bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree
Authors: Gadagkar Sudhindra R. , Rosenberg Michael S. , Kumar Sudhir 
Published: December 2004

AbstractPhylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super‐gene alignment, which is then analyzed to generate the species tree. In the other, phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree. Here, we have compared these two approaches by means of computer simulation, using 448 parameter sets, including evolutionary rate, sequence length, base composition, and transition/transversion rate bias. In these simulations, we emphasized a worst‐case scenario analysis in which 100 replicate datasets for each evolutionary parameter set (gene) were generated, and the replicate dataset that produced a tree topology showing the largest number of phylogenetic errors was selected to represent that parameter set. Both randomly selected and worst‐case replicates were utilized to compare the consensus and concatenation approaches primarily using the neighbor‐joining (NJ) method. We find that the concatenation approach yields more accurate trees, even when the sequences concatenated have evolved with very different substitution patterns and no attempts are made to accommodate these differences while inferring phylogenies. These results appear to hold true for parsimony and likelihood methods as well. The concatenation approach shows >95% accuracy with only 10 genes. However, this gain in accuracy is sometimes accompanied by reinforcement of certain systematic biases, resulting in spuriously high bootstrap support for incorrect partitions, whether we employ site, gene, or a combined bootstrap resampling approach. Therefore, it will be prudent to report the number of individual genes supporting an inferred clade in the concatenated sequence tree, in addition to the bootstrap support. J. Exp. Zool.(Mol. Dev. Evol.) 304B:000–000, 2005. © 2005 Wiley‐Liss, Inc.
Delayed extraction experiments using a repulsing potential before ion extraction: evidence of non‐covalent clusters as ion precursor in UV matrix‐assisted laser desorption/ionization. Part II—Dynamic effects with α‐cyano‐4‐hydroxycinnamic acid matrix
Authors: Fournier I. , Brunot A. , Tabet J. C. , Bolbach G. 
Published: December 2004

AbstractDelayed extraction experiments were undertaken to gain a better insight into the dynamic effects involved in the ion formation in UV matrix‐assisted laser desorption/ionization. Part I1 was devoted to a 2,5‐dihydroxybenzoic (2,5‐DHB) matrix. The results clearly demonstrated the existence and the role of high‐mass precursors corresponding to a non‐covalent matrix–analyte association in ion formation. In this complementary study, ion flight time and abundance were studied as a function of the delay extraction time using the matrix α‐cyano‐4‐hydroxycinnamic acid (HCCA). Under our instrumental conditions, where ejected ions experienced a low repulsing electric field before extraction, two main results were obtained: (i) two ion components are observed in the peak profiles depending on the repulsing field, a first, major component (I) similar to that observed for 2,5‐DHB and a second, minor component (II) apparently triggered by the delayed extraction pulse, and (ii) ion time‐of‐flight variation vs delay time remained lower than that noted with 2,5‐DHB matrix, indicating that the initial axial velocity is smaller. The initial kinetic energy of matrix and low molecular mass peptide ions for the component I is not high enough to overcome the repulsing potential in the delay time range (200–2200 ns) and we have to assume that ions have non‐covalent clusters as precursors. Complete desolvation of these clusters–aggregates would be achieved through the extraction step. Simulations of the ion time‐of‐flight as a function of the delay time allow the determination of the average size of the precursors, typically 4500, 40000 and 50000 u for HCCA, ACTH 7–38 and bovine insulin quasi‐molecular ion, respectively, assuming that the precursors are singly charged. The size of these ion precursors is greater than that of those generated for 2,5‐DHB. For component II, ions are probably not solvated and they are directly desorbed from the target. Taking into account the results on HCCA and 2,5‐DHB matrices and other results from the literature, a general model for ion formation based on clusters as ion precursors is proposed and discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Enzymatic Degradation of Poly(L‐lactide) and Poly(ε‐caprolactone) Electrospun Fibers
Authors: Zeng Jing , Chen Xuesi , Liang Qizhi , Xu Xiuling , Jing Xiabin 
Published: December 2004

