG63 cells. Addition of W‐7 significantly inhibited the SMF‐induced cellular response. We suggest that one possible mechanism by which SMFs affects osteoblastic maturation is through a calmodulin‐dependent mechanotransduction pathway. Bioelectromagnetics 31:255–261, 2010. © 2009 Wiley‐Liss, Inc.
MutL: conducting the cell's response to mismatched and misaligned DNA
Authors: Polosina Yaroslava Y. , Cupples Claire G. 
Published: December 2009

AbstractBase pair mismatches in DNA arise from errors in DNA replication, recombination, and biochemical modification of bases. Mismatches are inherently transient. They are resolved passively by DNA replication, or actively by enzymatic removal and resynthesis of one of the bases. The first step in removal is recognition of strand discontinuity by one of the MutS proteins. Mismatches arising from errors in DNA replication are repaired in favor of the base on the template strand, but other mismatches trigger base excision or nucleotide excision repair (NER), or non‐repair pathways such as hypermutation, cell cycle arrest, or apoptosis. We argue that MutL homologues play a key role in determining biologic outcome by recruiting and/or activating effector proteins in response to lesion recognition by MutS. We suggest that the process is regulated by conformational changes in MutL caused by cycles of ATP binding and hydrolysis, and by physiologic changes which influence effector availability.
The origins of larval forms: what the data indicate, and what they don't
Authors: Minelli Alessandro 
Published: December 2009

AbstractWhat is a larva, if it is not what survives of an ancestor's adult, compressed into a transient pre‐reproductive phase, as suggested by Haeckel's largely disreputed model of evolution by recapitulation? A recently published article hypothesizes that larva and adult of holometabolous insects are developmental expressions of two different genomes coexisting in the same animal as a result of an ancient hybridization event between an onychophoran and a primitive insect with eventless post‐embryonic development. More likely, however, larvae originated from late embryonic or early post‐embryonic stages of ancestors with direct development. Evolutionary novelties would thus be intercalary rather than terminal, with respect to the ancestor's ontogenetic schedule. This scenario, supported by current research on holometabolous insects and marine invertebrates with complex life cycles, offers a serious alternative to the traditional scenario (‘what is early in ontogeny is also early in phylogeny’) underlying the current perception of the evolution of genetic regulatory networks.
Secreted production of Renilla luciferase in Bacillus subtilis
Authors: Chiang Chung‐Jen , Chen Po Ting , Chao Yun‐Peng 
Published: December 2009

AbstractLuciferase (Rluc) from the soft coral Renilla reniformis has been widely used as a bioluminescent reporter, and its secreted production has been solely performed in mammalian cells thus far. To make the production more efficient, a series of approaches was attempted to overproduce Rluc extracellularly in Bacillus subtilis. First, Cys124 in the Rluc gene was substituted with Ala. The mutant gene was subsequently incorporated into a pUB110/R6K‐based plasmid, consequently, fusing with the P43 promoter and the sacB signal peptide. With the nitrogen‐rich medium, B. subtilis strain bearing the plasmid became able to secret a detectable amount of Rluc. Moreover, the secretion signal for the Rluc gene was replaced by the aprN leader peptide with or without the propeptide. The result led to a more than twofold increase in the secreted Rluc. Finally, by enhancing the transcription of the Rluc gene implementing the P43 and spac tandem promoter, it resulted in the secreted Rluc with a yield of 100 mg/L. Overall, this study illustrates a potential strategy for improving the secretion efficiency of heterologous proteins in B. subtilis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Experimental and theoretical assessment of maximum productivities for the microalgae Chlamydomonas reinhardtii in two different geometries of photobioreactors
Authors: Takache Hosni , Christophe Gwendoline , Cornet Jean‐François , Pruvost Jérémy 
Published: December 2009

