bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model
Authors: Rice William R. , Friberg Urban , Gavrilets Sergey 
Published: July 2013

AbstractWe recently synthesized and reinterpreted published studies to advance an epigenetic model for the development of homosexuality (HS). The model is based on epigenetic marks laid down in response to the XX vs. XY karyotype in embryonic stem cells. These marks boost sensitivity to testosterone in XY fetuses and lower it in XX fetuses, thereby canalizing sexual development. Our model predicts that a subset of these canalizing epigenetic marks stochastically carry over across generations and lead to mosaicism for sexual development in opposite‐sex offspring – the homosexual phenotype being one such outcome. Here, we begin by outlining why HS has been under‐appreciated as a commonplace phenomenon in nature, and how this trend is currently being reversed in the field of neurobiology. We next briefly describe our epigenetic model of HS, develop a set of predictions, and describe how epigenetic profiles of human stem cells can provide for a strong test of the model.
Molecular phylogeny of Neotropical bioluminescent beetles (Coleoptera: Elateroidea) in southern and central Brazil
Authors: Amaral DT , Arnoldi FGC , Rosa SP , Viviani VR 
Published: July 2013

ABSTRACTBioluminescence in beetles is found mainly in the Elateroidea superfamily (Elateridae, Lampyridae and Phengodidae). The Neotropical region accounts for the richest diversity of bioluminescent species in the world with about 500 described species, most occurring in the Amazon, Atlantic rainforest and Cerrado (savanna) ecosystems in Brazil. The origin and evolution of bioluminescence, as well as the taxonomic status of several Neotropical taxa in these families remains unclear. In order to contribute to a better understanding of the phylogeny and evolution of bioluminescent Elateroidea we sequenced and analyzed sequences of mitochondrial NADH2 and the nuclear 28S genes and of the cloned luciferase sequences of Brazilian species belonging to the following genera: (Lampyridae) Macrolampis, Photuris, Amydetes, Bicellonycha, Aspisoma, Lucidota, Cratomorphus; (Elateridae) Conoderus, Pyrophorus, Hapsodrilus, Pyrearinus, Fulgeochlizus; and (Phengodidae) Pseudophengodes, Phrixothrix, Euryopa and Brasilocerus. Our study supports a closer phylogenetic relationship between Elateridae and Phengodidae as other molecular studies, in contrast with previous morphologic and molecular studies that clustered Lampyridae/Phengodidae. Molecular data also supported division of the Phengodinae subfamily into the tribes Phengodini and Mastinocerini. The position of the genus Amydetes supports the status of the Amydetinae as a subfamily. The genus Euryopa is included in the Mastinocerini tribe within the Phengodinae/Phengodidae. Copyright © 2013 John Wiley & Sons, Ltd.
Towards kinetic modeling of genome‐scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
Authors: Chakrabarti Anirikh , Miskovic Ljubisa , Soh Keng Cher , Hatzimanikatis Vassily 
Published: July 2013

AbstractMathematical modeling is an essential tool for the comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possible to define limits on steady‐state metabolic behavior using flux balance analysis. However, detailed information on enzyme kinetics and enzyme regulation is needed to formulate kinetic models that can accurately capture the dynamic metabolic responses. The use of mechanistic enzyme kinetics is a difficult task due to uncertainty in the kinetic properties of enzymes. Therefore, the majority of recent works considered only mass action kinetics for reactions in metabolic networks. Herein, we applied the optimization and risk analysis of complex living entities (ORACLE) framework and constructed a large‐scale mechanistic kinetic model of optimally grown Escherichia coli. We investigated the complex interplay between stoichiometry, thermodynamics, and kinetics in determining the flexibility and capabilities of metabolism. Our results indicate that enzyme saturation is a necessary consideration in modeling metabolic networks and it extends the feasible ranges of metabolic fluxes and metabolite concentrations. Our results further suggest that enzymes in metabolic networks have evolved to function at different saturation states to ensure greater flexibility and robustness of cellular metabolism.
Peptides as models for the structure and function of viral capsid proteins: Insights on dengue virus capsid
Authors: Freire João Miguel , Veiga Ana Salomé , de la Torre Beatriz G. , Santos Nuno C. , Andreu David , Da Poian Andrea T. , Castanho Miguel A. R. B. 
Published: July 2013