AbstractSummary: Poly(L‐lactide) (PLLA) and poly(ε‐caprolactone) (PCL) ultrafine fibers were prepared by electrospinning. The influence of cationic and anionic surfactants on their enzymatic degradation behavior was investigated by measuring weight loss, molecular weight, crystallinity, and melting temperature of the fibers as a function of degradation time. Under the catalysis of proteinase K, the PLLA fibers containing the anionic surfactant sodium docecyl sulfate (SDS) exhibited a faster degradation rate than those containing cationic surfactant triethylbenzylammonium chloride (TEBAC), indicating that surface electric charge on the fibers is a critical factor for an enzymatic degradation. Similarly, TEBAC‐containing PCL fibers exhibited a 47% weight loss within 8.5 h whereas SDS‐containing PCL fibers showed little degradation in the presence of lipase PS. By analyzing the charge status of proteinase K and lipase PS under the experimental conditions, the importance of the surface charges of the fibers and their interactions with the charges on the enzymes were revealed. Consequently, a “two‐step” degradation mechanism was proposed: (1) the enzyme approaches the fiber surface; (2) the enzyme initiates hydrolysis of the polymer. By means of differential scanning calorimetry and wide‐angle X‐ray diffraction, the crystallinity and orientation changes in the PLLA and PCL fibers during the enzymatic degradation were investigated, respectively.SEM photographs of PCL‐TEBAC fiber samples before and after enzymatic degradation (2.75 h) at 37 °C.magnified imageSEM photographs of PCL‐TEBAC fiber samples before and after enzymatic degradation (2.75 h) at 37 °C.
Synthesis of Aliphatic‐Aromatic Copolyesters by a High Temperature Bulk Reaction Between Poly(ethylene terephthalate) and Cyclodi(ethylene succinate)
Authors: Salhi Slim , Tessier Martine , Blais Jean‐Claude , El Gharbi Rachid , Fradet Alain 
Published: December 2004

AbstractSummary: Cyclodi(ethylene succinate) (C2) easily reacts with poly(ethylene terephthalate) (PET) in the melt leading to the formation of high molar mass PET‐Poly(ethylene succinate) copolymers (PET‐PES). Copolyesters with a PET/C2 starting mass ratio of 90/10, 80/20, 70/30 and 50/50 were synthesized and characterized by 1H NMR and MALDI‐TOF MS. The 50/50 copolyester was almost random, while copolyesters with higher ethylene terephthalate contents exhibited some block copolymer character. MALDI‐TOF MS/SEC off‐line coupling was used to determine copolyester absolute average molar masses. The results indicate that the conventional SEC polystyrene calibration strongly overestimates copolyester molar masses. The melting temperatures and crystallinity of the 90/10, 80/20 and 70/30 copolyesters were significantly higher than those of comparable PET‐aliphatic polyester copolymers.
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A Study of the Synthesis and Properties of AM/AMPS Copolymer as Superabsorbent
Authors: Liu Yang , Xie Jian‐Jun , Zhu Mei‐Fang , Zhang Xin‐Ying 
Published: December 2004

AbstractSummary:A new superabsorbent polymer, PAMA, has been prepared in an aqueous solution using acrylamide (AM) and 2‐acrylamido‐2‐methyl‐propanesulfonic acid (AMPS) as monomers, potassium persulfate (PPS) as initiator, andN,N′‐methylenebisacrylamide (NMBA) as cross‐linker. The absorbing properties and water retention of PAMA have been investigated. It is found that the absorbency of PAMA can reach 2 451 and 119 g · g−1in distilled water and in 0.9 wt.‐% NaCl solution, respectively. This copolymer also can absorb a large amount of pure methanol (277 g · g−1), a property that has not been reported for the other superabsorbent polymers in the literature. The swelling behavior of PAMA in some water/organic solvent mixtures and water retention of PAMA in sand have been investigated.Water retention of the PAMA in sand at 80 °C. 1) Sample containing PAMA; 2) Sample without PAMA.imageWater retention of the PAMA in sand at 80 °C. 1) Sample containing PAMA; 2) Sample without PAMA.
Shish Kebab Morphology induced in Polyhydroxybutyrate under Shear Flow
Authors: Sharma Lakshmi , Ogino Yoshino , Kanaya Toshiji 
Published: December 2004

