bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectrum of Point Mutations in the Human Genome and Major Subpopulations
Authors: Zhao Zhongming , Vuong Huy , Jia Peilin 
Published: May 2013

Abstract

Point mutation, often referred to as single‐nucleotide polymorphism (SNP), does not occur randomly and is dependent on the GC content and sequence context in the human genome. The spectrum of mutations in the human genome can be reliably inferred by comparing SNPs with their ancestral sequences. The direction of mutations inferred by SNPs may be measured by three approaches: directly observed frequencies of nucleotide changes, relative frequencies of nucleotide changes by normalising the nucleotide content and frequencies of nucleotide changes after excluding the CpG effect. An examination of the spectrum of mutations indicates that point mutation varies between the categorised genomic regions and has been strongly influenced by the CpG effect. There is no major difference in the mutational spectrum among the common and rare variants or among major human subpopulations; however, rare variants have higher frequency of C→T mutations, reflecting the CpG effect in the human genome.

Key Concepts:

Point mutation does not occur randomly in the human genome and is dependent on the GC content and sequence context.

Single nucleotide polymorphisms (SNPs) are the most abundant genetic variants in the human genome.

Mutational spectrum in the human genome and genomic regions is important for our understanding of the mechanisms of mutations, genome sequence evolution and causes of disease.

The direction of mutations can be reliably inferred by comparing SNPs with their ancestral sequences.

CpG effect has a significant influence on mutational spectrum.

Spectrum of mutations can be measured by three approaches: the observed frequencies of nucleotide changes, the relative frequencies and exclusion of the CpG effect.

Rare variants more likely reflect the recent mutational events in human populations.
Evolutionary Origin of Orphan Genes
Authors: Tautz Diethard , Neme Rafik , Domazet‐Lošo Tomislav 
Published: May 2013

Abstract

Orphan genes are genes that occur in specific evolutionary lineages without similarity to genes outside of these lineages and have, therefore, alternatively been named taxonomically restricted genes. They were so far considered to emerge through duplication–divergence processes, but it is now becoming clear that they can also arise

de novo

out of noncoding deoxyribonucleic acid (DNA). This latter process may even occur much more frequently than previously assumed. It appears that genomes harbour many transcripts in a transition stage from nonfunctional to functional genes, also known as protogenes, which are exposed to evolutionary testing and can become fixed when they turn out to be useful. Orphan genes may have played key roles in generating lineage‐specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.

Key Concepts:

Orphan genes, or taxonomically restricted genes, have arisen at all levels of the phylogenetic hierarchy.

All genes that cannot be traced to the first cellular ancestor are orphan genes in some lineages.

New genes may not only arise through gene duplication, but also through
de novo
evolution.

Spurious transcripts can give rise to protogenes, from which new functional genes evolve.

Emergence of new genes from protogenes is an active process in all extant genomes.

New genes may first act as noncoding RNAs before obtaining a functional reading frame.

Overprinting of existing reading frames with new reading frames is another possibility of
de novo
evolution of gene functions.

Orphan genes may contribute to lineage‐specific adaptations.

Orphan genes may carry information on the evolutionary past that can be harnessed by the phylostratigraphic approach.

There is a continuous birth–death dynamics of gene evolution.
Effect of DMDBS (3 : 2, 4‐bis(3,4‐dimethyldibenzylidene) sorbitol) and NA11 (sodium 2,2′‐methylene‐bis(4,6‐di‐tertbutylphenyl)‐phosphate) on electret properties of polypropylene filaments
Authors: Kilic Ali , Shim Eunkyoung , Yeom Bong Yeol , Pourdeyhimi Behnam 
Published: May 2013

ABSTRACTPolypropylene (PP) composite filaments containing two different nucleating agents—DMDBS (3 : 2, 4‐bis(3,4‐dimethyldibenzylidene) sorbitol) and NA11 (sodium 2,2′‐methylene‐bis(4,6‐di‐tertbutylphenyl)‐phosphate) were melt spun to modify polymer electrostatic charging characteristics. Sample filaments were charged with a corona instrument and their surface potentials were measured. Initial surface potential as well as potential stability was monitored through an accelerated decay procedure. NA11 was found to be more efficient as an electret additive leading to a 50% increase in charge stability. Filaments with DMDBS exhibited a faster decay. Charging at elevated temperatures resulted in enhanced charge density and stability for both additives. The fiber microstructure was examined by Wide Angle X‐ray Diffraction and Differential Scanning Calorimetry. Rather than reducing the crystal sizes, X‐Ray diffractograms suggest that the crystal size increases with the addition of nucleating agents, while the degree of crystallinity appears to remain unaltered. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 2068–2075, 2013
Adaptive‐Like Vibration Control in Mechanical Systems with Unknown Paramenters and Signals
Authors: Beltrán‐Carbajal F. , Silva‐Navarro G. 
Published: May 2013

