bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Trait Locus Analysis Using Recombinant Inbred Intercrosses
Authors: Zou Fei , Gelfond Jonathan A L , Airey David C , Lu Lu , Manly Kenneth F , Williams Robert W , Threadgill David W 
Published: May 2005

AbstractWe describe a new approach, called recombinant inbred intercross (RIX) mapping, that extends the power of recombinant inbred (RI) lines to provide sensitive detection of quantitative trait loci (QTL) responsible for complex genetic and nongenetic interactions. RIXs are generated by producing F1 hybrids between all or a subset of parental RI lines. By dramatically extending the number of unique, reproducible genomes, RIXs share some of the best properties of both the parental RI and F2 mapping panels. These attributes make the RIX method ideally suited for experiments requiring analysis of multiple parameters, under different environmental conditions and/or temporal sampling. However, since any pair of RIX genomes shares either one or no parental RIs, this cross introduces an unusual population structure requiring special computational approaches for analysis. Herein, we propose an efficient statistical procedure for QTL mapping with RIXs and describe a novel empirical permutation procedure to assess genome-wide significance. This procedure will also be applicable to diallel crosses. Extensive simulations using strain distribution patterns from CXB, AXB/BXA, and BXD mouse RI lines show the theoretical power of the RIX approach and the analysis of CXB RIXs demonstrates the limitations of this procedure when using small RI panels.
The Coupon Collector and the Suppressor Mutation
Authors: Poon Art , Davis Bradley H , Chao Lin 
Published: May 2005

AbstractCompensatory mutation occurs when a loss of fitness caused by a deleterious mutation is restored by its epistatic interaction with a second mutation at a different site in the genome. How many different compensatory mutations can act on a given deleterious mutation? Although this quantity is fundamentally important to understanding the evolutionary consequence of mutation and the genetic complexity of adaptation, it remains poorly understood. To determine the shape of the statistical distribution for the number of compensatory mutations per deleterious mutation, we have performed a maximum-likelihood analysis of experimental data collected from the suppressor mutation literature. Suppressor mutations are used widely to assess protein interactions and are under certain conditions equivalent to compensatory mutations. By comparing the maximum likelihood of a variety of candidate distribution functions, we established that an L-shaped gamma distribution (α = 0.564, θ = 21.01) is the most successful at explaining the collected data. This distribution predicts an average of 11.8 compensatory mutations per deleterious mutation. Furthermore, the success of the L-shaped gamma distribution is robust to variation in mutation rates among sites. We have detected significant differences among viral, prokaryotic, and eukaryotic data subsets in the number of compensatory mutations and also in the proportion of compensatory mutations that are intragenic. This is the first attempt to characterize the overall diversity of compensatory mutations, identifying a consistent and accurate prior distribution of compensatory mutation diversity for theoretical evolutionary models.
Efficiency of the Use of Pedigree and Molecular Marker Information in Conservation Programs
Authors: Fernández Jesús , Villanueva Beatriz , Pong-Wong Ricardo , Toro Miguel Ángel 
Published: May 2005

Abstract
The value of molecular markers and pedigree records, separately or in combination, to assist in the management of conserved populations has been tested. The general strategy for managing the population was to optimize contributions of parents to the next generation for minimizing the global weighted coancestry. Strategies differed in the type of information used to compute global coancestries, the number and type of evaluated individuals, and the system of mating. Genealogical information proved to be very useful (at least for 10 generations of management) to arrange individuals' contributions via the minimization of global coancestry. In fact, the level of expected heterozygosity after 10 generations yielded by this strategy was 88–100% of the maximum possible improvement obtained if the genotype for all loci was known. Marker information was of very limited value if used alone. The amount and degree of polymorphism of markers to be used to compute molecular coancestry had to be high to mimic the performance of the strategy relying on pedigree, especially in the short term (for example, &gt;10 markers per chromosome with 10 alleles each were needed if only the parents' genotype was available). When both sources of information are combined to calculate the coancestry conditional on markers, clear increases in effective population size (Ne) were found, but observed diversity levels (either gene or allelic diversity) in the early generations were quite similar to the ones obtained with pedigree alone. The advantage of including molecular information is greater when information is available on a greater number of individuals (offspring and parents vs. parents only). However, for realistic situations (i.e., large genomes) the benefits of using information on offspring are small. The same conclusions were reached when comparing the use of the different types of information (genealogical or/and molecular) to perform minimum coancestry matings.
Comparison of the X and Y Chromosome Organization in Silene latifolia
Authors: Zluvova Jitka , Janousek Bohuslav , Negrutiu Ioan , Vyskot Boris 
Published: May 2005