AbstractSummary: In‐situ rheo small‐angle X‐ray scattering (SAXS), rheo‐light scattering, and rheo‐optical methods were employed to investigate the resultant morphology of polyhydroxybutyrate (PHB) under varying shear flow conditions. Immediately after shear flow application, a highly orientated structure emerged and row nucleation was identified at high shears. Only the initial stages of shish growth (we term the partial shish) were confirmed at excessively high shear conditions. However, only the kebabs were identified at medium shears, below this neither the shish nor kebab were observed. We believe this partial shish is a result of insufficient stability resulting from using such a low‐molecular‐weight species. We conclude that from our observations the shish kebab mechanism appears to display similarities to the Janeschitz‐Kriegl model of precursor formation.Left: In‐situ rheo‐SAXS two‐dimensional pattern; kebab morphology observed at 100 s−1 for 1 s shear after 160 s. Right: In‐situ rheo‐optical micrograph; PHB row‐nucleated morphology observed at 100 s−1 for 1 s shear after 1 min.imageLeft: In‐situ rheo‐SAXS two‐dimensional pattern; kebab morphology observed at 100 s−1 for 1 s shear after 160 s. Right: In‐situ rheo‐optical micrograph; PHB row‐nucleated morphology observed at 100 s−1 for 1 s shear after 1 min.
Synthesis of Polycaprolactone Using Free/Supported Enzymatic and Non‐Enzymatic Catalysts
Authors: Foresti María Laura , Ferreira María Luján 
Published: December 2004

AbstractSummary: Polymerization of caprolactone using lipases from Candida antarctica B, Rhizomucor meihei, Candida rugosa, and Pseudomonas fluorescens is highly effective, with 97% conversion into polycaprolactone. Poly(propylene)‐supported Candida rugosa lipase achieves higher conversion values (85–92%) than free lipase (75%). Acidic and basic non‐conventional catalysis with butanol yields 50–85% conversion. Simple UV/visible techniques gave the same results for measuring conversion than other studies. Applications are opened for the non‐conventional catalysts.Mechanism of the polymerization of caprolactone polymerization using a basic catalyst.imageMechanism of the polymerization of caprolactone polymerization using a basic catalyst.
Isotactic Poly(propylene)/Monoalkylimidazolium‐Modified Montmorillonite Nanocomposites: Preparation by Intercalative Polymerization and Thermal Stability Study
Authors: He Aihua , Hu Haiqing , Huang Yingjuan , Dong Jin‐Yong , Han Charles C. 
Published: December 2004

AbstractSummary: Poly(propylene)/monoalkylimidazolium‐modified montmorillonite (PP/IMMT) nanocomposites were prepared by in situ intercalative polymerization of propylene with TiCl4/MgCl2/MMT catalyst. The PP synthesized possessed high isotacticity and molecular weight. Both wide‐angle X‐ray diffraction (XRD) and transmission electron microscopy (TEM) examinations evidenced the nanocomposite formation with exfoliated MMT homogeneously distributed in the PP matrix. A thermal stability study revealed that the nanocomposites possess good thermal stability.X‐ray diffraction patterns of PP/IMMT (MMT = 2.2 wt.‐%) nanocomposite before and after processing.imageX‐ray diffraction patterns of PP/IMMT (MMT = 2.2 wt.‐%) nanocomposite before and after processing.
Regioselective Dendritic Functionalization of Cellulose
Authors: Hassan Mohammad L. , Moorefield Charles N. , Newkome George R. 
Published: December 2004

AbstractSummary: A series of regioselectively dendronized cellulose derivatives has been prepared by the treatment of cellulose in a N,N‐dimethylacetamide/LiCl solvent system with dendrons possessing isocyanate focal substituents. These new materials were characterized using FT‐IR and 13C NMR spectroscopies, and thermogravimetric analysis; the products were highly soluble in a wide range of organic solvents.Substitution pattern of the dendronized cellulose.imageSubstitution pattern of the dendronized cellulose.
Histone H3 acetylation is associated with reduced p21WAF1/CIP1 expression by gastric carcinoma
Authors: Mitani Yoshitsugu , Oue Naohide , Hamai Yoichi , Aung Phyu Phyu , Matsumura Shunji , Nakayama Hirofumi , Kamata Nobuyuki , Yasui Wataru 
Published: December 2004