AbstractThis paper describes the application of an on‐line algebraic identification methodology for parameter and signal estimation in vibrating mechanical systems. An important property of the algebraic identification is that the parameter identification is not asymptotic but algebraic, that is, the parameters are computed as fast as the system dynamics are being excited by some external input or by changes in the initial conditions. The algebraic identification is then employed to estimate mass, stiffness, and viscous damping in simple mechanical systems using only position measurements. This approach is also used in the identification of frequency, phase, and amplitude of exogenous vibrations affecting a mechanical system. The algebraic identification is then combined with a certainty equivalence controller to asymptotically stabilize the system response and, simultaneously, cancel harmonic vibrations. The proposed adaptive‐like control scheme is fast and robust against unknown parameters and frequency variations. Some numerical and experimental results illustrate the dynamic and robust performance of the algebraic identification and the active vibration controller.
Synthesis and Properties of Porous Organic Polymers from a Rigid Macrocyclic Building Block
Authors: Song Jingru , Huang Zhitang , Zheng Qiyu 
Published: May 2013

AbstractTwo rigid macrocyclic CTV‐based porous organic polymers, Click‐POP‐1 and Click‐POP‐2, have been synthesized by Click reaction of a cyclotriveratrylene analogue with alkyne groups and aromatic azides in one pot. FTIR, solid 13C NMR and elemental analysis confirmed the formation of the polymers. Both of them possess high thermo‐stability which is up to 410 and 900°C, respectively, and moderate hydrogen storage properties with 0.46 wt% at 77 K. Their nitrogen uptake showed type‐I isotherm with BET surface areas up to 342 and 317 m2·g−1.
Self‐assembly of Pyrene‐modified Rhomboidal Metallodendrimers via Directional Metal‐ligand Bonding Approach
Authors: He Menglan , Han Qing , He Jiuming , Li Quanjie , Abliz Zeper , Tan Hongwei , Xu Lin , Yang Haibo 
Published: May 2013

AbstractThe design and self‐assembly of pyrene‐modified rhomboidal metallodendrimers R1–R6 via directional metal‐ligand bonding approach is described. By employing pyrene‐containing 120° di‐Pt(II) acceptor and appropriate 60° dendritic dipyridyl donors, a variety of [G‐1]–[G‐3] pyrene‐modified rhomboidal metallodendrimers with well‐defined shape and size were prepared under mild conditions in high yields. The supramolecular dendrimers were characterized with multinuclear NMR (1H and 31P) and mass spectrometry (CSI‐TOF‐MS). Isotopically resolved mass spectrometry data support the existence of the pyrene‐modified dendrimers with rhomboidal cavities, and NMR data were consistent with the formation of all ensembles. The shape and size of all rhomboidal dendrimers were investigated with the PM6 semiempirical molecular orbital method. Their primary photochemical properties were studied as well.
Complexation Selectivities of Pillar[5]arenes with Primary Ammonium Salts
Authors: Liu Luzhi , Chen Yu , Wang Lingyun , Meier Herbert , Cao Derong 
Published: May 2013

AbstractThe complexation of alkyl‐substituted pillar[5]arenes with primary ammonium salts is investigated. 1,4‐Bis(methoxy)pillar[5]arene (MeP5) can form strong complexes with the primary ammonium salts in CDCl3. However, 1,4‐bis(ethoxy)pillar[5]arene (EtP5) shows weak interaction with these guests, and 1,4‐bis(butoxy)pillar[5]arene (BuP5) can not form such a complex at all. These results indicate that the modified alkyl chains of pillar[5]arene play an important role in the complexation selectivity.
Stereoselective Photochemical Reaction of Cyclohexyl Phenyl Ketone within Lytropic Liquid Crystals Formed by Chiral Ionic Liquids
Authors: Yang Xiujie , Li Xinwei , Chen Bin , Wu Lizhu , Zhang Liping , Zheng Liqiang , Tung Chenho 
Published: May 2013

