bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching foundational topics and scientific skills in biochemistry within the conceptual framework of HIV protease
Authors: Johnson R. Jeremy 
Published: March 2014

AbstractHIV protease has served as a model protein for understanding protein structure, enzyme kinetics, structure‐based drug design, and protein evolution. Inhibitors of HIV protease are also an essential part of effective HIV/AIDS treatment and have provided great societal benefits. The broad applications for HIV protease and its inhibitors make it a perfect framework for integrating foundational topics in biochemistry around a big picture scientific and societal issue. Herein, I describe a series of classroom exercises that integrate foundational topics in biochemistry around the structure, biology, and therapeutic inhibition of HIV protease. These exercises center on foundational topics in biochemistry including thermodynamics, acid/base properties, protein structure, ligand binding, and enzymatic catalysis. The exercises also incorporate regular student practice of scientific skills including analysis of primary literature, evaluation of scientific data, and presentation of technical scientific arguments. Through the exercises, students also gain experience accessing computational biochemical resources such as the protein data bank, Proteopedia, and protein visualization software. As these HIV centered exercises cover foundational topics common to all first semester biochemistry courses, these exercises should appeal to a broad audience of undergraduate students and should be readily integrated into a variety of teaching styles and classroom sizes. © 2014 by The International Union of Biochemistry and Molecular Biology, 42(4):299–304, 2014.
Terpendole E and its Derivative Inhibit STLC‐ and GSK‐1‐Resistant Eg5
Authors: Tarui Yuka , Chinen Takumi , Nagumo Yoko , Motoyama Takayuki , Hayashi Toshiaki , Hirota Hiroshi , Muroi Makoto , Ishii Yasuyuki , Kondo Hisae , Osada Hiroyuki , Usui Takeo 
Published: March 2014

AbstractTerpendole E is first natural product found to inhibit mitotic kinesin Eg5, but its inhibitory mechanism remains to be revealed. Here, we report the effects of terpendole E and 11ketopaspaline (a new natural terpendole E analogue) on the Eg5–microtubule interaction and in several Eg5 mutants. 11‐Ketopaspaline is a shunt product from terpendole E, and it shows potent inhibitory activity against the microtubule‐stimulated ATPase activity of Eg5. Unlike other Eg5 inhibitors, such as S‐trityl‐L‐cysteine (STLC) and GSK‐1, both terpendole E and 11‐ketopaspaline only partially inhibited Eg5–microtubule interaction. Furthermore, terpendole E and 11‐ketopaspaline inhibited several Eg5 mutants that are resistant to STLC (Eg5D130A, Eg5L214A) or GSK‐1 (Eg5I299F, Eg5A356T), but with the same extent of inhibition against wild‐type Eg5. Because Eg5D130A and Eg5L214A show cross‐resistance to most known Eg5 inhibitors, which bind the L5 loop, these results suggest that terpendole E and its analogues have a different binding site and/or inhibitory mechanism to those for L5 loop‐binding type Eg5 inhibitors.
Helical Carbon Segment in Carbon–Boron–Nitride Heteronanotubes: Structure and Nonlinear Optical Properties
Authors: Zhong Rong‐Lin , Sun Shi‐Ling , Xu Hong‐Liang , Qiu Yong‐Qing , Su Zhong‐Min 
Published: March 2014

AbstractCarbon–boron–nitride heteronanotubes have attracted much interest owing to their adjustable properties and wide applications in many fields. In this work, the structures and first hyperpolarizabilities (β0) of a series of HA‐n and isoelectronic PA‐n heteronanotubes are investigated, in which HA‐n is composed of a helical C segment and BN segment, and PA‐n is composed of an arc C segment and BN segment. Interestingly, the helix C segment in HA‐9 leads to a fascinating long‐range charge‐transfer character. As a result, the β0 value of HA‐9 is 1.80×104 a.u., which is much larger than that of PA‐9 (4.99×103 a.u.). Significantly, the β0 value of the C segment in HA‐9 is 1.72×104 a.u., whereas that of the BN segment in HA‐9 is much smaller (7.48×102 a.u.). In this context, the larger β0 value of HA‐9 is essentially induced by the helix topological effect of the C segment. It is our expectation that this new knowledge about heteronanotubes might provide more ideas for further exploration of sp2‐hybridized carbon segments with special topologies.
Early left‐right asymmetries during axial morphogenesis in the chick embryo
Authors: Otto Annalena , Pieper Tobias , Viebahn Christoph , Tsikolia Nikoloz 
Published: March 2014

