bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lone Star Pterosaurs
Authors: Andres Brian , Myers Timothy S. 
Published: September 2013

ABSTRACTThe state of Texas has one of the greatest records of pterosaurs in the world, surpassing all other US states and most countries in the number of occurrences. Uniquely, this record extends over the entire 150+ million history of the Pterosauria. A review of this pterosaur record confirms at least 30 pterosaurs known from 13 occurrences, including five valid species. The holotypes of two of these species have been described before and are diagnosed and erected here as the new speciesRadiodactylus langstoni, gen. et sp. nov., named in honour of Dr. Wann Langston Jr, the father of Texas pterosaurology, andAlamodactylus byrdi, gen. et sp. nov.. Phylogenetic analysis of all Texas pterosaurs that can be coded for more than one character confirms that these species are distinct from others and occupy phylogenetic positions close to their original classifications.Radiodactylus langstoniis recovered as a non-azhdarchid azhdarchoid,Quetzalcoatlus northropias an azhdarchid,Alamodactylus byrdias a non-pteranodontoid pteranodontian,Aetodactylusas a pteranodontoid, andColoborhynchus wadleighias an ornithocheirid. The presence of eudimorphodontid, dsungaripterid, as well as other azhdarchid and pteranodontoid pterosaurs, is also confirmed in Texas.
The development of “modern” palaeontological laboratory methods: a century of progress
Authors: Brown Matthew A. 
Published: September 2013

ABSTRACTVertebrate fossils have been converted from natural history objects into research specimens through the act of preparation for over 200 years. All of the basic techniques applied to specimens in the 21st Century were already in use in palaeontological laboratories by the first decade of the 1900s. It behoves any worker in the field to be intimately familiar with processes for treatment of specimens, as these procedures almost always permanently alter material available for interpretation. Historic treatments also complicate attempts to re-treat or re-prepare specimens. Sometimes this results in damage to fossils and loss of information, and often in wasted resources. Most palaeontologists are unaware of the historical evolution of laboratory methods through this time; much of the documentation of this process is considered to be obscure. However, there is in fact a robust body of literature that chronicles the development of procedures for the preparation of fossils. Awareness of the past development of methods is crucial to guiding future directions in the palaeontological laboratory. Regular reporting of laboratory methods in the technical literature at a pace matching that of other analytical methods is integral to the function of palaeontology as a science.
Herpetofaunas from the “overburden” (Quaternary) of western Canada
Authors: Jass Christopher N. , Gardner James D. 
Published: September 2013

ABSTRACTQuaternary herpetofaunas from eight palaeontological localities in western Canada (British Columbia: Bear Flat; Alberta: Eagle Cave, January Cave, Rat's Nest Cave, Hand/Wintering Hills, Fletcher Site, Stampede Site and Little Fish Lake) are described in detail for the first time. Identifications of taxa from these localities include frogs (Ranasp.,Bufosp., and Anura indet.), salamanders (cf.Ambystomasp.), and snakes (cf.Thamnophissp. and cf.Pituophissp.). Preglacial and postglacial herpetofaunas are distinctly separated by a boundary resulting from the advance and retreat of glacial ice across northern North America. The taxonomic records presented here represent a conservative, morphology-based approach to identification that resulted in less taxonomic resolution than is commonly found in literature on Quaternary herpetofaunas. Nonetheless, the resultant data set was useful for establishing a framework that is indicative of biogeographic stability in Quaternary reptiles and amphibians of western Canada. We hypothesise that the observed stability may be related to evolutionary adaptations (e.g. cold-tolerance) in specific lineages.
Information Measure for Long-Range Correlated Sequences: the Case of the 24 Human Chromosomes
Authors: Carbone A. 
Published: September 2013

AbstractA new approach to estimate the Shannon entropy of a long-range correlated sequence is proposed. The entropy is written as the sum of two terms corresponding respectively to power-law (ordered) and exponentially (disordered) distributed blocks (clusters). The approach is illustrated on the 24 human chromosome sequences by taking the nucleotide composition as the relevant information to be encoded/decoded. Interestingly, the nucleotide composition of the ordered clusters is found, on the average, comparable to the one of the whole analyzed sequence, while that of the disordered clusters fluctuates. From the information theory standpoint, this means that the power-law correlated clusters carry the same information of the whole analysed sequence. Furthermore, the fluctuations of the nucleotide composition of the disordered clusters are linked to relevant biological properties, such as segmental duplications and gene density.
The alternative oxidases: simple oxidoreductase proteins with complex functions
Authors: Young Luke , Shiba Tomoo , Harada Shigeharu , Kita Kiyoshi , Albury Mary S. , Moore Anthony L. 
Published: September 2013

