bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily
Authors: Lecompte Emilie , Aplin Ken , Denys Christiane , Catzeflis François , Chades Marion , Chevret Pascale 
Published: July 2008

AbstractBackgroundWithin the subfamily Murinae, African murines represent 25% of species biodiversity, making this group ideal for detailed studies of the patterns and timing of diversification of the African endemic fauna and its relationships with Asia. Here we report the results of phylogenetic analyses of the endemic African murines through a broad sampling of murine diversity from all their distribution area, based on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR).ResultsA combined analysis of one mitochondrial and two nuclear gene sequences consistently identified and robustly supported ten primary lineages within Murinae. We propose to formalize a new tribal arrangement within the Murinae that reflects this phylogeny. The diverse African murine assemblage includes members of five of the ten tribes and clearly derives from multiple faunal exchanges between Africa and Eurasia. Molecular dating analyses using a relaxed Bayesian molecular clock put the first colonization of Africa around 11 Mya, which is consistent with the fossil record. The main period of African murine diversification occurred later following disruption of the migration route between Africa and Asia about 7–9 Mya. A second period of interchange, dating to around 5–6.5 Mya, saw the arrival in Africa ofMus(leading to the speciose endemicNannomys), and explains the appearance of several distinctive African lineages in the late Miocene and Pliocene fossil record of Eurasia.ConclusionOur molecular survey of Murinae, which includes the most complete sampling so far of African taxa, indicates that there were at least four separate radiations within the African region, as well as several phases of dispersal between Asia and Africa during the last 12 My. We also reconstruct the phylogenetic structure of the Murinae, and propose a new classification at tribal level for this traditionally problematic group.
A method for visualizing surface-exposed and internal PfEMP1 adhesion antigens in Plasmodium falciparum infected erythrocytes
Authors: Bengtsson Dominique , Sowa Kordai M , Salanti Ali , Jensen Anja TR , Joergensen Louise , Turner Louise , Theander Thor G , Arnot David E 
Published: July 2008

AbstractBackgroundThe insertion of parasite antigens into the host erythrocyte membrane and the structure and distribution ofPlasmodium falciparumadhesion receptors on that membrane are poorly understood. Laser scanning confocal microscopy (LSCM) and a novel labelling and fixation method have been used to obtain high resolution immuno-fluorescent images of erythrocyte surface PfEMP1 and internal antigens which allow analysis of the accumulation of PfEMP1 on the erythrocyte membrane during asexual development.MethodsA novel staining technique has been developed which permits distinction between erythrocyte surface PfEMP1 and intracellular PfEMP1, in parasites whose nuclear material is exceptionally well resolved. Primary antibody detection by fluorescence is carried out on the live parasitized erythrocyte. The surface labelled cells are then fixed using paraformaldehyde and permeabilized with a non-ionic detergent to permit access of antibodies to internal parasite antigens. Differentiation between surface and internal antigens is achieved using antibodies labelled with different fluorochromes and confocal microscopyResultsSurface exposed PfEMP1 is first detectable by antibodies at the trophozoite stage of intracellular parasite development although the improved detection method indicates that there are differences between different laboratory isolates in the kinetics of accumulation of surface-exposed PfEMP1.ConclusionA sensitive method for labelling surface and internal PfEMP1 with up to three different fluorochromes has been developed for laser scanning confocal optical microscopy and the analysis of the developmental expression of malaria adhesion antigens.
Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer
Authors: Anglim Paul P , Galler Janice S , Koss Michael N , Hagen Jeffrey A , Turla Sally , Campan Mihaela , Weisenberger Daniel J , Laird Peter W , Siegmund Kimberly D , Laird-Offringa Ite A 
Published: July 2008