SummaryThe primitive node is the “hub” of early left‐right patterning in the chick embryo: (1) it undergoes asymmetrical morphogenesis immediately after its appearance at Stage 4; (2) it is closely linked to the emerging asymmetrical expression of nodal and shh at Stage 5; and (3) its asymmetry is spatiotemporally related to the emerging notochord, the midline barrier maintaining molecular left‐right patterning from Stage 6 onward. Here, we study the correlation of node asymmetry to notochord marker expression using high‐resolution histology, and we test pharmacological inhibition of shh signaling using cyclopamine at Stages 4 and 5. Just as noggin expression mirrors an intriguing structural continuity between the right node shoulder and the notochord, shh expression in the left node shoulder confirms a similar continuity with the future floor plate. Shh inhibition at Stage 4 or 5 suppressed nodal in both its paraxial or lateral plate mesoderm domains, respectively, and resulted in randomized heart looping. Thus, the “primordial” paraxial nodal asymmetry at Stage 4/5 (1) appears to be dependent on, but not instructed by, shh signaling and (2) may be fixed by asymmetrical roots of the notochord and the floor plate, thereby adding further twists to the node's pivotal role during left‐right patterning. genesis 52:614–625, 2014. © 2014 Wiley Periodicals, Inc.
110 Years of change in urban tree stocks and associated carbon storage
Authors: Díaz‐Porras Daniel F. , Gaston Kevin J. , Evans Karl L. 
Published: March 2014

AbstractUnderstanding the long‐term dynamics of urban vegetation is essential in determining trends in the provision of key resources for biodiversity and ecosystem services and improving their management. Such studies are, however, extremely scarce due to the lack of suitable historical data. We use repeat historical photographs from the 1900s, 1950s, and 2010 to assess general trends in the quantity and size distributions of the tree stock in urban Sheffield and resultant aboveground carbon storage. Total tree numbers declined by a third from the 1900s to the 1950s, but increased by approximately 50% from the 1900s–2010, and by 100% from the 1950s–2010. Aboveground carbon storage in urban tree stocks had doubled by 2010 from the levels present in the 1900s and 1950s. The initial decrease occurred at a time when national and regional tree stocks were static and are likely to be driven by rebuilding following bombing of the urban area during the Second World War and by urban expansion. In 2010, trees greater than 10 m in height comprised just 8% of those present. The increases in total tree numbers are thus largely driven by smaller trees and are likely to be associated with urban tree planting programmes. Changes in tree stocks were not constant across the urban area but varied with the current intensity of urbanization. Increases from 1900 to 2010 in total tree stocks, and smaller sized trees, tended to be greatest in the most intensely urbanized areas. In contrast, the increases in the largest trees were more marked in areas with the most green space. These findings emphasize the importance of preserving larger fragments of urban green space to protect the oldest and largest trees that contribute disproportionately to carbon storage and other ecosystem services. Maintaining positive trends in urban tree stocks and associated ecosystem service provision will require continued investment in urban tree planting programmes in combination with additional measures, such as revisions to tree preservation orders, to increase the retention of such trees as they mature.
Use of posterior predictive checks as an inferential tool for investigating individual heterogeneity in animal population vital rates
Authors: Chambert Thierry , Rotella Jay J. , Higgs Megan D. 
Published: March 2014

AbstractThe investigation of individual heterogeneity in vital rates has recently received growing attention among population ecologists. Individual heterogeneity in wild animal populations has been accounted for and quantified by including individually varying effects in models for mark–recapture data, but the real need for underlying individual effects to account for observed levels of individual variation has recently been questioned by the work of Tuljapurkar et al. (Ecology Letters, 12, 93, 2009) on dynamic heterogeneity. Model‐selection approaches based on information criteria or Bayes factors have been used to address this question. Here, we suggest that, in addition to model‐selection, model‐checking methods can provide additional important insights to tackle this issue, as they allow one to evaluate a model's misfit in terms of ecologically meaningful measures. Specifically, we propose the use of posterior predictive checks to explicitly assess discrepancies between a model and the data, and we explain how to incorporate model checking into the inferential process used to assess the practical implications of ignoring individual heterogeneity. Posterior predictive checking is a straightforward and flexible approach for performing model checks in a Bayesian framework that is based on comparisons of observed data to model‐generated replications of the data, where parameter uncertainty is incorporated through use of the posterior distribution. If discrepancy measures are chosen carefully and are relevant to the scientific context, posterior predictive checks can provide important information allowing for more efficient model refinement. We illustrate this approach using analyses of vital rates with long‐term mark–recapture data for Weddell seals and emphasize its utility for identifying shortfalls or successes of a model at representing a biological process or pattern of interest.
Crystal and Electronic Structures and Magnetic Properties of Eu3Tt2As4 (Tt = Si, Ge)
Authors: Liu Xiao‐Cun , Xia Sheng‐Qing , Lei Xiao‐Wu , Pan Ming‐Yan , Tao Xu‐Tang 
Published: March 2014