Abstract
Here we compare gene orders on the Silene latifolia sex chromosomes. On the basis of the deletion mapping results (11 markers and 23 independent Y chromosome deletion lines used), we conclude that a part of the Y chromosome (covering a region corresponding to at least 23.9 cM on the X chromosome) has been inverted. The gradient in silent-site divergence suggests that this inversion took place after the recombination arrest in this region. Because recombination arrest events followed by Y chromosome rearrangements also have been found in the human Y chromosome, this process seems to be a general evolutionary pathway.
Epistasis and the Adaptability of an RNA Virus
Authors: Sanjuán Rafael , Cuevas José M , Moya Andrés , Elena Santiago F 
Published: May 2005

Abstract
We have explored the patterns of fitness recovery in the vesicular stomatitis RNA virus. We show that, in our experimental setting, reversions to the wild-type genotype were rare and fitness recovery was at least partially driven by compensatory mutations. We compared compensatory adaptation for genotypes carrying (1) mutations with varying deleterious fitness effects, (2) one or two deleterious mutations, and (3) pairs of mutations showing differences in the strength and sign of epistasis. In all cases, we found that the rate of fitness recovery and the proportion of reversions were positively affected by population size. Additionally, we observed that mutations with large fitness effect were always compensated faster than mutations with small fitness effect. Similarly, compensatory evolution was faster for genotypes carrying a single deleterious mutation than for those carrying pairs of mutations. Finally, for genotypes carrying two deleterious mutations, we found evidence of a negative correlation between the epistastic effect and the rate of compensatory evolution.
Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile
Authors: Lin Jer-Young , Jacobus Barbara Hass , SanMiguel Phillip , Walling Jason G , Yuan Yinan , Shoemaker Randy C , Young Nevin D , Jackson Scott A 
Published: May 2005

Abstract
Little is known about the physical makeup of heterochromatin in the soybean (Glycine max L. Merr.) genome. Using DNA sequencing and molecular cytogenetics, an initial analysis of the repetitive fraction of the soybean genome is presented. BAC 076J21, derived from linkage group L, has sequences conserved in the pericentromeric heterochromatin of all 20 chromosomes. FISH analysis of this BAC and three subclones on pachytene chromosomes revealed relatively strict partitioning of the heterochromatic and euchromatic regions. Sequence analysis showed that this BAC consists primarily of repetitive sequences such as a 102-bp tandem repeat with sequence identity to a previously characterized ∼120-bp repeat (STR120). Fragments of Calypso-like retroelements, a recently inserted SIRE1 element, and a SIRE1 solo LTR were present within this BAC. Some of these sequences are methylated and are not conserved outside of G. max and G. soja, a close relative of soybean, except for STR102, which hybridized to a restriction fragment from G. latifolia. These data present a picture of the repetitive fraction of the soybean genome that is highly concentrated in the pericentromeric regions, consisting of rapidly evolving tandem repeats with interspersed retroelements.
The Inactivation of KlNOT4, a Kluyveromyces lactis Gene Encoding a Component of the CCR4-NOT Complex, Reveals New Regulatory Functions
Authors: Mazzoni Cristina , Serafini Agnese , Falcone Claudio 
Published: May 2005

Abstract
We have isolated the KlNOT4 gene of the yeast Kluyveromyces lactis, which encodes a component of the evolutionarily conserved CCR4-NOT complex. We show that inactivation of the gene leads to pleiotropic defects that were differentially suppressed by the NOT4 gene of S. cerevisiae, indicating that these genes have overlapping, but not identical, functions. K. lactis strains lacking Not4p are defective in fermentation and show reduced transcription of glucose transporter and glycolytic genes, which are phenotypes that are not found in the corresponding mutant of S. cerevisiae. We also show that Not4 proteins control the respiratory pathway in both yeasts, although with some differences. They activate transcription of KlACS2 and KlCYC1, but repress KlICL1, ScICL1, ScACS1, and ScCYC1. Altogether, our results indicate that Not4p is a pivotal factor involved in the regulation of carbon metabolism in yeast.
Nonuniform radiation modeling of a corrugated plate photocatalytic reactor
Authors: Shang Huilan , Zhang Zisheng , Anderson William A. 
Published: May 2005