AbstractBackgroundLung cancer is the leading cause of cancer death in men and women in the United States and Western Europe. Over 160,000 Americans die of this disease every year. The five-year survival rate is 15% – significantly lower than that of other major cancers. Early detection is a key factor in increasing lung cancer patient survival. DNA hypermethylation is recognized as an important mechanism for tumor suppressor gene inactivation in cancer and could yield powerful biomarkers for early detection of lung cancer. Here we focused on developing DNA methylation markers for squamous cell carcinoma of the lung. Using the sensitive, high-throughput DNA methylation analysis technique MethyLight, we examined the methylation profile of 42 loci in a collection of 45 squamous cell lung cancer samples and adjacent non-tumor lung tissues from the same patients.ResultsWe identified 22 loci showing significantly higher DNA methylation levels in tumor tissue than adjacent non-tumor lung. Of these, eight showed highly significant hypermethylation in tumor tissue (p < 0.0001): GDNF, MTHFR, OPCML, TNFRSF25, TCF21, PAX8, PTPRN2 and PITX2. Used in combination on our specimen collection, this eight-locus panel showed 95.6% sensitivity and specificity.ConclusionWe have identified 22 DNA methylation markers for squamous cell lung cancer, several of which have not previously been reported to be methylated in any type of human cancer. The top eight markers show great promise as a sensitive and specific DNA methylation marker panel for squamous cell lung cancer.
Examining warfarin underutilization rates in patients with atrial fibrillation: Detailed chart review essential to capture contraindications to warfarin therapy
Authors: Srivastava Ajay , Hudson Michael , Hamoud Ihab , Cavalcante Joao , Pai Chetan , Kaatz Scott 
Published: July 2008

Abstract

Introduction
Atrial fibrillation affects an estimated 2.5 million Americans and incurs an average annual stroke risk of 4.5% per year. Despite warfarin reducing stroke risk by approximately 66%, prior studies show warfarin usage rates to be about 50%. However, the methods that define warfarin as "inappropriate underutilization" might not be sensitive enough to pick up relative contraindications. We assessed the inappropriate underutilization of warfarin in atrial fibrillation patients at our hospital by abstracting individual patient charts.

Methods
Medical records were reviewed to determine stroke risk factors, warfarin use, and documented contraindications to warfarin use in 364 consecutive patients with atrial fibrillation.

Results
Amongst 364 atrial fibrillation patients, 54.6% received warfarin anticoagulation. Overall, 29.5 % of patients had documented reasons for not prescribing warfarin. Primary reasons listed by treating physicians included: gastrointestinal bleed 10.7%, secondary/transient atrial fibrillation 8.2%, and fall risk 6.3%. Only 7.1% of the patients had no documented reasons for the lack of warfarin use.

Conclusion
Consistent with previous reports, 45.4% of patients in this atrial fibrillation cohort were not prescribed warfarin. However, after reviewing medical charts for documented reasons why warfarin was not used, the inappropriate underutilization rate was only 7.1%. These findings suggest that studies utilizing administrative database and ICD-9 CM coding might overestimate warfarin underutilization.
Altered behavior and digestive outcomes in adult male rats primed with minimal colon pain as neonates
Authors: Wang Jing , Gu Chunping , Al-Chaer Elie D 
Published: July 2008

Abstract

Background
Neonatal colon irritation (CI; pain or inflammation) given for 2 weeks prior to postnatal day 22 (PND22), causes long-lasting functional disorders in rats that can be seen 6 months after the initial insult. This study looked at the effect of varying the frequency and duration of neonatal CI on the rate of growth, digestive outcomes, exploratory activity, and colon and skin sensitivity in adult rats.

Methods
Male Sprague-Dawley rats were given CI using repeated colorectal distension (CRD) at different time intervals and for varying durations starting at PND 8, 10 or 14. Control rats were handled by the investigator without any intracolonic insertion. Further experiments were done on adult rats. Digestive outcomes (food and water consumption, fecal and urinary outputs) were measured using metabolic cages. Exploratory behavior was measured using digital video tracking in an open field. Cutaneous sensitivity was assessed by measuring the responses to mechanical and heat stimuli applied to the shaved abdomen or hind paws. Visceral sensitivity was measured by recording electromyographic responses, under light isoflurane anesthesia, from the external oblique muscles in response to CRD.

Results
No significant weight differences were observed between CI and control rats. Exploratory behavior was reduced in rats with neonatal CI compared to control. Digestive outputs and somatic and visceral sensitivity changed between different treatment groups with earlier and more frequent insults yielding a higher deviation from normal.

Conclusion
The diversity of behavioral and digestive symptoms in these rats parallels the diversity of symptoms in patients with functional gastrointestinal disorders and is consistent with global plastic changes affecting more than one system in the organism.
A retrospective evaluation of patients switched from buprenorphine (subutex) to the buprenorphine/naloxone combination (suboxone)
Authors: Simojoki Kaarlo , Vorma Helena , Alho Hannu 
Published: July 2008

Abstract

Background
In Finland, buprenorphine (Subutex) is the most abused opioid. In order to curb this problem, many treatment centres transferred ("forced transfer") their buprenorphine patients to the buprenorphine plus naloxone (Suboxone) combination product in late 2003.