AbstractTwo new europium‐containing Zintl phases, Eu3Si2As4 and Eu3Ge2As4, were discovered from metal flux reactions and their structures were identified by using single‐crystal X‐ray diffraction. Both compounds crystallize in the monoclinic space group P21/c and are isotypic to Sr3Ge2As4. Magnetic property studies were performed and the results proved the long‐range antiferromagnetic behavior for Eu3Ge2As4 but with a positive Weiss constant, which suggested the coexistence of both ferromagnetic and antiferromagnetic order of Eu 4f electrons in the structure. Density functional calculations were incorporated to understand the related magnetic properties as well.
Involvement of immune‐ and inflammatory‐related factors in flucloxacillin‐induced liver injury in mice
Authors: Takai Shohei , Higuchi Satonori , Yano Azusa , Tsuneyama Koichi , Fukami Tatsuki , Nakajima Miki , Yokoi Tsuyoshi 
Published: March 2014

ABSTRACTDrug‐induced liver injury (DILI) is a serious problem in pre‐clinical stages of drug development and clinical pharmacotherapy, but the pathogenesis of DILI has not been elucidated. Flucloxacillin (FLX), which is a β‐lactam antibiotic of the penicillin class that is used widely in Europe and Australia, rarely causes DILI. Clinical features suggest that FLX‐induced liver injury is caused by immune‐ and inflammatory‐related factors, but the mechanism of FLX‐induced liver injury is unknown. The purpose of this study was to elucidate the mechanisms of FLX‐induced liver injury in vivo. Plasma alanine aminotransferase, aspartate aminotransferase and total‐bilirubin levels were significantly elevated in FLX‐administered mice [1000 mg kg–1, intraperitoneally (i.p.)]. Toll‐like receptor 4 (TLR4) ligands, such as high‐mobility group box 1 (HMGB1) and S100A8/A9, were significantly increased in FLX‐administered mice, and inflammatory factors, such as interleukin (IL)‐1β, tumor necrosis factor‐alpha (TNF‐α), macrophage inflammatory protein (MIP)‐2, CXC chemokine‐ligand‐1 (CXCL1) and monocyte chemoattractant protein (MCP)‐1, were also significantly elevated. IL‐17‐related transcriptional factors and cytokines were increased, and the administration of recombinant IL‐17 (2 mg per body weight, i.p.) resulted in an exacerbation of the FLX‐induced liver injury. TLR4‐associated‐signal transduction may be involved in FLX‐induced liver injury, and IL‐17 is an exacerbating factor. Copyright © 2014 John Wiley & Sons, Ltd.
Disadvantages of interfragmentary shear on fracture healing—mechanical insights through numerical simulation
Authors: Steiner Malte , Claes Lutz , Ignatius Anita , Simon Ulrich , Wehner Tim 
Published: March 2014

ABSTRACTThe outcome of secondary fracture healing processes is strongly influenced by interfragmentary motion. Shear movement is assumed to be more disadvantageous than axial movement, however, experimental results are contradictory. Numerical fracture healing models allow simulation of the fracture healing process with variation of single input parameters and under comparable, normalized mechanical conditions. Thus, a comparison of the influence of different loading directions on the healing process is possible. In this study we simulated fracture healing under several axial compressive, and translational and torsional shear movement scenarios, and compared their respective healing times. Therefore, we used a calibrated numerical model for fracture healing in sheep. Numerous variations of movement amplitudes and musculoskeletal loads were simulated for the three loading directions. Our results show that isolated axial compression was more beneficial for the fracture healing success than both isolated shearing conditions for load and displacement magnitudes which were identical as well as physiological different, and even for strain‐based normalized comparable conditions. Additionally, torsional shear movements had less impeding effects than translational shear movements. Therefore, our findings suggest that osteosynthesis implants can be optimized, in particular, to limit translational interfragmentary shear under musculoskeletal loading. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 32:865–872, 2014.
Reduction of aflatoxin B1 to aflatoxicol: A comprehensive DFT study provides clues to its toxicity
Authors: Karabulut Sedat , Paytakov Guvanchmyrat , Leszczynski Jerzy 
Published: March 2014

