bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational features of benzo‐homologated yDNA duplexes by molecular dynamics simulation
Authors: Aparna P. , Varughese Mary , Varghese Mathew K. , Haris P. , Sudarsanakumar C. 
Published: September 2015

ABSTRACTyDNA is a base‐modified nucleic acid duplex containing size‐expanded nucleobases. Base‐modified nucleic acids could expand the genetic alphabet and thereby enhance the functional potential of DNA. Unrestrained 100 ns MD simulations were performed in explicit solvent on the yDNA NMR sequence [5′(yA T yA yA T yA T T yA T)2] and two modeled yDNA duplexes, [5′(yC yC G yC yC G G yC G G)2] and [(yT5′ G yT A yC yG C yA yG T3′)•(yA5′ C T C yG C G yT A yC A3′)]. The force field parameters for the yDNA bases were derived in consistent with the well‐established AMBER force field. Our results show that DNA backbone can withstand the stretched size of the bases retaining the Watson‐Crick base pairing in the duplexes. The duplexes retained their double helical structure throughout the simulations accommodating the strain due to expanded bases in the backbone torsion angles, sugar pucker and helical parameters. The effect of the benzo‐expansion is clearly reflected in the extended C1′‐C1′ distances and enlarged groove widths. The size expanded base modification leads to reduction in base pair twist resulting in larger overlapping area between the stacked bases, enhancing inter and intra strand stacking interactions in yDNA in comparison with BDNA. This geometry could favour enhanced interactions with the groove binders and DNA binding proteins., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 55–64, 2016
A rapid and sensitive LC‐MS/MS method for the determination of linarin in small‐volume rat plasma and tissue samples and its application to pharmacokinetic and tissue distribution study
Authors: Feng Xinchi , Liu Youping , Wang Xin , Di Xin 
Published: September 2015

AbstractA rapid and sensitive LC‐MS/MS method was developed for the determination of linarin in small‐volume rat plasma and tissue sample. Sample preparation was employed by the combination of protein precipitation (PPT) and liquid–liquid extraction (LLE) to allow measurement over a 5‐order‐of‐magnitude concentration range. Fast chromatographic separation was achieved on a Hypersil Gold column (100 × 2.1 mm i.d., 5 µm). Mass spectrometric detection was achieved using a triple‐quadrupole mass spectrometer equipped with an electrospray ionization interface operating in positive ionization mode. Quantification was performed using selected reaction monitoring of precursor‐product ion transitions at m/z 593 → 285 for linarin and m/z 447 → 271 for baicalin (internal standard). The total run time was only 2.8 min per sample. The calibration curves were linear over the concentration range of 0.4–200 µg/mL for PPT and 0.001–1.0 µg/mL for LLE. A lower limit of quantification of 1.0 ng/mL was achieved using only 20 μL of plasma or tissue homogenate. The intra‐ and inter‐day precisions in all samples were ≤14.7%, while the accuracy was within ±5.2% of nominal values. The validated method has been successfully applied to pharmacokinetic and tissue distribution study of linarin. Copyright © 2015 John Wiley & Sons, Ltd.
Bioresorbable vascular scaffold for the treatment of coronary bifurcations: What have we learned?
Authors: Belardi Jorge A. , Albertal Mariano 
Published: September 2015

Key points

Bioresorbable vascular scaffolds (BVS) remain experimental for the treatment of coronary bifurcations (B) and further clinical data is needed before widespread adoption in this setting.
Preliminary, clinical outcome in B using a provisional stenting or double stenting approach with BVS is encouraging and close to the one observed with next‐generation drug‐eluting stent.
Improvements in device navigability, reduction in strut bulk and reabsorption time may render the device more predictable and simpler to use.
Intramolecular Enantiomerism in S(+)2,2‐dimethyl ‐1,3‐dioxolane‐4‐methanol: The Interpretation of Raman Optical Activity Intensity
Authors: Wu Guozhen , Wang Peijie 
Published: September 2015