The alternative oxidases are membrane-bound monotopic terminal electron transport proteins found in all plants and in some agrochemically important fungi and parasites including Trypansoma brucei, which is the causative agent of trypanosomiasis. They are integral membrane proteins and reduce oxygen to water in a four electron process. The recent elucidation of the crystal structure of the trypanosomal alternative oxidase at 2.85 Å (1 Å=0.1 nm) has revealed salient structural features necessary for its function. In the present review we compare the primary and secondary ligation spheres of the alternative oxidases with other di-iron carboxylate proteins and propose a mechanism for the reduction of oxygen to water.
Molecular mechanism and physiological role of active–deactive transition of mitochondrial complex I
Authors: Babot Marion , Galkin Alexander 
Published: September 2013

The unique feature of mitochondrial complex I is the so-called A/D transition (active–deactive transition). The A-form catalyses rapid oxidation of NADH by ubiquinone (k ~104 min−1) and spontaneously converts into the D-form if the enzyme is idle at physiological temperatures. Such deactivation occurs in vitro in the absence of substrates or in vivo during ischaemia, when the ubiquinone pool is reduced. The D-form can undergo reactivation given both NADH and ubiquinone availability during slow (k ~1–10 min−1) catalytic turnover(s). We examined known conformational differences between the two forms and suggested a mechanism exerting A/D transition of the enzyme. In addition, we discuss the physiological role of maintaining the enzyme in the D-form during the ischaemic period. Accumulation of the D-form of the enzyme would prevent reverse electron transfer from ubiquinol to FMN which could lead to superoxide anion generation. Deactivation would also decrease the initial burst of respiration after oxygen reintroduction. Therefore the A/D transition could be an intrinsic protective mechanism for lessening oxidative damage during the early phase of reoxygenation. Exposure of Cys39 of mitochondrially encoded subunit ND3 makes the D-form susceptible for modification by reactive oxygen species and nitric oxide metabolites which arrests the reactivation of the D-form and inhibits the enzyme. The nature of thiol modification defines deactivation reversibility, the reactivation timescale, the status of mitochondrial bioenergetics and therefore the degree of recovery of the ischaemic tissues after reoxygenation.
Assembly of the Escherichia coli FoF1 ATP synthase involves distinct subcomplex formation
Authors: Deckers-Hebestreit Gabriele 
Published: September 2013

The ATP synthase (FoF1) of Escherichia coli couples the translocation of protons across the cytoplasmic membrane by Fo to ATP synthesis or hydrolysis in F1. Whereas good knowledge of the nanostructure and the rotary mechanism of the ATP synthase is at hand, the assembly pathway of the 22 polypeptide chains present in a stoichiometry of ab2c10α3β3γδϵ has so far not received sufficient attention. In our studies, mutants that synthesize different sets of FoF1 subunits allowed the characterization of individually formed stable subcomplexes. Furthermore, the development of a time-delayed in vivo assembly system enabled the subsequent synthesis of particular missing subunits to allow the formation of functional ATP synthase complexes. These observations form the basis for a model that describes the assembly pathway of the E. coli ATP synthase from pre-formed subcomplexes, thereby avoiding membrane proton permeability by a concomitant assembly of the open H+-translocating unit within a coupled FoF1 complex.
Dynamic structural science: recent developments in time-resolved spectroscopy and X-ray crystallography
Authors: Trincao Jose , Hamilton Michelle L. , Christensen Jeppe , Pearson Arwen R. 
Published: September 2013