Methods
Data from a retrospective study involving five different treatment centers, examining the effects of switching patients to Suboxone, were gathered from 64 opioid-dependent patients who had undergone the medication transfer.

Results
Most patients (90.6%) switched to Suboxone at the same dose of buprenorphine that they had been receiving as Subutex (average 22 mg). The majority of these patients (71.9%) were maintained at the same dose of Suboxone throughout the 4-week study period. During the first 4 weeks, 50% of the patients reported adverse events and at the four month time point, 26.6% reported adverse events. However, due to adverse events one patient only discontinued treatment with Suboxone during the 4-week study period, and five during the four month follow-up period. Of the 26 patients in the follow-up period, Suboxone was misused intravenously once each by 4 patients and twice by 1 patient. These 5 patients all reported that injecting Suboxone was like injecting "nothing" with any euphoria, or that it was a bad experience.

Conclusion
We conclude that when patients are transferred from high doses (> 22 mg) of buprenorphine to the combination product, dose adjustments may be necessary especially in the later phase of the treatment. We recommend that a transfer from Subutex to Suboxone should be carefully discussed and planned in advance with the patients and after the transfer adverse events should be regularly monitored. With regard of buprenorphine IV abuse, the combination product seems to have a less abuse potential than buprenorphine alone.
A monoclonal antibody marker for the exclusion-zone filaments of Trypanosoma brucei
Authors: Bonhivers Mélanie , Landrein Nicolas , Decossas Marion , Robinson Derrick R 
Published: July 2008

Abstract

Background

Trypanosoma brucei is a haemoflagellate pathogen of man, wild animals and domesticated livestock in central and southern Africa. In all life cycle stages this parasite has a single mitochondrion that contains a uniquely organised genome that is condensed into a flat disk-like structure called the kinetoplast. The kinetoplast is essential for insect form procyclic cells and therefore is a potential drug target. The kinetoplast is unique in nature because it consists of novel structural proteins and thousands of circular, interlocking, DNA molecules (kDNA). Secondly, kDNA replication is critically timed to coincide with nuclear S phase and new flagellum biogenesis. Thirdly, the kinetoplast is physically attached to the flagellum basal bodies via a structure called the tripartite attachment complex (TAC). The TAC consists of unilateral filaments (within the mitochondrion matrix), differentiated mitochondrial membranes and exclusion-zone filaments that extend from the distal end of the basal bodies. To date only one protein, p166, has been identified to be a component of the TAC.

Results
In the work presented here we provide data based on a novel EM technique developed to label and characterise cytoskeleton structures in permeabilised cells without extraction of mitochondrion membranes. We use this protocol to provide data on a new monoclonal antibody reagent (Mab 22) and illustrate the precise localisation of basal body-mitochondrial linker proteins. Mab 22 binds to these linker proteins (exclusion-zone filaments) and provides a new tool for the characterisation of cytoskeleton mediated kinetoplast segregation.

Conclusion
The antigen(s) recognised by Mab 22 are cytoskeletal, insensitive to extraction by high concentrations of non-ionic detergent, extend from the proximal region of basal bodies and bind to the outer mitochondrial membrane. This protein(s) is the first component of the TAC exclusion-zone fibres to be identified. Mab 22 will therefore be important in characterising TAC biogenesis.
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids
Authors: Loh Yong-Hwee E , Katz Lee S , Mims Meryl C , Kocher Thomas D , Yi Soojin V , Streelman J Todd 
Published: July 2008

Abstract
Background
Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity. In 2006, the Joint Genome Institute completed low coverage survey sequencing of the genomes of five phenotypically and ecologically diverse Lake Malawi species. We report a computational and comparative analysis of these data that provides insight into the mechanisms that make closely related species different from one another.

Results
We produced assemblies for the five species ranging in aggregate length from 68 to 79 megabase pairs, identified putative orthologs for more than 12,000 human genes, and predicted more than 32,000 cross-species single nucleotide polymorphisms (SNPs). Nucleotide diversity was lower than that found among laboratory strains of the zebrafish. We collected around 36,000 genotypes to validate a subset of SNPs within and among populations and across multiple individuals of about 75 Lake Malawi species. Notably, there were no fixed differences observed between focal species nor between major lineages. Roughly 3% to 5% of loci surveyed are statistical outliers for genetic differentiation (FST) within species, between species, and between major lineages. Outliers for FST are candidate genes that may have experienced a history of natural selection in the Malawi lineage.