ABSTRACTThe structural organization of viral particles is among the most astonishing examples of molecular self‐assembly in nature, involving proteins, nucleic acids, and, sometimes, lipids. Proper assembly is essential to produce well structured infectious virions. A great variety of structural arrangements can be found in viral particles. Nucleocapsids, for instance, may display highly ordered geometric shapes or consist in macroscopically amorphous packs of the viral genome. Alphavirus and flavivirus are viral genera that exemplify these extreme cases, the former comprising viral particles structured with a T = 4 icosahedral symmetry, whereas flavivirus capsids have no regular geometry. Dengue virus is a member of flavivirus genus and is used in this article to illustrate how viral protein‐derived peptides can be used advantageously over full‐length proteins to unravel the foundations of viral supramolecular assemblies. Membrane‐ and viral RNA‐binding data of capsid protein‐derived dengue virus peptides are used to explain the amorphous organization of the viral capsid. Our results combine bioinformatic and spectroscopic approaches using two‐ or three‐component peptide and/or nucleic acid and/or lipid systems. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 325–336, 2013.
Peptide antagonists of the calcitonin gene‐related peptide (CGRP) receptor with improved pharmacokinetics and pharmacodynamics
Authors: Miranda Les P. , Shi Licheng , Holder Jerry R. , Wright Marie , Gegg Colin V. , Johnson Eileen , Wild Kenneth , Stenkilsson Michael , Doellgast George , Manning Barton H. , Salyers Kevin 
Published: July 2013

ABSTRACTAntagonism of the calcitonin gene‐related peptide (CGRP) receptor may be a useful approach for migraine treatment. Selective PEGylated peptide antagonists to the CGRP receptor are described, derived from CGRP(8–37) with polymer derivatization at an engineered lysine‐25 residue. Potent PEGylated peptides with improved pharmacokinetics were identified through peptide side‐chain modification to mitigate metabolic liabilities. PEGylated Ac‐Trp‐[Cit11,18,hArg24,Lys25,Asp31,Pro34,1‐Nal35]CGRP(8–37)‐NH2, 9, elicits a dose‐dependent reduction of intradermal CGRP‐induced local blood flow in rodents with an ED50 of 0.52 mg kg−1 without any overt adverse effects. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 422–430, 2013.
Advances in turbulent mixing techniques to study microsecond protein folding reactions
Authors: Kathuria Sagar V. , Chan Alexander , Graceffa Rita , Paul Nobrega R. , Robert Matthews C. , Irving Thomas C. , Perot Blair , Bilsel Osman 
Published: July 2013

ABSTRACTRecent experimental and computational advances in the protein folding arena have shown that the readout of the one‐dimensional sequence information into three‐dimensional structure begins within the first few microseconds of folding. The initiation of refolding reactions has been achieved by several means, including temperature jumps, flash photolysis, pressure jumps, and rapid mixing methods. One of the most commonly used means of initiating refolding of chemically denatured proteins is by turbulent flow mixing with refolding dilution buffer, where greater than 99% mixing efficiency has been achieved within 10's of microseconds. Successful interfacing of turbulent flow mixers with complementary detection methods, including time‐resolved Fluorescence Spectroscopy (trFL), Förster Resonance Energy Transfer, Circular Dichroism, Small‐Angle X‐ray Scattering, Hydrogen Exchange followed by Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy, Infrared Spectroscopy (IR), and Fourier Transform IR Spectroscopy, has made this technique very attractive for monitoring various aspects of structure formation during folding. Although continuous‐flow (CF) mixing devices interfaced with trFL detection have a dead time of only 30 µs, burst phases have been detected in this time scale during folding of peptides and of large proteins (e.g., CheY and TIM barrels). Furthermore, a major limitation of the CF mixing technique has been the requirement of large quantities of sample. In this brief communication, we will discuss the recent flurry of activity in micromachining and microfluidics, guided by computational simulations, which are likely to lead to dramatic improvements in time resolution and sample consumption for CF mixers over the next few years. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 888–896, 2013.
Characterization of hyaluronic acid and synovial fluid in stagnation point elongational flow
Authors: Haward Simon J. 
Published: July 2013