AbstractCorrugated plate photocatalytic reactors provide a promising photoreactor design due to its potential in enhancing energy efficiency. A detailed model of such reactors is needed for engineering applications and process design. The model for the light absorption in a corrugated plate reactor using a nonuniform radiation source is developed based on first principles. The local area‐specific rate of energy absorption (LASREA) distribution on the corrugated plates is examined via simulation. The effect of the design parameters on LASREA is investigated. The results from this research provide feasible basis for design and optimization of corrugated plate photoreactors. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Structural and dynamic properties of cytochrome P450 BM‐3 in pure water and in a dimethylsulfoxide/water mixture
Authors: Roccatano Danilo , Wong Tuck Seng , Schwaneberg Ulrich , Zacharias Martin 
Published: May 2005

AbstractSolvent molecules play an important role for the structural and dynamical properties of proteins. A major focus of current protein engineering is the development of enzymes that are catalytically active in the presence of organic solvents. The monooxygenase P450 BM‐3 is one of the best‐studied enzymes and promising for industrial applications but with limited activity in the presence of organic solvents or cosolvents. To gain insights into the structural and dynamical properties of the heme domain of this enzyme in solution, molecular dynamics simulations in pure water and in a 14% DMSO/water mixture were performed. The results of the simulations show overall similar structural fluctuations in both solvent systems, with no indication of partial or global unfolding. In 14% DMSO, the regions comprising the helices E, F, and the EF loop (implicated in controlling the entry to the active site channel) undergo a large shift. Significant changes were also observed near the active site access channel at the residue R47. During the simulation, no DMSO molecule penetrated the active site. However, a significant accumulation of DMSO molecules close to the substrate‐binding site and to the Flavin Mononucleotide (FMN) reductase domain interface was observed. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 259–267, 2005
Randomized trial of traditional dissection with electrocautery versus ultrasonic fundus-first dissection in patients undergoing laparoscopic cholecystectomy
Authors: Cengiz Y , Jänes A , Grehn Å , Israelsson L A 
Published: May 2005

Abstract

Background
In laparoscopic cholecystectomy dissection can be with monopolar electrocautery or with ultrasonic shears, and can start at the triangle of Calot or at the fundus of the gallbladder.

Methods
Thirty-seven patients undergoing laparoscopic cholecystectomy were randomized to electrocautery dissection from the triangle of Calot and 43 to fundus-first dissection with ultrasonic shears. All procedures were strictly standardized, and patients and their postoperative carers were blinded to the operation performed.

Results
Ultrasonic fundus-first dissection was associated with a shorter duration of operation (mean 46 versus 61 min), fewer overnight hospital stays (two versus eight), lower pain scores 4 and 24 h after surgery, less nausea at 2, 4 and 24 h, and a shorter period of sick leave (mean 5·5 versus 9·3 days) compared with electrocautery from the triangle of Calot.

Conclusion
Ultrasonic fundus-first dissection during laparoscopic cholecystectomy was quicker and associated with less nausea and pain than electrocautery dissection from the triangle of Calot.
Simple Synthesis of Aminoquinoline/Ethylaniline Copolymer Semiconducting Nanoparticles
Authors: Li Xin‐Gui , Hua Yi‐Min , Huang Mei‐Rong 
Published: May 2005

AbstractPure copolymer nanoparticles from 8‐aminoquinoline (AQ) and 2‐ethylaniline (EA) were easily synthesized by a chemically oxidative polymerization in three different aqueous media. The potential and temperature of polymerization solution were used to successfully follow the polymerization progress. The molecular and morphological structures of the resulting AQ/EA copolymer particles were systematically characterized by IR, UV/Vis, NMR, gel permeation chromatography, laser particle‐size analysis, atomic force and transmission electron microscopy. The oxidation potential of the monomers as well as the polymerization yield, structure, and properties of the particles were found to significantly depend on AQ/EA ratio, polymerization temperature and medium. It is surprisingly found that AQ homopolymerization and AQ/EA (50:50) copolymerization at 5 °C in HCl simply afford nano‐ellipsoids with the major/minor axis diameters of 24/14 nm and 80/67 nm, respectively. A simple method of synthesizing semiconducting pure nanoparticles by introducing the AQ units with positively charged quaternary ammonium groups but in the absence of adscititious stabilizer or sulfonic substituent on the monomers is established first. Both the molecular weight and bulk electroconductivity of the copolymers exhibit a maximum at AQ content of 10 mol %. The solubility and film formability of the copolymers are good in highly polar solvents and reach the optimal at the AQ content of 20 and 10 mol %, respectively.
Enhanced chemotherapy delivery by intraarterial infusion and blood‐brain barrier disruption in malignant brain tumors
Authors: Fortin David , Desjardins Annick , Benko Andrew , Niyonsega Theophylle , Boudrias Marie 
Published: May 2005