AbstractIrradiation of cyclohexyl phenyl ketone (1) results in either intra‐ or intermolecular hydrogen abstraction to afford compounds 1‐phenylhept‐6‐en‐1‐one (2) and α‐cyclohexyl benzyl alcohol (3) as photoproducts, in which 3 has a pair of enantiomers. Herein, two types of chiral hexagonal liquid crystals were prepared to direct the enantioselective photochemical reaction of 1. One of the hexagonal liquid crystals is composed of 1‐tetradecyl‐3‐methylimidazolium bromide/p‐xylene/H2O with the modification by a chiral inductor. The other one is formed by chiral (S)‐3‐hexadecyl‐1‐(1‐hydroxy‐propan‐2‐yl)‐imidazolium bromide/p‐xylene/H2O. The product analysis shows that the latter one can be used as a microreactor to achieve stereoselective photochemical reaction, while the former one produced compound 3 with no enantioselectivity at all.
Multidrug resistance in relapsed acute myeloid leukemia: Evidence of biological heterogeneity
Authors: Patel Chirayu , Stenke Leif , Varma Sudhir , Lindberg Marita Lagergren , Björkholm Magnus , Sjöberg Jan , Viktorsson Kristina , Lewensohn Rolf , Landgren Ola , Gottesman Michael M. , Gillet Jean‐Pierre 
Published: May 2013

BACKGROUNDStudies of mechanisms mediating resistance to chemotherapy led to the discovery of the multidrug transporter ABCB1 (ATP‐binding cassette, subfamily B, member 1), often expressed in leukemic cells of patients with acute myeloid leukemia (AML). Most clinical trials evaluating the strategy of inhibiting efflux‐mediated chemotherapeutic resistance have been unsuccessful, clearly indicating the need for a better approach.METHODSThis study investigated the clinical relevance of 380 genes whose expression has been shown to affect the response to chemotherapy, mostly through in vitro studies, in 11 paired samples obtained at AML diagnosis and at relapse. The expression profiling of these 380 genes was performed using TaqMan‐based quantitative reverse‐transcription polymerase chain reaction. Patients had a median age of 58 years at diagnosis, a median duration of complete remission of 284.5 days, and a median overall survival of 563 days. Cytogenetic abnormalities were detected at diagnosis in 4 patients, whereas 5 displayed a normal karyotype and 2 were not investigated.RESULTSHierarchical clustering shows that samples taken at diagnosis and relapse clustered in pairs for 6 patients of the 11 studied, suggesting recurrence of the same leukemic blast, whereas for the other 5 patients, the data indicate their relapse blasts arose from different origins. A patient‐by‐patient analysis of the paired samples led to the striking observation that each had a unique gene signature representing different mechanisms of resistance.CONCLUSIONSThe data underline the need for personalized molecular analysis to tailor treatment for patients with AML. Cancer 2013;119:3076—3083. © 2013 American Cancer Society.
Paranasal sinus squamous cell carcinoma incidence and survival based on Surveillance, Epidemiology, and End Results data, 1973 to 2009
Authors: Ansa Benjamin , Goodman Michael , Ward Kevin , Kono Scott A. , Owonikoko Taofeek K. , Higgins Kristin , Beitler Jonathan J. , Grist William , Wadsworth Trad , El‐Deiry Mark , Chen Amy Y. , Khuri Fadlo Raja , Shin Dong M. , Saba Nabil F. 
Published: May 2013

BACKGROUNDParanasal sinus squamous cell carcinomas (PNSSCC) account for 3% of all head and neck malignancies. There has been little information on the trends in incidence and survival, and no randomized trials have been conducted to guide therapy.METHODSPatients with PNSSCC reported to the Surveillance, Epidemiology, and End Results (SEER) Program from 1973 through 2009 were categorized by sex, age, year of diagnosis, primary site, stage, and treatment. The incidence and survival were then compared across different demographic and disease‐related categories by calculating rate ratios (RRs) and mortality hazard ratios along with the corresponding 95% confidence intervals (CIs).RESULTSIn total, 2553 patients with PNSSCC were identified. While incidence of PNSSCC showed a gradual decline, survival remained largely unchanged. The proportion of patients with advanced disease decreased from 14.7% during the period from 1983 to 1992 to 12.4% during 1993‐2002 and to 9.5% during 2003‐2009. Compared with whites, incidence was higher among African Americans (RR 1.63; 95% CI, 1.39, 1.90) and among all other racial groups (RR, 1.78; 95% CI: 1.53‐2.07). After adjusting for age, sex, disease stage, tumor site, and treatment, mortality among African American patients also was increased (hazard ratio, 1.22; 95% CI, 1.04‐1.43). Among patients with localized disease, the relation between race and mortality was no longer evident once the results were controlled for tumor classification.CONCLUSIONSThe current findings point to racial disparities in the incidence of PNSSCC and, to a lesser extent, in the outcome of patients with PNSSCC. Although there has been a decline in the proportion of patients presenting with advanced PNSSCC, the overall survival remained stable over time. Cancer 2013;119:2602–2610. © 2013 American Cancer Society.
Inclusion of minorities and women in cancer clinical trials, a decade later: Have we improved?
Authors: Kwiatkowski Kat , Coe Kathryn , Bailar John C. , Swanson G. Marie 
Published: May 2013