ABSTRACTHyaluronic acid (HA) is an important biomacromolecule, which fulfils a number of vital physiological functions (especially in the joint synovial fluid) and also has consumer and pharmaceutical applications. HA solution properties have already been quite thoroughly characterized in response to steady shear flows but are less well understood in highly deforming extensional flows. In this study, flow‐induced birefringence measurements are made as a function of the strain rate in planar elongational flow at the stagnation point of a cross‐slot device using HA solutions of a range of molecular weightsand at dilute concentrations. The results provide macromolecular relaxation times, molecular weight distributions and the extensional viscosities and Trouton ratios of the fluids. The HA relaxation time is found to vary as1.8, which is consistent with a partially solvated, expanded coil. An intrinsic Trouton ratio is defined, which varies as2. The measurement of birefringence with strain rate is shown to be highly sensitive to the molecular weight distribution and can resolve subtle changes due to macromolecular degradation and the presence of fracture products. Mechanical degradation experiments in the cross‐slots indicate midchain scission of HA macromolecules, strongly suggesting near full extension of the high‐molecular weight fraction in the stagnation point extensional flow field. Taken together the results suggest a possible method for analysis of the HA in synovial fluid, and this concept is tested using synovial fluid obtained from porcine tarsal joint. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 287–305, 2014.
LC‐ESI‐MS/MS analysis and pharmacokinetics of jolkinolide B, a potential antitumor active component isolated from Euphorbia fischeriana, in rat plasma
Authors: Li Yang , Liu Xiao‐Li , Cai Zhen‐Gang , Zhang Si‐Xi 
Published: July 2013

ABSTRACTA simple, specific and reproducible liquid chromatography–electrospray ionization mass spectrometry was developed and validated for the determination of jolkinolide B, a potential antitumor active component isolated from Euphorbia fischeriana, in rat plasma. Chromatographic separation was achieved on a Venusil MP‐C18 column using an isocratic elution. Jolkinolide B and osthole (internal standard) were monitored by positive electrospray ionization in the selected reaction monitoring mode. Good linearity (r2 > 0.996) was achieved by a weighted (1/x2) linear least‐squares regression over a concentration range of 6.50–2600 ng/mL. The accuracy and precision of the assay were satisfactory and the method proved to be applicable to pharmacokinetics following a single intravenous bolus injection of jolkinolide B to rats. Copyright © 2013 John Wiley & Sons, Ltd.
Phytal: A Candidate Sex Pheromone Component of the Moroccan Locust Dociostaurus maroccanus
Authors: Fürstenau Benjamin , Muñoz Lourdes , Coca‐Abia Milagro , Rosell Gloria , Guerrero Angel , Quero Carmen 
Published: July 2013

AbstractOutbreaks of locusts cause enormous economic losses to agriculture in many countries. To develop environmentally friendly strategies for their control, much research has been focused on the factors that influence locust biology, particularly infochemical‐mediated interactions. We present herein the identification and synthesis of both Z and E isomers of phytal (3,7,11,15‐tetramethylhexadec‐2‐enal, 1), which are involved in chemical communication and behaviour of the Moroccan locust, Dociostaurus maroccanus, a serious agricultural pest. The compound was identified by comparison of its chromatographic and spectrometric features and microchemical reactions with those of a synthetic sample. The natural compound was shown to have the R,R configuration by chiral HPLC analysis, and its structure is unique as an insect pheromone component. Both isomers of phytal are produced by sexually mature adult males and elicit electroantennographic responses in antennae of both sexes. In two‐choice olfactometer bioassays, males and females significantly preferred the stream enriched with racemic phytal to the control. In contrast, hydrogenated phytal was behaviourally inert. Both isomers of phytal are specific to D. maroccanus as they are absent in the closely related, habitat‐sharing species Dociostaurus jagoi and Calliptamus wattenwylianus. Legs and wings are the main release sites of the compound: approximately 90 % of that emitted by living individuals. In biosynthetic studies, phytal appears to proceed from oxidation of phytol (2) after injection of deuterated phytol into the abdomen of the insect or after administration in the diet. Our results demonstrate that phytal is a candidate sex pheromone component of the Moroccan locust; it is produced by mature males, and might be eavesdropped upon by conspecific males.
Strand Invasion of DNA Quadruplexes by PNA: Comparison of Homologous and Complementary Hybridization
Authors: Gupta Anisha , Lee Ling‐Ling , Roy Subhadeep , Tanious Farial A. , Wilson W. David , Ly Danith H. , Armitage Bruce A. 
Published: July 2013