AbstractBACKGROUNDAflatoxicol (AFL) is one of most the important metabolites of aflatoxin B1 (AFB1). AFL can be formed through enzymatic or synthetic reduction of AFB1. Various experimental and theoretical studies have been focused on the AFB1 due to its high toxicity and carcinogenicity.RESULTSThe selective reduction of AFB1 carbonyls, molecular structure of AFL and its effect on toxicity has been studied here by the density functional theory (DFT) method. Although the toxicity of AFL is 18 times lower than that of AFB1, it has been concluded that both molecular structures have similar potency to form an exo‐epoxide (AFEP) analogue which can bind to DNA.CONCLUSIONCalculations revealed that only one of the three possible tautomers of AFL is stable, both in the gas phase and water. The electronic properties of aflatoxicol are calculated as similar to aflatoxin B1 and this may be an explanation of similar carcinogenicity and toxicity of these compounds, which has been proved by experimental results. © 2014 Society of Chemical Industry
Otoscopy simulation training in a classroom setting: A novel approach to teaching otoscopy to medical students
Authors: Davies Joel , Djelic Lucas , Campisi Paolo , Forte Vito , Chiodo Albino 
Published: March 2014

Objectives/HypothesisTo determine the effectiveness of using of an otoscopy stimulator to teach medical students the primary principles of otoscopy in large group training sessions and improve their confidence in making otologic diagnoses.Study DesignCross‐sectional survey design.MethodsIn March 2013, the Department of Otolaryngology–Head and Neck Surgery held a large‐scale otoscopy simulator teaching session at the MaRS Innovation Center for 92 first and second year University of Toronto medical students. Following the training session, students were provided with an optional electronic, nine‐question survey related to their experience with learning otoscopy using the simulators alone, and in comparison to traditional methods of teaching.ResultsThirty‐four medical students completed the survey. Ninety‐one percent of the respondents indicated that the overall quality of the event was either very good or excellent. A total of 71% of respondents either agreed, or strongly agreed, that the otoscopy simulator training session improved their confidence in diagnosing pathologies of the ear. The majority (70%) of students indicated that the training session had stimulated their interest in otolaryngology–head and neck surgery as a medical specialty.ConclusionsOrganizing large‐group otoscopy simulator training sessions is one method whereby students can become familiar with a wide variety of pathologies of the ear and improve both their diagnostic accuracy and their confidence in making otologic diagnoses.Level of EvidenceNA Laryngoscope, 124:2594–2597, 2014
Small‐fiber neuropathy with cardiac denervation in postural tachycardia syndrome
Authors: Haensch Carl‐Albrecht , Tosch Marco , Katona Istvan , Weis Joachim , Isenmann Stefan 
Published: March 2014

ABSTRACTIntroduction: Postural tachycardia syndrome (POTS) is a disorder of orthostatic intolerance characterized by excessive tachycardia of unknown etiology. Our objective in this study was to evaluate the correlation between C‐fiber involvement as shown by skin biopsy and adrenergic cardiac metaiodobenzylguanadine (MIBG) uptake in POTS patients. Methods: Skin biopsies of 84 patients with POTS were examined by Protein Gene Product 9.5 (PGP9.5) immunohistochemistry and were compared with MIBG myocardial scintigraphy imaging data. Results: Mean intraepidermal nerve fiber (IENF) density was in the lower normal age‐adjusted range, 7.2 ± 2.9/mm (normal ≥7/mm), and was slightly below the normal range in 45% of POTS patients. MIBG uptake was reduced in 21% of patients. Low IENF density correlated with reduced cardiac MIBG uptake (r = 0.39, P = 0.001). Conclusions: A subset of neuropathic POTS patients may harbor mild small fiber neuropathy with abnormalities of unmyelinated nerve fibers in the skin associated with reduced myocardial postganglionic sympathetic innervation. Muscle Nerve 50: 956–961, 2014
Antibiotic therapy for inpatients with community‐acquired pneumonia in a developing country
Authors: Trinh Hieu T. , Hoang Phuong H. , Cardona‐Morrell Magnolia , Nguyen Hai T. , Vu Dinh Hoa , Dong Phuong T. X. , Cao Thao T. B. , Nguyen Son T. , Pham Van T. T. , Moss Le , Dinh Kathryn , Dartnell Jonathan , Nguyen Huong T. L. 
Published: March 2014