BACKGROUNDInclusion of diverse groups of participants in cancer clinical trials is an important methodological and clinical issue. The quality of the science and generalizability of results depends on the inclusion of study participants who represent all populations among whom these treatment and prevention approaches will be used.METHODSWe conducted a systematic review using OVID as the primary source of reports included. Based on 304 peer‐reviewed publications, diversity in the inclusion and reporting of study participants during a decade of cancer treatment and prevention trials (2001‐2010) is summarized. Recommendations are made for improvements in the science and reporting of cancer clinical trials.RESULTSOf the 277 treatment trials and 27 prevention trials included in this report, more than 80% of participants were white and 59.8% were male. In the recent decade, race and sex are rarely used as selection criteria unless the trial is focused on a sex‐specific cancer.CONCLUSIONSWomen and racial/ethnic minorities remain severely underrepresented in cancer clinical trials, thus limiting the generalizability of cancer clinical research. Cancer 2013;119:2956—2963. © 2013 American Cancer Society.
Immunohistochemical analysis of E‐cadherin and zeste homolog 2 expression in endoscopic ultrasound‐guided fine‐needle aspiration of pancreatic adenocarcinoma
Authors: Gao Ling , Antic Tatjana , Hyjek Elizabeth , Gong Can , Mueller Jeffrey , Waxman Irving , DeMay Richard M. , Reeves Ward 
Published: May 2013

BACKGROUNDRecent studies have demonstrated that partial or complete loss of E‐cadherin (EC) and nuclear accumulation of zeste homolog 2 (EZH2) are hallmarks of poorly differentiated pancreatic adenocarcinoma (PAC). Depletion of EZH2 sensitizes cancer cells to chemotherapy in vitro. The objective of this study was to determine EC and EZH2 expression by immunohistochemistry (IHC) in samples obtained by endoscopic ultrasound‐guided fine‐needle aspiration (EUS‐FNA) as potential biomarkers for treatment and disease prognosis.METHODSThirty‐eight EUS‐FNA samples from patients with a PAC diagnosis were analyzed by IHC for EC and EZH2 expression. Seven corresponding surgical resection specimens were included in the study. The intensity of EZH2 and EC expression in PAC and in normal gastrointestinal pick‐ups (internal positive control) was scored by using a 4‐tier grading system.RESULTSEC demonstrated a focal, weak‐to‐moderate decrease in 24 PAC samples. Complete loss of EC expression was observed in the poorly differentiated areas represented by single tumor cells. The average staining intensity of EC in samples of poorly differentiated PAC was significantly lower than that of moderately differentiated PAC samples (P = .0005). EZH2 was variably positive in 31 of 38 PAC samples. The average staining intensity of EZH2 in moderately and poorly differentiated PACs did not differ significantly (P = .81).CONCLUSIONSEC and EZH2 expression was determined reliably by IHC on paraffin sections of EUS‐FNA cell block specimens. The current results were consistent with prior reports indicating a decrease or loss of EC expression in poorly differentiated PAC. However, EZH2 expression did not always correlate inversely with EC expression and was more heterogeneous. Cancer (Cancer Cytopathol) 2013;121:644–52. © 2013 American Cancer Society.
Extraction of Noble and Rare‐Earth Metals from Aqueous Solutions by DNA Cross‐Linked Hydrogels
Authors: Maeda Yuko , Zinchenko Anatoly , Lopatina Larisa I. , Sergeyev Vladimir G. , Murata Shizuaki 
Published: May 2013