AbstractBACKGROUNDThe treatment of malignant brain tumors is hampered by the presence of the blood‐brain barrier, which limits chemotherapy penetration to the central nervous system (CNS). In recent years, different strategies have been designed to circumvent this physiologic barrier. The osmotic blood‐brain barrier disruption (BBBD) procedure is one such strategy, and has been studied extensively in preclinical and clinical studies. The authors detail their experience so far with the procedure in the context of an open Phase II study in the treatment of malignant brain tumors.METHODSPatients with histologically proven malignant gliomas, primitive neuroectodermal tumors, primary CNS lymphomas, and metastatic disease to the brain were eligible. Patients enrolled were treated every 4 weeks (1 cycle) for ≤ 12 cycles. A methotrexate‐based regimen was offered to patients with lymphomas, whereas a carboplatin‐based regimen was offered to patients with all other histologies. Before intraarterial chemotherapy infusion, patients were submitted to an osmotic BBBD procedure.RESULTSSeventy‐two patients were included in the current report. The overall median survival times (MST) from treatment initiation for glioblastoma multiforme (GBM), anaplastic oligodendrogliomas, primary CNS lymphomas, and metastases were, respectively, 9.1, 13.9, not reached, and 9.9 months, whereas time to disease progression was 4.1, 9.2, 12.3, and 3.3 months. The MST from diagnosis was 32.2 months for GBM.CONCLUSIONSThese encouraging results prompted the authors to further refine their knowledge of the potential contribution of this procedure in the treatment of brain tumors. These authors designed a randomized Phase III study for patients with GBM that is now open. Cancer 2005. © 2005 American Cancer Society.
Genetic interaction between Wnt7a and Lrp6 during patterning of dorsal and posterior structures of the mouse limb
Authors: Adamska Maja , Billi Allison C. , Cheek Susannah , Meisler Miriam H. 
Published: May 2005

AbstractWnt7a and the Wnt coreceptor Lrp6 are both required for development of posterior digits and dorsal structures of the limb. We report that Lrp6 null mice lack Lmx1b expression in the distal mesenchyme, as previously described for Wnt7a mutants. The loss of Lmx1b expression in Wnt7a−/−Lrp6+/− double mutants did not differ from that in Wnt7a−/− mice. These data suggest that Wnt7a acts through Lrp6 to regulate Lmx1b expression during dorsal specification. The loss of posterior skeletal elements in the Wnt7a−/−Lrp6+/− double mutant was much more severe than in Wnt7a−/− mice, suggesting that the Wnt7a−/− limb is protected by the action of other Lrp6 ligands. The data are consistent with the view that Wnt7a acts through Lrp6 and the canonical Wnt signaling pathway during dorsal and posterior limb development in the mouse. Developmental Dynamics 233:368–372, 2005. © 2005 Wiley‐Liss, Inc.
MultiPEGs: High Molecular Weight Multifunctional Poly(ethylene glycol)s Assembled by a Dendrimer‐Like Approach
Authors: Ballico Maurizio , Drioli Sara , Bonora Gian M. 
Published: May 2005