AbstractThe validity of a simple, reliable, and useful recently published formula enabling to calculate the maximum volumetric biomass productivities in photobioreactors (PBRs) was investigated through the cultivation of the microalga Chlamydomonas reinhardtii. Experimental maximum kinetic performances accurately obtained in two different, artificially lightened torus‐plane and cylindrical reactors having the same specific illuminated area confirmed the availability, power, and robustness of such formula. The predictive kinetic parameters previously proposed and validated with cyanobacteria were then proved general and robust in case of eukaryotic microalgae, as postulated in the founding article. In this case, an additional criterion requiring rigorous control of the working illuminated fraction γ = 1 ± (15%) inside the reactor is demonstrated. For this, the usefulness and reliability of a generalized two‐flux model accurately describing the radiation field inside turbid culture media of C. reinhardtii were also established in this article. These important results contribute to identify the main engineering factors governing light‐limited PBRs functioning and then to clarify some misinterpretations widely reported in the literature. Together with the referenced previous work, this article gives a framework toward optimal conception of PBRs on a strong physical basis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010
An Alternative Approach to Quantify Partition Processes in Confined Environments: The Electrochemical Behavior of PRODAN in Unilamellar Vesicles
Authors: Moyano Fernando , Molina Patricia G. , Silber Juana J. , Sereno Leonides , Correa N. Mariano 
Published: November 2009

AbstractHerein, we investigate the behavior of the electroactive molecular probe 6‐propionyl‐2‐dimethyl amino naphthalene (PRODAN) in large unilamellar vesicles (LUV) formed with the phospholipid 1,2‐di‐oleoyl‐sn‐glycero‐3‐phosphatidylcholine (DOPC) by using cyclic voltammetry (CV). The CV studies in pure water confirm our previous spectroscopic results that PRODAN self‐aggregates due to its low water solubility. Moreover, the electrochemical results also reveal that the PRODAN aggregated species are non‐electroactive within the studied electrochemical potential region. In DOPC LUV media, the redox behavior of PRODAN shows how the LUV bilayer interacts with PRODAN aggregated species to form PRODAN monomer species. Moreover, the electrochemical response of PRODAN allows us to propose a model for explaining the electrochemical experimental results and—in conjunction with our measurements—for calculating the value of the partition constant (Kp) of PRODAN between the water and LUV bilayer pseudophases. This value coincides with that obtained through an independent technique. Moreover, our electrochemical model allows us to calculate the diffusion coefficient (D) for the DOPC LUV, which coincides with the D value obtained through dynamic light scattering (DLS). Thus, our data clearly show that electrochemical measurements could be a powerful alternative approach to investigate the behavior of nonionic electroactive molecules embed in a confined environment such as the LUV bilayer. Moreover, we believe that this approach can be used to investigate the behavior of non‐optical molecular drugs embedded in bilayer media.
Fine needle aspiration of renal cortical lesions in adults
Authors: Adeniran Adebowale J. , Al‐Ahmadie Hikmat , Iyengar Pratibha , Reuter Victor E. , Lin Oscar 
Published: December 2009

AbstractThe role of fine needle aspiration (FNA) biopsy of renal cortical lesions was controversial in the past because the result of the FNA did not affect clinical management. All renal cortical lesions, except metastasis, were subject to surgical resection. However, with the advances in neoadjuvant targeted therapies, knowledge of the renal cortical tumor histological subtype is critical for tailoring clinical trials and follow‐up strategies. At present, there are clinical trials involving the use of novel kinase inhibitors for conventional (clear cell) and papillary renal cell carcinoma. We studied 143 consecutive cases of renal cortical lesions, evaluated after radical or partial nephrectomies over a 2‐year period. An air‐dried smear and a Thinprep® slide were prepared in all cases. The slides were Diff‐Quick and Papanicolaou stained, respectively. The cytology specimens were reviewed and the results were then compared with the histologic diagnosis. Cytology was highly accurate to diagnose conventional RCC, while the accuracy for papillary RCC, chromophobe RCC, and papillary urothelial carcinoma was much lower. Our results indicate that ancillary studies might have an important role in the subclassification of renal cortical neoplasms for targeted treatment. Diagn. Cytopathol. 2010;38:710–715. © 2009 Wiley‐Liss, Inc.
Enhancing the scope of conventional cervical cytology for detecting HPV infection
Authors: Nijhawan Raje , Mittal Neha , Suri Vanita , Rajwanshi Arvind 
Published: December 2009