AbstractA bond polarizability algorithm was developed and applied to interpret the Raman optical activity (ROA) intensity. It is demonstrated that for the chiral molecule such as S(+)2,2‐dimethyl‐1,3‐dioxolane‐4‐methanol there exists approximate (or symmetry breaking) mirror reflection that reverses the signs of the differential bond polarizabilities of the pair bond coordinates that are related to each other by the mirror reflection, just like that between the right and left enantiomers. The magnitude difference of the differential bond polarizabilities of the pair bond coordinates becomes smaller as they are farther away from the asymmetric atom. Hence, that the asymmetric atom (center) plays a central role in ROA is confirmed from a spectroscopic viewpoint. Meanwhile, the concept of intramolecular enantiomerism is proposed. Chirality 27:820–825, 2015. © 2015 Wiley Periodicals, Inc.
Barriers to health care contribute to delays in follow‐up among women with abnormal cancer screening: Data from the Patient Navigation Research Program
Authors: Ramachandran Ambili , Snyder Frederick R. , Katz Mira L. , Darnell Julie S. , Dudley Donald J. , Patierno Steven R. , Sanders Mechelle R. , Valverde Patricia A. , Simon Melissa A. , Warren‐Mears Victoria , Battaglia Tracy A. ,   on behalf of the Patient Navigation Research Program Investigators
Published: September 2015

BACKGROUNDThere is limited understanding of the association between barriers to care and clinical outcomes within patient navigation programs.METHODSSecondary analyses of data from the intervention arms of the Patient Navigation Research Program were performed, which included navigated participants with abnormal breast and cervical cancer screening tests from 2007 to 2010. Independent variables were: 1) the number of unique barriers to care (0, 1, 2, or ≥3) documented during patient navigation encounters; and 2) the presence of socio‐legal barriers originating from social policy (yes/no). The median time to diagnostic resolution of index screening abnormalities was estimated using Kaplan‐Meier cumulative incidence curves. Multivariable Cox proportional hazards regression examined the impact of barriers on time to resolution, controlling for sociodemographics and stratifying by study center.RESULTSAmong 2600 breast screening participants, approximately 75% had barriers to care documented (25% had 1 barrier, 16% had 2 barriers, and 34% had ≥3 barriers). Among 1387 cervical screening participants, greater than one‐half had barriers documented (31% had 1 barrier, 11% had 2 barriers, and 13% had ≥3 barriers). Among breast screening participants, the presence of barriers was associated with less timely resolution for any number of barriers compared with no barriers. Among cervical screening participants, only the presence of ≥2 barriers was found to be associated with less timely resolution. Both types of barriers, socio‐legal and other barriers, were found to be associated with delay among breast and cervical screening participants.CONCLUSIONSNavigated women with barriers resolved cancer screening abnormalities at a slower rate compared with navigated women with no barriers. Further innovations in navigation care are necessary to maximize the impact of patient navigation programs nationwide. Cancer 2015;121:4016–4024. © 2015 American Cancer Society.
Fluorescence‐based retention assays reveals sustained release of vascular endothelial growth factor from bone grafts
Authors: Kang Wonmo , Yun Ye‐Rang , Lee Dong‐Sung , Kim Tae‐Hyun , Kim Joong‐Hyun , Kim Hae‐Won , Jang Jun‐Hyeog 
Published: September 2015

AbstractThe sustained release of growth factors following their implantation in vivo is essential for successful outcomes in bone tissue engineering. In this study, we evaluated the release kinetics and delivery efficacies of vascular endothelial growth factor (VEGF), a potent angiogenic growth factor, incorporated into calcium phosphate bone grafts (BGs). We evaluated the release profile of VEGF from BGs using a novel fluorescence‐based retention assay, which revealed that VEGF loaded on BGs can be released in a sustained manner without an initial burst (near zero‐order cumulative release) with a controlled release rate of 13.6% per week for up to 7 weeks. In contrast, an ELISA‐based release assay showed VEGF to have an early burst‐release profile for the first week. However, the biological activity of VEGF released from the BGs was preserved over the 7‐week release period, which is consistent with the sustained‐release profile observed in the fluorescence‐based retention assay. Furthermore, the in vivo bone‐forming action of the VEGF‐loaded BGs was well demonstrated in a rat subcutaneous model. Taken together, the sustained release of VEGF loaded onto BGs was effective in stimulating proliferation, angiogenesis and osteogenesis, suggesting the ultimate value of VEGF‐engineered BGs for bone tissue engineering. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 283–290, 2016.
Broadband spin‐controlled focusing via logarithmic‐spiral nanoslits of varying width
Authors: Mehmood M. Q. , Liu Hong , Huang Kun , Mei Shengtao , Danner Aaron , Luk'yanchuk Boris , Zhang Shuang , Teng Jinghua , Maier Stefan A. , Qiu Cheng‐Wei 
Published: September 2015