AbstractNew multifunctional, soluble and biocompatible polymeric systems exhibiting good physicochemical properties and good binding capacity have been obtained by assembly of smaller PEG components, selectively protected, purified and activated, by use of appropriate polyfunctional linkers. A general process for the synthesis of those derivatives was characterized by: a) selective derivatization of a PEG unit with a defined MW with an appropriate protecting group and activation of residual functional groups, and b) multiple condensation reactions of PEG units and linkers to provide multifunctional polyethylene glycol derivatives (MultiPEGs) of the desired size and complex structure. These complex‐structured MultiPEGs have larger numbers of functional groups, and probably better biodegradability, than commercial PEGs of comparable molecular weight. They can be advantageously used as carriers or stabilizers of pharmacologically or biologically active substances, and also as soluble supports for reagents and catalysts in liquid‐phase synthesis reactions. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Cobalt Bis(dicarbollides)(1–) Covalently Attached to the Calix[4]arene Platform: The First Combination of Organic Bowl‐Shaped Matrices and Inorganic Metallaborane Cluster Anions
Authors: Grüner Bohumír , Mikulášek Libor , Báča Jiří , Císařová Ivana , Böhmer Volker , Danila Crenguta , Reinoso‐García Marta M. , Verboom Willem , Reinhoudt David N. , Casnati Alessandro , Ungaro Rocco 
Published: May 2005

AbstractVarious calix[4]arene and resorc[4]arene ionic compounds substituted by cobalt bis(dicarbollide) anions (1) have been prepared for the first time. From tBu‐calix[4]arene (A) the complete series of mono‐, di‐, tri‐ and tetrasubstituted derivatives bearing one to four cluster anions on the lower rim (3–6) have been obtained in the form of their alkali‐metal salts by O‐alkylation with the 1‐dioxane derivative [8‐O(CH2CH2)2O(+)‐1,2‐C2B9H10)‐(1',2'‐C2B9H11)‐3,3'‐Co] (2), all of which are syn or cone isomers. In contrast, disubstitution of the dipropyl ether of tBu‐calix[4]arene (B) led to a mixture of the cone and 1,3‐alternate conformers 7a and 7b, respectively. Starting from tetrapropoxy‐calix[4]arene functionalised at the upper rim by carboxylic acid groups in distal positions (C) and an amino‐bridged derivative [8,8'‐μ‐H2N<(1,2‐C2B9H10)2‐3,3'‐Co] (8), calix[4]arene 9, disubstituted at the upper rim, was obtained as the main product along with the monosubstituted species 10. Di‐ and tetrasubstituted ionic products (11–15) were also obtained from resorcarene‐based cavitands by O‐alkylation with the 1‐dioxane derivative 2. A pair of regioisomeric disubstitution products, 11a,b, was isolated in the case of the hydroxy cavitand D, while E, functionalised by hydroxymethyl groups on the wide rim, and F, bearing hydroxy groups on the alkylidene bridges, gave the 1,3‐di‐ (12 and 14) and the tetrasubstituted compounds (13 and 15), respectively. The molecular structure of the electroneutral dicaesium complex of the dianion 4 was determined by single‐crystal X‐ray diffraction analysis. The two Cs+ cations are found in different coordination spheres in the structure of Cs24. Coordination of the Na+ cation by the diethylene glycol chain and one calixarene lower rim oxygen atom was found in the crystal structure of the Na complex of the monoanion 3. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Synthesis of Tricyclic Quinolones and Naphthyridones by Intramolecular Heck Cyclization of Functionalized Electron‐Rich Heterocycles
Authors: Beccalli Egle M. , Broggini Gianluigi , Martinelli Michela , Paladino Giuseppe , Zoni Caterina 
Published: May 2005

AbstractStarting from commercially available pyrrole‐ and thiophene‐2‐carboxylic acids 1 or thiophene‐ and furan‐3‐carboxylic acids 6, we report the synthesis of tricyclic fused quinolone and naphthyridone derivatives, in only three steps, by an intramolecular Heck cyclization. We also report the use of microwave irradiation to obtain, in some cases, better yields of cyclized products. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
First Asymmetric Synthesis and Determination of the Absolute Configuration of a Lignan Isolated from Virola sebifera
Authors: Enders Dieter , Milovanovic Mile , Voloshina Elena , Raabe Gerhard , Fleischhauer Jörg 
Published: May 2005

AbstractThe first asymmetric synthesis of a lignan isolated from the seeds of Virola sebifera, one of the most widely spread Myristicaceae species in Brazil, in four steps (48 % overall yield) and with excellent stereoselectivity (de, ee ≥ 96 %) is described. The key step is the asymmetric Michael addition of a lithiated enantiopure α‐amino nitrile to an enone, followed by α‐methylation and cleavage of the amino nitrile. The absolute configuration of the naturally occurring 1,4‐diketone was determined by polarimetry as well as by CD spectroscopy and quantum chemical calculations. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)