To understand the mechanism of biological processes, time-resolved methodologies are required to investigate how functionality is linked to changes in molecular structure. A number of spectroscopic techniques are available that probe local structural rearrangements with high temporal resolution. However, for macromolecules, these techniques do not yield an overall high-resolution description of the structure. Time-resolved X-ray crystallographic methods exist, but, due to both instrument availability and stringent sample requirements, they have not been widely applied to macromolecular systems, especially for time resolutions below 1 s. Recently, there has been a resurgent interest in time-resolved structural science, fuelled by the recognition that both chemical and life scientists face many of the same challenges. In the present article, we review the current state-of-the-art in dynamic structural science, highlighting applications to enzymes. We also look to the future and discuss current method developments with the potential to widen access to time-resolved studies across discipline boundaries.
A long road towards the structure of respiratory complex I, a giant molecular proton pump
Authors: Sazanov Leonid A. , Baradaran Rozbeh , Efremov Rouslan G. , Berrisford John M. , Minhas Gurdeep 
Published: September 2013

Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the ‘minimal’ bacterial version contains 14 highly conserved ‘core’ subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe–S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe–S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via long-range conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review.
Prevalence of Epstein–Barr Virus in a population of patients with inflammatory bowel disease: a prospective cohort study
Authors: Linton M. S. , Kroeker K. , Fedorak D. , Dieleman L. , Fedorak R. N. 
Published: September 2013

SummaryBackgroundThe Epstein–Barr Virus (EBV) is truly prolific, with a prevalence of more than 90% in the adult human population. There are, however, little data available on the prevalence of EBV among patients with Inflammatory Bowel Disease (IBD), a population that is frequently immunosuppressed and thus at risk for severe, often fatal, primary infection.AimTo identify the prevalence of EBV in a population of patients with IBD and to compare it with that of the general population.MethodsA database of 2500 IBD patients previously followed at the University of Alberta IBD Centre was queried; 60 of these patients were randomly chosen to participate. A total of 220 patients attending the IBD Centre for clinical appointment were also prospectively asked to participate. Participants completed serological testing for VCA‐IgM, VCA‐IgG and EBNA‐IgG, to determine prior EBV exposure.ResultsA total of 263 patients underwent testing. Results for EBV seroprevalence of specific age groups were as follows: 18–20 years (n = 17), 29% seronegative; 21–25 years (n = 31), 29% seronegative; 26–30 years (n = 35), 31–35 years (n = 18) and 36–40 years (n = 25), 100% seropositive. Finally, 3% of those older than 40 (n = 117) were seronegative. EBV seroprevalence was similar for Crohn's disease and ulcerative colitis. Azathioprine was associated with seropositivity (P = 0.048).ConclusionThe prevalence of EBV seronegativity in the IBD population aged 18–25 years was similar to that described in the general population, and above age 25 years, seropositivity approached 100%.
Enrichment of Anaerobic Ammonium Oxidation (Anammox) Bacteria for Biological Nitrogen Removal of Wastewater
Authors: Yusof Norjan , Abdullah Hanisom , Samsudin Syakirah , Hassan Mohd Ali 
Published: September 2013

Anaerobic ammonium oxidation (anammox) bacteria enrichment was explored for the potential application of ammonium rich wastewater removal. Samples of sludge from mature and young landfill leachate treatment plants were screened and used as inocula for anammox enrichment cultures. Enrichments were monitored for N-NH3, N-NO2- and N-NO3- to detect anammox potential activity. Six of the twelve enrichment cultures showed anammox activity after more than five months of enrichment period. All enrichment cultures that gave positive results were obtained from bottom part of sequencing batch reactor (SBR) lagoon indicating localization of anammox bacteria in anaerobic condition. Polymerase Chain Reaction (PCR) with specific primers targeting anammox and planctomycete were able to amplify the 16S rRNA sequence for anammox bacteria under PCR optimum condition. However, only three of six positive samples were successfully sequenced. DNA sequence analysis using NCBI (BLAST) and RDP showed that the anammox bacterial sequences of the investigated samples were identified as Candidatus Kuenenia stuttgartiensis with similarity of 100% (NCBI) and 99.3% (RDP).
Pembentukan TPS dalam Pembuatan Lean: Satu Kajian Perbandingan
Authors: Ab Rahman Mohd Nizam , A Ghani Jaharah , Ho Chan Kien , Afandi Abusin Muhammad Amir 
Published: September 2013