AbstractHistone acetylation appears to play an important role in transcriptional regulation. Inactivation of chromatin by histone deacetylation is involved in the transcriptional repression of several tumour suppressor genes, including p21WAF1/CIP1. However, the in vivo status of histone acetylation in human cancers, including gastric carcinoma, is not well understood. This study shows that histone H3 in the p21WAF1/CIP1 promoter region is hypoacetylated and that this hypoacetylation is associated with reduced p21WAF1/CIP1 expression in gastric carcinoma specimens. Chromatin immunoprecipitation assays revealed that histone H3 was hypoacetylated in the p21WAF1/CIP1 promoter and coding regions in 10 (34.5%) and 10 (34.5%) of 29 gastric carcinoma specimens, respectively. Hypoacetylation of histone H4 in the p21WAF1/CIP1 promoter and coding regions was observed in 6 (20.7%) and 16 (55.2%) of 29 gastric carcinoma specimens, respectively. p21WAF1/CIP1 mRNA levels were associated with histone H3 acetylation status in the p21WAF1/CIP1 promoter region (p = 0.047) but not p53 mutation status (p = 0.460). In gastric carcinoma cell lines, expression of p21WAF1/CIP1 protein was induced by trichostatin A, a histone deacetylase inhibitor. This induction was associated with hyperacetylation of histone H3 in the p21WAF1/CIP1 promoter region. Hyperacetylation of histone H4 in the p21WAF1/CIP1 promoter region did not appear to be associated with increased expression. Induction of p21WAF1/CIP1 protein expression was associated with hyperacetylation of histones H3 and H4 in the p21WAF1/CIP1 coding region. Expression of a dominant‐negative mutant of p53 reduced expression of p21WAF1/CIP1 protein. Histone H4 acetylation in both the promoter and coding regions of the p21WAF1/CIP1 gene in cells expressing dominant‐negative p53 was less than half of that in cells expressing wild‐type p53, whereas histone H3 acetylation in both the promoter and coding regions was slightly reduced (by approximately 20%) in cells expressing the dominant‐negative p53. These findings provide evidence that alteration of histone acetylation occurs in human cancer tissue specimens such as those from gastric carcinoma. Copyright © 2004 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Red dots near the fovea found during diabetic retinopathy screening: what should we do?
Authors: Ryder REJ , Basu A , Illahi W , Khan M , Carey S 
Published: December 2004

AbstractThe National Service Framework for Diabetes is working towards a national programme for diabetic retinopathy screening. The digital retinal cameras that will be used very easily detect red dots near the fovea. In a consecutive series of 175 patients undergoing eye screening, 25/175 (14%) had macula red dots but no other significant lesions.In the case report presented here, on digital retinal photography a 46‐year‐old man with type 2 diabetes and a normal visual acuity had four red dots within a disc diameter of the centre of the fovea but little other diabetic retinopathy. Repeat photography seven months later showed progression to well‐established exudative maculopathy. This patient's case was considered in the light of the European referral criteria, the grading system in the report of the UK National Screening Committee, the National Institute for Clinical Excellence guidelines, the guidelines of the Royal College of Ophthalmologists, the Welsh Community Diabetic Retinopathy Study grading system, the Scottish Intercollegiate Guidelines Network guidelines and the Scottish Diabetic Retinopathy Grading System.The results showed that the guidelines are inconsistent and could lead, at the time of the first eye screening, to the patient being referred to an ophthalmologist, re‐screened in 12 months or ‘observed at regular intervals’ depending on which guidelines are followed and whether the screener believes the red dots are microaneurysms or dot haemorrhages.In conclusion, the natural history of retinopathy in patients with red dots near the fovea needs to be systematically studied. Pending the outcome of such studies, all patients with red dots clearly visible on retinal photographs within a disc diameter of the centre of the fovea, with normal visual acuity and without other retinopathy suggesting that they should be referred, should be re‐screened at least six monthly. Copyright © 2004 John Wiley & Sons, Ltd.
Targeted first‐trimester prenatal diagnosis before fetal reduction in triplet gestations and subsequent outcome
Authors: Geipel A. , Berg C. , Katalinic A. , Plath H. , Hansmann M. , Smrcek J. , Gembruch U. , Germer U. 
Published: December 2004