AbstractMolecular recognition of DNA quadruplex structures is envisioned to be a strategy for regulating gene expression at the transcriptional level and for in situ analysis of telomere structure and function. The recognition of DNA quadruplexes by peptide nucleic acid (PNA) oligomers is presented here, with a focus on comparing complementary, heteroduplex‐forming and homologous, heteroquadruplex‐forming PNAs. Surface plasmon resonance and optical spectroscopy experiments demonstrated that the efficacy of a recognition mode depended strongly on the target. Homologous PNA readily invades a quadruplex derived from the promoter regulatory region found upstream of the MYC proto‐oncogene to form a heteroquadruplex at high potassium concentration mimicking the intracellular environment, whereas complementary PNA exhibits virtually no hybridization. In contrast, complementary PNA is superior to the homologous in hybridizing to a quadruplex modeled on the human telomere sequence. The results are discussed in terms of the different structural morphologies of the quadruplex targets and the implications for in vivo recognition of quadruplexes by PNAs.
Complete percutaneous approach for arterial access in transfemoral transcatheter aortic valve replacement: A comparison with surgical cut‐down and closure
Authors: Nakamura Mamoo , Chakravarty Tarun , Jilaihawi Hasan , Doctor Niraj , Dohad Suhail , Fontana Gregory , Cheng Wen , Makkar Raj R. 
Published: July 2013

ObjectivesThis study sought to investigate the immediate safety and feasibility of complete percutaneous access/closure of arteriotomy for device deployment compared to the surgical approach for transfemoral transcatheter aortic valve replacement (TAVR).BackgroundThe percutaneous approach for arterial access for device deployment in transfemoral TAVR is a potential alternative to the surgical approach.MethodsIn 274 patients who underwent transfemoral TAVR using Edward Sapien heart valve, 140 had a complete percutaneous approach using a “pre‐closure” technique whereas 134 had surgical cut‐down/repair for arterial access/closure of device deployment. Immediate vascular access/closure success, associated complications and clinical outcomes were compared.ResultsWhile overall acute success of access/closure and in‐hospital access‐related events were similar, significant isolated stenosis/dissection at the access site developed more frequently in the percutaneous group (7.1% vs. 0.7%, P = 0.007). Contrary, wound infections requiring prolonged antibiotics use or surgical debridement occurred more frequently in the surgical group (0.7% vs. 6.7%, P = 0.007). Although the rate of major vascular complications was not different, the surgical group developed more frequent minor bleeding (27.1% vs. 38.8%, P = 0.04) and underwent transfusion of packed red blood cells of ≤3 units (25.7% vs. 43.3%, P = 0.002). Median hospital stay was shorter in the percutaneous group (3 days vs. 4 days, P = 0.002).ConclusionsThe percutaneous approach is a feasible access/closure method with a potential of lowering access site infection and bleeding, and shortening hospital stay, while maintaining similar rates of major vascular complications compared to the surgical approach. © 2013 Wiley Periodicals, Inc.
The long‐term outcomes of transcoronary ablation of septal hypertrophy compared to surgical myectomy in patients with symptomatic hypertrophic obstructive cardiomyopathy
Authors: Samardhi Himabindu , Walters Darren L , Raffel Christopher , Rateesh Shruti , Harley Catherine , Burstow Darryl , Pohlner Peter , Aroney Con 
Published: July 2013