Pembuatan Lean dan Toyota Production System (TPS) merupakan amalan atau falsafah pengurusan kualiti yang popular di kalangan pengusaha pembuatan. Tujuan utamanya adalah untuk meminimumkan pembaziran dalam pengeluaran dan memberi fokus kepada aktiviti yang mampu menambah nilai. Selain daripada mencari persamaan ataupun perbezaan, kajian ini menggabung serta merungkaikan teori pembuatan lean dan TPS. Kajian kes juga telah dijalankan, dan melibatkan temu bual di tiga syarikat yang terpilih. Pelbagai faktor yang membezakan pembuatan lean dengan TPS telah dibincangkan bagi membuktikan kedua-dua falsafah ini adalah berlainan. Keputusan perbandingan menunjukkan bahawa pembuatan lean dan TPS adalah berbeza dari segi faktor masa, prinsip, tujuan, matlamat, penjenamaan, teknik dan pelaksanaan.. Syarikat-syarikat lebih cenderung mengamalkan lima prinsip pembuatan lean dan sebahagian prinsip TPS dengan mengaplikasikan lima teknik atau konsep amalan kualiti utama iaitu 5S, Kerja Terpiawai, VSM, JIT dan Kaizen. Melalui kajian kes ini, didapati bahawa kekurangan kerjasama daripada pembekal serta pemahaman dan kesedaran pekerja yang rendah merupakan halangan utama dalam pelaksanaan pembuatan lean atau TPS. Kajian ini boleh dijadikan sebagai satu rujukan kepada pembaca dan syarikat-syarikat yang bercadang untuk melaksanakan pembuatan lean atau TPS.
The Breakdown of Symmetry in Word Pairs in 1,092 Human Genomes
Authors: Afreixo Vera , P. Garcia Sara , M. O. S. Rodrigues João 
Published: September 2013

Single strand symmetry has been observed in several genomes, and some authors have associated this phenomenon to genome evolution. However, it is still not clear how strong and exceptional this phenomenon is. We use next-generation sequencing data from a sample of 1,092 human individuals made available by the 1000 Genomes Project. To evaluate the phenomenon of symmetry of single-strand human genomic DNA, we explore and analyze these 1,092 human genomes and 1,092 randomly generated sequences, each forced to mimic the nucleotide frequency distribution of their real counterpart. Our methodology is based on measurements, traditional and equivalence statistical tests using different parameters. By statistical testing we find that the global symmetries phenomenon is significant for word lengths smaller than 8. When we evaluate the global symmetry scores, we obtain strong values for all word lengths and both types of sequences under study. However, the symmetry scores in human genomes reach higher values and have lower dispersion than those in random sequences. We also find that human and random symmetry scores are significantly different. We conclude that in the human genome, the differences between symmetric words are higher than in random sequences, but the correlation between symmetric words in human genomes is higher.
Estimating Kinetic Parameters for Essential Amino Acid Production in Arabidopsis Thaliana by Using Particle Swarm Optimization
Authors: Ng Siew Teng , Chong Chuii Khim , Choon Yee Wen , Chai Lian En , Deris Safaai , Illias Rosli Md , Shamsir Mohd Shahir , Mohamad Mohd Saberi 
Published: September 2013

Parameter estimation is one of nine phases in modelling, which is the most challenging task that is used to estimate the parameter values for biological system that is non-linear. There is no general solution for determining the nonlinearity of the dynamic model. Experimental measurement is expensive, hard and time consuming. Hence, the aim for this research is to implement Particle Swarm Optimization (PSO) intoSBToolbox to solve the mentioned problems. As a result, the optimum kinetic parameters for simulating essential amino acid metabolism in plant model Arabidopsis Thaliana are obtained. There are four performance measurements used, namely computational time, average of error rate, standard deviation and production of graph. As a finding of this research, PSO has the smallest standard deviation and average of error rate. The computational time in parameter estimation is smaller in comparison with others, indicating that PSO is a consistent method to estimate parameter values compared to the performance of Simulated Annealing (SA) and downhill simplex method after the implementation into SBToolbox.
Suppression of thymosin β10 increases cell migration and metastasis of cholangiocarcinoma
Authors: Sribenja Sirinapa , Sawanyawisuth Kanlayanee , Kraiklang Ratthaphol , Wongkham Chaisiri , Vaeteewoottacharn Kulthida , Obchoei Sumalee , Yao Qizhi , Wongkham Sopit , Chen Changyi 
Published: September 2013