AbstractPurposeThe aim of this study was to identify antibiotic prescription patterns for community‐acquired pneumonia (CAP) in Vietnam.MethodsMedical records for CAP adult patients admitted to 10 hospitals across the country were randomly selected from admission lists during the peak pneumonia season. CAP cases were identified from manual record reviews by clinical pharmacists. Data was collected using a standard data collection tool including patient clinical features on admission, comorbidities, microbiological culture results, and antibiotic regimens. Pneumonia severity was estimated using the CURB‐65 score.ResultsA total of 649 medical records for adult patients (55.2% male and 52.3% urban residents, median age 68 years) met the selection criteria for CAP. Pneumonia severity was assessed as mild (64.1% of patients), moderate (23.0%), and severe (9.2%). Antibiotics were most frequently administered intravenously (93.4%) and as combination therapy (dual therapy 54.4%, monotherapy 42.5%, and triple therapy 3.1% of patients) regardless of CAP severity. Third‐generation cephalosporins were used most frequently (29.3% as monotherapy and 40.4% as combination therapy). Third‐generation cephalosporins were most commonly combined with penicillins and/or quinolones.ConclusionsThis first nationwide study provides a baseline profile of antibiotic use in the treatment of CAP. Third‐generation cephalosporins were widely used for initial empirical management of CAP, often in combination with quinolones, regardless of CAP severity. The study will assist in providing an evidence base to inform new national antibiotic guidelines for CAP management and will contribute locally relevant data for the national master plan addressing antibiotic resistance and the development of educational interventions to improve CAP management. Copyright © 2014 John Wiley & Sons, Ltd.
AlGaN/GaN HEMTs on Si by MBE with regrown contacts and fT = 153 GHz
Authors: Ganguly Satyaki , Song Bo , Hwang Wan Sik , Hu Zongyang , Zhu Mingda , Verma Jai , Xing Huili (Grace) , Jena Debdeep 
Published: March 2014

AbstractAlGaN/GaN high‐electron‐mobility transistors (HEMT) have been grown by radio frequency molecular beam epi‐taxy (RF‐MBE) on 3″ Si substrates. A record low contact resistance Rc ˜ 0.11 Ω.mm has been achieved for GaN HEMTs on Si by using non alloyed ohmic contacts regrown by MBE. Owing to the low contact resistance a 75‐nm gate length unpassivated HEMT shows intrinsic current gain cut‐off frequency fT =153 GHz, a high saturation drain current density> 1.3 A/mm and a low RON of 1 Ω.mm, among the best reported for HEMTs on Si. With further scaling GaN HEMTs on Si can compete in the high‐performance RF arena with similar devices on SiC, while exploiting the many advantages of integration with Si. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Experimental and theoretical study of dephasing processes in the kinetics of photoexcited carriers in GaN
Authors: Garrett Gregory A. , Shishehchi Sara , Rudin Sergey , Malinovsky Vladimir , Wraback Michael , Bellotti Enrico 
Published: March 2014

AbstractThe scattering and dephasing processes that accompany the initial photoexcitation of electron‐hole pairs in the semiconductor GaN are studied by sub‐picosecond time‐resolved photoluminescence. The rise time of the carrier recombination at the band edge after excitation 750 meV above the band gap is analyzed as a function of initial photoexcited carrier density and sample temperature. To elucidate the findings, simulations were performed based on a two band model with a non‐parabolic conduction band and using a generalized Monte‐Carlo technique. Results showed a small dependence in the rise time on the initial carrier density but a strong dependence on the sample temperature, where simulation and experiment scaled proportionately. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Layer‐by‐layer AuCl3 doping of stacked graphene films
Authors: Oh Sooyeoun , Kim Byung‐Jae , Kim Jihyun 
Published: March 2014

AbstractWe investigated the effect of layer‐by‐layer AuCl3 doping on the electrical and optical properties of stacked graphene films. Graphene grown by the chemical‐vapor deposition method on a Cu‐foil was chemically doped by AuCl3 solution with a concentration of 20 mM. Eight different configurations were prepared and analyzed by using four‐point probe measurements, optical transmittance measurements, scanning electron microscopy, and micro‐Raman spectroscopy to compare the optical and electrical characteristics of the different graphene samples. In our study, the top‐layer doping method was very effective because better performances considering both sheet resistance and optical transmittance were observed from the configurations with the top‐layer doped. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)