AbstractInvited for this month’s cover is the group of Prof. Shizuaki Murata and Dr. Anatoly Zinchenko from Nagoya University and the group of Prof. Vladimir Sergeyev from Moscow State University. The cover picture shows the accumulation of noble and rare‐earth metals by DNA cross‐linked hydrogel. Read the full text of the article on page 619 ff..
Benchmark of Simplified Formulations for the Electrical Conductivity of Non‐Ideal Plasmas
Authors: Clérouin J. 
Published: May 2013

AbstractWe discuss simplified formulations for the electrical conductivity [1] and compare them with experimental results of various expanded metals recently published [2]. We use formulations designed for fully ionized hydrogen in a broader range of non‐fully ionized materials of various atomic number through the use of an effective coupling parameter based on estimations of the ionization. The ionizations are deduced from average‐atom calculations and compared with faster Thomas‐Fermi‐Dirac estimations. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Calculation of Canonical Properties of a Quantum System by Path Integral Numerical Methods
Authors: Voznesenskiy M. A. , Vorontsov‐Velyaminov P. N. 
Published: May 2013

AbstractWe propose a new approach in obtaining the partition function of a system of several interacting particles (fermions) in external field within path integral Monte Carlo method based on direct averaging of the exchange contributions over the positive weight determined by non‐closed trajectories. This procedure is performed at fixed temperatures, ranging to rather low values. The complete partition function for each temperature is then obtained within an expanded ensemble procedure. We found a good agreement of data obtained by the new method with results of previously proposed path‐integral‐expanded‐ensemble Monte Carlo calculations [1, 2]. The new approach allows to reach observably lower temperatures compared to method [1, 2], thus providing a significant reduce of the sign problem. It yields an independent way to treat thermal properties of quantum systems, so the good agreement with previous data [1, 2] allows us to test and state the validity of both approaches. Simulations for systems of 2 up to 5 non‐interacting particles and particles interacting with Coulomb repulsion in 3D harmonic field were performed. The presented approach allows one to carry out calculations for low temperatures that makes it possible to extract data for the ground‐state energy and low‐temperature thermodynamics. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron Kinetics in Femtosecond X‐Ray Irradiated SiO2
Authors: Medvedev N. , Ziaja B. , Cammarata M. , Harmand M. , Toleikis S. 
Published: May 2013

AbstractA theoretical study of the ultrafast electron kinetics in solid SiO2, irradiated with a femtosecond X‐ray laser pulse, is presented. A Monte Carlo code for event‐by‐event simulations of individual particles is applied to model the electron kinetics within the irradiated SiO2 bulk. The simulation includes photoionization, elastic and inelastic scatterings of electrons, Auger decays of core holes, and electron‐hole recombination via exciton self‐trapping mechanism. Transient electron density is followed, at different photon energies and pulse durations. The change of the optical properties (reflectance, transmittance) of the material is estimated with the help of the Drude model. The analysis of the results allows us to conclude that within the X‐ray excited dielectric, the holes in the valence band give the predominant contribution to the transient changes of optical properties within the material. The increase rate of the free electron density is limited by the duration of secondary electron cascading. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Atomistic Modelling and Simulation of Warm Dense Matter. Conductivity and Reflectivity
Authors: Norman G. , Saitov I. , Stegailov V. , Zhilyaev P. 
Published: May 2013

AbstractWarm dense matter conductivity and reflectivity are investigated by means of density functional theory. Both one‐ and two‐temperature cases are considered. One‐temperature mode is related to equilibrium state where temperature of electrons and ions are equal. As an example of one‐temperature system xenon plasma is studied. The reflectivity of shock‐compressed dense xenon plasma is calculated and compared with experimental data. Two‐temperature mode is associated with different temperature of electrons and ions. The thermal conductivity of aluminium and gold in such mode is examined. The comparison of obtained results with theoretical model based on Boltzmann equation is conducted. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
SAHA‐S Thermodynamic Model of Solar Plasma
Authors: Gryaznov V.K. , Iosilevskiy I.L. , Fortov V.E. , Starostin A.N. , Roerich V.K. , Baturin V. A. , Ayukov S. V. 
Published: May 2013

AbstractThe model SAHA‐S based on the chemical picture for the equation of state of the solar plasma is presented. The effects of Coulomb interaction, exchange and diffraction effects, free electron degeneracy, relativistic corrections, radiation pressure contributions are taken into account. The solar model based on SAHA‐S taking into account extended element composition and variation of heavy element abundance is represented and discussed. The comparison of the SAHA‐S equation of state data for a hydrogen plasma with the results of other models applicable to the description of the solar plasma equation of state and the results obtained with the first principle methods are demonstrated and discussed. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)