ObjectivesThe aim of this study was to compare the long‐term outcomes of transcoronary ablation of septal hypertrophy (TASH) with open surgical myomectomy (SM) in patients with symptomatic hypertrophic obstructive cardiomyopathy (HOCM).MethodsWe reviewed patients who underwent either procedure at our institution. The demographics, clinical outcomes, echocardiographic parameters, and complications were compared.ResultsSeventy patients with HOCM were treated with either TASH (n = 47, 26 male) or SM (n = 23, 10 male). Compared to those treated with SM, patients undergoing TASH were older (57+/− 14.7 years versus 47 +/− 20.6 years, P = 0.021) and more symptomatic. A higher proportion of patients had syncope as a presenting feature in the TASH group compared to the SM group (57.5% vs. 17.4%, P = 0.002) respectively. They were also more likely to be in New York Heart Association (NYHA) class III/IV compared to the patients who underwent SM (85.1% vs. 39.1%; P < 0.001). Patients were followed for a mean period of 43 months (TASH) and 46 months (SM). Repeat procedures were more common in the TASH group (17% vs. 0%, P = 0.04) but mitral valve replacement was more common in the SM group (0% vs. 8.7%, P = 0.105). Symptom improvement, the rate of complications and all cause mortality rates were similar in both groups.ConclusionsTASH compares favorably with surgical myectomy with regard to symptom resolution, rate of complications and mortality in a tertiary referral centre and should be seen as an attractive alternative to surgical myectomy in the appropriate patient population. © 2013 Wiley Periodicals, Inc.
Two‐week interval optical coherence tomography: Imaging evidence on neointimal coverage completion after implantation of the endeavor zotarolimus‐eluting stent
Authors: Nishinari Makoto , Shimohama Takao , Tojo Taiki , Shiono Takaaki , Shinagawa Hisahito , Kameda Ryo , Aoyama Naoyoshi , Izumi Tohru 
Published: July 2013

ObjectiveTo obtain imaging evidence by 2‐week optical coherence tomography (OCT) on the completion of neointimal coverage (NIC; the percentage of stent strut coverage and thickness of the formed neointima) completion after implantation of the Endeavor zotarolimus‐eluting stent (E‐ZES).BackgroundDespite the fact that NIC is a cardinal process in the pathomechanism of late stent thrombosis, little imaging information is available on morphological changes thereof on a short‐time interval basis.Methods27 Japanese patients with stable angina pectoris and de novo native coronary artery lesions were enrolled, and 27 lesions (30 implantations) were examined. OCT was performed at weeks 2, 4, 6, 8, and 10 after E‐ZES implantation. NIC was examined using cross‐sectional OCT images obtained at the 1.0‐mm intervals.ResultsIn total, 621 cross‐sectional OCT images, which depicted 7,747 stent struts, were analyzed. The mean percentages of stent strut coverage at weeks 2, 4, 6, 8, and 10 after E‐ZES implantation were 12.3, 70.4, 67.9, 86.0, and 99.2%, respectively; a marked increase was found between weeks 2 and 4. The mean thicknesses of the formed neointima were 40.2, 52.1, 48.1, 86.5, and 146.2 μm at respective weeks, with the high‐signal and thick neointima (146 µm) at week 10. An intracoronary thrombus was detected in only one stent at week 4.ConclusionsThe full circumferential coverage of the vessel wall by the high‐signal neointima was found at as early as week 10 after E‐ZES implantation, imparting a surrogate index for vascular healing by NIC. © 2013 Wiley Periodicals, Inc.
Formation of Propane in the Aqueous‐Phase Processing of 1‐Propanol over Platinum: A DFT Study
Authors: Chiu Cheng‐chau , Genest Alexander , Rösch Notker 
Published: July 2013

AbstractThe reaction pathways for alkane formation from alcohols in aqueous‐phase (AP) processing was studied computationally for the model system 1‐propanol over flat and stepped surfaces of Pt. We examined the dehydration–hydrogenation (DH) mechanism in an acidic environment and alcohol hydrogenolysis (AH) under neutral conditions. The highest (relative) barrier of the DH mechanism was calculated at approximately 90 kJ mol−1on Pt(1 1 1), which occurs in the hydrogenation step after cleavage of the CO bond. The highest relative barrier of the AH mechanism, if the CO bond is cleaved on Pt(1 1 1), is slightly higher, 105 kJ mol−1. The corresponding elementary reaction step does not start from the alcohol, but a dehydrogenated intermediate. On Pt(2 2 1), transition state geometries differ somewhat and the highest relative barriers of both mechanisms, AH and DH, are lower by 8–40 kJ mol−1, than the corresponding barriers on Pt(1 1 1).