Conclusion
We present a novel genome sequencing strategy, which is useful when evolutionary diversity is the question of interest. Lake Malawi cichlids are phenotypically and behaviorally diverse, but they appear genetically like a subdivided population. The unique structure of Lake Malawl cichlid genomes should facilitate conceptually new experiments, employing SNPs to identity genotype-phenotype association, using the entire species flock as a mapping panel.
Administrative “Health Courts” For Medical Injury Claims: The Federal Constitutional Issues
Authors: Elliott E. Donald , Narayan Sanjay A. , Nasmith Moneen S. 
Published: July 2008

Our article analyzes whether the federal government may constitutionally supplant a traditional system of common-law trials before state judges and juries with new federal institutions designed by statute for compensating victims of medical injuries. Specifically, this article examines the federal constitutional issues raised by various proposals to replace traditional medical malpractice litigation in state courts with a federal system of administrative “health courts.” In doing so, we address the following constitutional issues:Is there federal authority to preempt state law (the commerce clause and spending clause issues)? May jurisdiction be created in non - article 3 tribunals, and may claims be decided without trial by jury (the separation of powers and Seventh Amendment issues)? Would pilot programs that require some claims to be pursued in a federal administrative forum while other claimants are left to pursue traditional state tort law remedies be constitutional (the equal protection issue)?The article concludes that a federal compensation system through administrative health courts should be constitutional provided the statute is appropriately drafted and that appropriate factual findings are made concerning the benefits to patients and the public as well as to doctors and their insurers.
Synthesis of Rubrivivax gelatinosus Lipid A and Analogues for Investigation of the Structural Basis for Immunostimulating and Inhibitory Activities
Authors: Fukase Yoshiyuki , Fujimoto Yukari , Adachi Yo , Suda Yasuo , Kusumoto Shoichi , Fukase Koichi 
Published: July 2008

Abstract
To elucidate the structural requirements for the endotoxic and antagonistic activities of lipid A derivatives, we have focused on the effects of the acyl moieties and acidic groups at the 1- and 4′-positions in the present study. We have synthesized new analogues corresponding to Rubrivivax gelatinosus lipid A, which has a characteristic symmetrical distribution of its acyl groups on its two glucosamine residues with shorter acyl groups (decanoyl groups (C10) and lauryl groups (C12)) than Escherichia coli lipid A’s. Carboxymethyl (CM) analogues in which one of the phosphates was replaced with a CM group were also synthesized with a different distribution of acyl groups. Biological tests revealed that the acyl group distribution in the lipid A analogue, strongly affected its bioactivity. The synthetic Ru. gelatinosus type lipid A showed potent antagonistic activity against LPS, whereas its 1-O-carboxymethyl analogue showed weak endotoxic activity. These results demonstrate that when lipid A has shorter (C10 and C12) hexa-acyl groups, its bioactivity is more easily affected by small structural differences, such as differences in acidic groups or acyl group distribution, and that they can change bioactivity from endotoxic to agonistic or vice versa at this structural boundary for the bioactivity.
Geometrical and Kinetic Isotope Effects on R–H(D)···R Type Intramolecular Hydrogen Bonds (R = CH2, NH, and O) Using a Multi-Component Molecular Orbital Method
Authors: Kikuta Yoko , Ishimoto Takayoshi , Nagashima Umpei 
Published: July 2008