AbstractBackgroundThymosin β10 (Tβ10) expression is associated with malignant phenotypes in many cancers. However, the role and mechanisms of Tβ10 in liver fluke-associated cholangiocarcinoma (CCA) are not fully understood. In this study, we investigated the expression of Tβ10 in CCA tumor tissues and cell lines as well as molecular mechanisms of Tβ10 in tumor metastasis of CCA cell lines.MethodsTβ10 expression was determined by real time RT-PCR or immunocytochemistry. Tβ10 silence or overexpression in CCA cells was achieved using gene delivery techniques. Cell migration was assessed using modified Boyden chamber and wound healing assay. The effect of silencing Tβ10 on CCA tumor metastasis was determined in nude mice. Phosphorylation of ERK1/2 and the expression of EGR1, Snail and matrix metalloproteinases (MMPs) were studied.ResultsTen pairs of CCA tissues (primary and metastatic tumors) and 5 CCA cell lines were studied. With real time RT-PCR and immunostaining analysis, Tβ10 was highly expressed in primary tumors of CCA; while it was relatively low in the metastatic tumors. Five CCA cell lines showed differential expression levels of Tβ10. Silence of Tβ10 significantly increased cell migration, invasion and wound healing of CCA cellsin vitro; reversely, overexpression of Tβ10 reduced cell migration compared with control cells (P<0.05). In addition, silence of Tβ10 in CCA cells increased liver metastasis in a nude mouse model of CCA implantation into the spleen. Furthermore, silence of Tβ10 activated ERK1/2 and increased the expression of Snail and MMPs in CCA cell lines. Ras-GTPase inhibitor, FPT inhibitor III, effectively blocked Tβ10 silence-associated ERK1/2 activation, Snail expression and cell migration.ConclusionsLow expression of Tβ10 is associated with metastatic phenotype of CCAin vitroandin vivo, which may be mediated by the activation of Ras, ERK1/2 and upregulation of Snail and MMPs. This study suggests a new molecular pathway of CCA pathogenesis and a novel strategy to treat or prevent CCA metastasis.
Class III β-tubulin is a predictive marker for taxane-based chemotherapy in recurrent and metastatic gastric cancer
Authors: Hwang Jun-Eul , Hong Ji-Yun , Kim Karham , Kim Seung-Hun , Choi Won-Young , Kim Min-Jee , Jung Sung-Hoon , Shim Hyun-Jeong , Bae Woo-Kyun , Hwang Eu-Chang , Lee Kyung-Hwa , Lee Jae-Hyuk , Cho Sang-Hee , Chung Ik-Joo 
Published: September 2013

Abstract

Background
Class III β-tubulin (TUBB3) is a prognostic marker in various tumors, but the role of TUBB3 in advanced gastric cancer is not clearly defined. We analyzed the significance of TUBB3 expression, along with that of excision repair cross-complementation group 1 (ERCC1) in recurrent and metastatic gastric cancer patients receiving taxane-based first-line palliative chemotherapy.

Methods
We reviewed the cases of 146 patients with advanced gastric adenocarcinoma who received taxane-based first-line palliative chemotherapy between 2004 and 2010 at Chonnam National University Hwasun Hospital (Gwangju, Korea). Immunohistochemical staining for TUBB3 and ERCC1 was performed using paraffin wax-embedded tumor tissues. We evaluated the patients’ response to chemotherapy, progression-free survival (PFS), and overall survival (OS).

Results
In total, 146 patients with advanced gastric cancer received docetaxel and cisplatin (n = 15) or paclitaxel and cisplatin (n = 131). The median PFS was significantly shorter for patients with high-level TUBB3 expression than for patients with low-level TUBB3 expression (3.63 vs. 6.67 months, P = 0.001). OS was not associated with TUBB3 expression (13.1 vs. 13.1 months, P = 0.769). By multivariate analysis, only TUBB3 was related to a shorter PFS (HR 2.74, 95% CI 1.91-3.91, P = 0.001). Patients with high-level ERCC1 expression showed a lower response rate than patients with low-level ERCC1 expression (24 vs. 63.2%, P = 0.001); however, ERCC1 had no clinical effect on PFS or OS.

Conclusions
TUBB3 was a strong predictive marker in recurrent and metastatic gastric cancer patients receiving taxane-based first-line palliative chemotherapy. No clinical impact of ERCC1 was evident in this setting.