AbstractObjectiveTo assess the feasibility of targeted first‐trimester ultrasound evaluation in triplet gestations and to report the outcome in reduced and expectantly managed triplets.MethodsThis was a retrospective analysis of 127 triplets at 11–14 weeks with targeted ultrasound examination including nuchal translucency (NT) screening.ResultsOne or more abnormal findings were observed in 33 of 381 fetuses (8.7%), including increased NT (n = 18), malformations (n = 4), aneuploidy (n = 3), relative intrauterine growth restriction (n = 2) or spontaneous demise (n = 13). Of 63 patients (49%) who chose reduction, selective termination due to abnormal findings was performed in 13 fetuses. The rates of complete abortion <24 weeks were 9.8% and 3.2% for those with expectant management and fetal reduction, respectively. Expectantly managed triplets delivered significantly earlier (31.1 ± 3.8 vs. 35.6 ± 3.3 weeks) (P < 0.01) with a lower mean birth weight (1483 ± 552 g vs. 2305 ± 557 g) (P < 0.01) and a lower number of liveborn fetuses (85.6% vs. 97.4%) (P < 0.01) than those reduced.ConclusionTargeted first‐trimester ultrasound is feasible and reliable in triplet gestations and should be an integral part of the counseling process. It results in more accurate selection for those who consider fetal reduction. Our data further support fetal reduction as a valuable strategy to improve perinatal outcome in triplet pregnancies. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Relationships among nutrition and reproduction and relevance for wild animals
Authors: Allen Mary E. , Ullrey Duane E. 
Published: December 2004

AbstractThis review discusses aspects of feeding ecology, nutrition, and dietary husbandry that are particularly relevant to reproductive success in wild animals. Emphasis has been placed on recently published literature. Special attention has been given to requirements for energy and protein and the unique roles of essential amino acids, essential fatty acids, calcium, phosphorus, zinc, copper, selenium, and vitamins A, C, D, and E. Information has been drawn from research with mammals, birds, reptiles, amphibians, and fish, including the domestic and laboratory species that play such a large role in elucidating mechanisms connecting nutrition and reproduction. Zoo Biol 23:475–487, 2004. © 2004 Wiley‐Liss, Inc.
Contrasting anesthetic sensitivities of T‐type Ca2+ channels of reticular thalamic neurons and recombinant Cav3.3 channels
Authors: Joksovic Pavle M , Brimelow Barbara C , Murbartián Janet , Perez‐Reyes Edward , Todorovic Slobodan M 
Published: December 2004

Reticular thalamocortical neurons express a slowly inactivating T‐type Ca2+ current that is quite similar to that recorded from recombinant Cav3.3b (α1Ib) channels. These neurons also express abundant Cav3.3 mRNA, suggesting that it underlies the native current.
Here, we test this hypothesis by comparing the anesthetic sensitivities of recombinant Cav3.3b channels stably expressed in HEK 293 cells to native T channels in reticular thalamic neurons (nRT) from brain slices of young rats.
Barbiturates completely blocked both Cav3.3 and nRT currents, with pentobarbital being about twice more potent in blocking Cav3.3 currents. Isoflurane had about the same potency in blocking Cav3.3 and nRT currents, but enflurane, etomidate, propofol, and ethanol exhibited 2–4 fold higher potency in blocking nRT vs Cav3.3 currents.
Nitrous oxide (N2O; laughing gas) blocked completely nRT currents with IC50 of 20%, but did not significantly affect Cav3.3 currents at four‐fold higher concentrations. In addition, we observed that in lower concentration, N2O reversibly increased nRT but not Cav3.3 currents.
In conclusion, contrasting anesthetic sensitivities of Cav3.3 and nRT T‐type Ca2+ channels strongly suggest that different molecular structures of Ca2+ channels give rise to slowly inactivating T‐type Ca2+ currents. Furthermore, effects of volatile anesthetics and ethanol on slowly inactivating T‐type Ca2+ channel variants may contribute to the clinical effects of these agents.

British Journal of Pharmacology (2005) 144, 59–70. doi:10.1038/sj.bjp.0706020