AbstractCervical neoplasia is attributed to a persistent Human Papilloma Virus infection. The Pap smear being the mainstay of cervical cancer screening in low‐resource settings, we studied the nonclassical features which might indicate HPV infection. These included abortive koilocytes, mild dyskeratosis, parakeratosis, mild nuclear hyperchromasia, bi/multinucleation, measles cells, and keratohyaline‐like granules. Two hundred and eight women with a satisfactory Pap smear and a Hybrid Capture II test were compared against the “HPV Gold Standard” for validation of the nonclassical signs. This was defined as one with any/all of the following: definite HPV‐related lesions on Pap smear (LSIL and above), hrHPV positivity, and CIN I, or above on histology. The highest PPV and NPV were achieved by bi/multinucleation and mild nuclear hyperchromasia, respectively. The mean number of nonclassical signs for HPV Gold Standard‐positive and ‐negative groups was 5.52 and 3.12 per smear, respectively (P < 0.0005). Abortive koilocytes, mild dyskeratosis, mild nuclear hyperchromasia, bi/multinucleation, parakeratosis, and diffuse keratohyaline granules had the best correlation with the gold standard (P < 0.05). Addition of nonclassical signs to established intraepithelial lesions on Pap smear increased the sensitivity from 52.31to 59.10% and reduced the specificity from 100 to 98%. To maximize the benefit from grouping of these signs, various combinations were studied. The best was: abortive koilocytes, mild nuclear hyperchromasia, and bi/multinucleation. Another was abortive koilocytes, mild nuclear hyperchromasia, bi/multinucleation, and mild dyskeratosis. In conclusion, these signs proved useful for identifying HPV infection. Population‐based studies are required to corroborate our findings. Diagn. Cytopathol. 2010;38:645–651. © 2009 Wiley‐Liss, Inc.
Factors influencing the challenges of modelling and treating fecal indicator bacteria in surface waters
Authors: Surbeck Cristiane Q. 
Published: November 2009

AbstractIn the United States, thousands of creeks, rivers, and coastal zones are listed as impaired in the Clean Water Act's 303(d) list. The number one general cause of impairments is denoted as ‘pathogens’, which can include known pathogenic organisms or, more commonly, fecal indicator bacteria (FIB), such as fecal coliform bacteria, Escherichia coli, and enterococci bacteria. Despite efforts by water quality managers to reduce FIB in surface waters via treatment, successful and significant reduction of FIB has been difficult to achieve to meet water quality standards. In addition, current efforts to numerically model FIB concentrations in surface waters do not consider many complexities associated with FIB as a pollutant. Reasons for the challenge of treating and modelling FIB are their varied sources and mechanisms of survival and decay in the environment. This technical note addresses this challenge by discussing the nature of FIB, their sources, and their fate and transport mechanisms. Sources of FIB to surface waters include wastewater, stormwater and dry‐weather runoff, and animals. Mechanisms of pathogen indicator occurrence in surface waters are transport in stormwater, ecological proliferation, and interaction with sediments. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis and Stereochemical Properties of “Extended” Biphenols Bridged by ortho‐, meta‐, and para‐Phenylene Spacers
Authors: Gruza Mariusz M. , Chambron Jean‐Claude , Espinosa Enrique , Aubert Emmanuel 
Published: December 2009

AbstractA series of isomeric biphenols based on para‐ (1), meta‐ (2), and ortho‐ (3) terphenyl backbones was synthesized. Suzuki cross‐coupling methodology was employed for the construction of the terphenyl backbone of their methyl‐protected precursors (respectively 8, 13, and 16). Using K2CO3 as the base, the best reaction conditions involved DMF at 100 °C as solvent. Anhydrous conditions greatly improved the yields of the sterically crowded systems (particularly 16). ortho‐Terphenyls 3 and 16 exist as mixtures of syn/anti atropisomers in solution. Compound 16 crystallizes in the anti‐in form. DFT calculations at the B3LYP/6‐311+G(d,p) level indicate that for both compounds the anti‐in form is more stable than the syn form by 6.07 and 2.07 kJ mol–1 for 16 and 3, respectively. These ΔΔG0 values are higher by the same factor (of two) than those obtained in solution at 240 K (3.17 and 0.93 kJ mol–1). The atropisomeric properties of 16 and 3 are finally discussed in the context of ortho‐terphenyls in the literature. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Enantioselective Synthesis of Unsymmetrical Triarylmethanes by Chiral Brønsted Acids
Authors: Sun Feng‐Lai , Zheng Xiao‐Jian , Gu Qing , He Qing‐Li , You Shu‐Li 
Published: November 2009

AbstractChiral Brønsted acid catalyzed Friedel–Crafts alkylation of electron‐rich arenes with (3‐indolyl)methanamines has been realized to provide an efficient synthesis of enantioenriched unsymmetrical triarylmethanes. With 5 mol‐% of a newly developed chiral phosphoric acid, the enantioenriched unsymmetrical triarylmethanes were obtained in excellent yields with up to 91 % ee.