Abstract
We theoretically analyzed the geometrical isotope effect and kinetic isotope effect for R–H(D)···R type proton (deuteron) transfer on the intramolecular hydrogen bond of (Z)-1,3-pentadiene (R=CH2), 3-imino-1-propen-1-amine (R=NH), and malonaldehyde (R=O) by using Hartree–Fock (HF) and second-order Møller–Plesset (MP2) levels of a multi-component molecular orbital (MC_MO) method to treat the quantum effects of nuclei. As the protonic and deuteronic basis functions, our proposed exponent values of 24.1725 and 35.6214 for the single protonic and deuteronic Gaussian-type functions were employed, respectively. In the case of R=NH and O, the calculated R5–D6 and R1···D6 bond lengths are shorter and longer than those of the R5–H6 and R1···H6 bonds due to the anharmonicity of the potential. The charge densities around the deuteron for all R=CH2, NH, and O cases are larger than those around the proton because the deuteron is more localized than the proton. The ratio of rate constant (kaH⁄kaD) obtained by MP2 level theory of the MC_MO method is estimated as 10.16, which is in reasonable agreement with the experimental result (12.2). For the systematic analysis of the intramolecular proton (deuteron)-transfer reaction, we also estimated the kaH⁄kaD of R=NH and O.
Aromatic Conjugation Pathways in Porphyrins
Authors: Aihara Jun-ichi , Kimura Eiichi , Krygowski Tadeusz Marek 
Published: July 2008

Abstract
The π-current density induced in a polycyclic π-system is strongly dependent on molecular geometry, so that information on main aromatic pathways cannot be extracted straightforwardly from the π-current density. Using our graph theory of aromaticity and ring-current diamagnetism, we re-interpreted the π-current densities and aromatic stabilization energies of porphyrins consistently and found that main pathways of π-electron circulation along the macroscopic ring are not those of aromatic stabilization. Four five-site circuits instead proved to be the main origin of aromaticity in porphyrins. In general, currents are induced in all possible circuits in a π-system. Superposition of all these circuit currents gives rise to the apparent bifurcation of the π-current across each pyrrolic unit. Local π-currents induced in pyrrolic rings represent those induced in the corresponding five-site circuits.
Hydrogen Adsorption Properties of Lantern-Type Dinuclear M(BDC)(DABCO)1⁄2
Authors: Takei Tohru , Kawashima Jiro , Ii Takato , Maeda Akihiro , Hasegawa Mika , Kitagawa Tamami , Ohmura Tetsushi , Ichikawa Masao , Hosoe Mitsuya , Kanoya Izuru , Mori Wasuke 
Published: July 2008

Abstract
The hydrogen adsorption properties and uptake capacities of three-dimensional microporous materials of lantern-type dinuclear M(BDC)(DABCO)1⁄2 (M=CoII, CuII, and ZnII; BDC = 1,4-benzenedicarboxylate, DABCO = 1,4-diazabicyclo[2.2.2]octane; Co(BDC)(DABCO)1⁄2 (1), Cu(BDC)(DABCO)1⁄2 (2), Zn(BDC)(DABCO)1⁄2 (3)) were investigated at various temperatures of 77–333 K and pressures up to 10 MPa using a PCT automatic measuring system (Sievert-type apparatus). The results indicated that uptake to 4.11, 2.70, and 3.17 wt % of hydrogen can be stored on 1, 2, and 3, respectively, at 77 K. The amounts of hydrogen are adsorbed by all complexes at around room temperature (293 K) and high-pressures are much lower (&lt;0.5 wt %). Adsorption isotherms at around room temperature show a linear uptake relationship; all of them follow the Henry’s law. By measuring nitrogen gas adsorption/desorption, all complexes exhibit approximately Type-I isotherms according to the IUPAC classification and possess BET surface areas in the range of 1165 (for 3) to 1595 m2 g−1 (for 1). Further, the thermal stability of all complexes is high, in the range of about 500 K (for 3) to 600 K (for 1). These complexes were synthesized and characterized by X-ray powder diffraction pattern, TG/DTA, FT-IR, surface area analysis, and hydrogen adsorption measurements.
Formation of 4-Hydroxy-3-(oxan-3-yl)coumarin from Photochemical Reaction between 4-Hydroxycoumarin and 3,4-Dihydro-2H-pyran and MO Analysis
Authors: Shimo Tetsuro , Sato Kenya , Wang Weidong , Obata Toru , Iwanaga Tetsuo , Shinmyozu Teruo , Somekawa Kenichi 
Published: July 2008

Abstract
Photochemical reaction of 4-hydroxycoumarin with 3,4-dihydro-2H-pyran gave 4-hydroxy-3-(oxan-3-yl)coumarin whose formation was explained by considering a hydrogen shift and successive keto–enol isomerization from a head–tail biradical intermediate (A). The reaction mechanism was confirmed by molecular orbital analysis to be induced by intermolecular hydrogen bonding between the 4-OH and pyran oxygen at the transition state.