AbstractThis work presents analytical, numerical and experimental demonstrations of light diffracted through a logarithmic spiral (LS) nanoslit, which forms a type of switchable and focus‐tunable structure. Owing to a strong dependence on the incident photon spin, the proposed LS‐nanoslit converges incoming light of opposite handedness (to that of the LS‐nanoslit) into a confined subwavelength spot, while it shapes light with similar chirality into a donut‐like intensity profile. Benefitting from the varying width of the LS‐nanoslit, different incident wavelengths interfere constructively at different positions, i.e., the focal length shifts from 7.5 μm (at λ = 632.8 nm) to 10 μm (at λ = 488 nm), which opens up new opportunities for tuning and spatially separating broadband light at the micrometer scale.
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Vesicle‐to‐Rod Transition of Polymer Aggregates upon Irradiation
Authors: Menon Sajith , Ongungal Rahul M. , Das Suresh 
Published: September 2015

Atom transfer radical polymerization is utilized to synthesize an amphiphilic photoresponsive triblock copolymer poly(trifluorostilbene methacrylate)‐b‐polystyrene‐b‐polyethylene oxide (PTFS‐b‐PSt‐b‐PEO). Adding water into tetrahydrofuran solution of PTFS‐b‐PSt‐b‐PEO results in the formation of spherical vesicular aggregates brought about as a result of the association of the water insoluble TFS and St blocks. UV irradiation of the colloidal solution causes trans–cis isomerization of the TFS units which result in morphological transition of the spherical vesicular aggregates to rod‐like particles. This morphological transition is studied using dynamic light scattering, scanning electron microscopy, atomic force microscopy, transmission electron microscopy, and UV–vis and fluorescence spectroscopy. The trans‐stilbene units have almost zero dipole moment whereas the corresponding cis‐form has a definite dipole moment. This polarity difference associated with structural change is expected to be the main reason for the structural transformation of the aggregates. It is also found that PTFS‐b‐PSt‐b‐PEO aggregates have the ability of trapping organic dyes inside their hydrophobic cavity thereby making them water soluble. Subsequently the encapsulated dye can be partially released upon UV irradiation.
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“I know exactly what I'm going into”: recommendations for pre‐nursing experience from an evaluation of a pre‐nursing scholarship in rural Scotland
Authors: Smith Annetta , Beattie Michelle , Kyle Richard G. 
Published: September 2015

AbstractAimTo develop a model of pre‐nursing experience from evaluation of a pre‐nursing scholarship for school pupils in Scotland.DesignAction research study.MethodsSchool pupils (n = 42) completed questionnaire surveys and participated in anecdote circles. Student nurses acting as pupil ‘buddies’ (n = 33) participated in focus groups. Descriptive quantitative data and thematic analyses of qualitative data were integrated across cohorts and campuses.ResultsTen recommended components of a model of pre‐nursing experience were identified: educational experience of: (1) face‐to‐face on‐campus teaching; (2) hands‐on clinical skills sessions; and (3) andragogy, practice exposure to (4) nursing language; (5) nurses’ emotional labour; (6) patients’ stories; (7) pupils socializing with buddies; (8) buddies planning placement activities; and (9) supporting pupils during placements. Academic attainment was not a central component of the model due to pupils’ need to (10) prioritize examined work for further/higher education entry.
NMR analysis of the interaction of picornaviral proteinases Lb and 2A with their substrate eukaryotic initiation factor 4GII
Authors: Aumayr Martina , Fedosyuk Sofiya , Ruzicska Katharina , Sousa‐Blin Carla , Kontaxis Georg , Skern Tim 
Published: September 2015

AbstractMessenger RNA is recruited to the eukaryotic ribosome by a complex including the eukaryotic initiation factor (eIF) 4E (the cap‐binding protein), the scaffold protein eIF4G and the RNA helicase eIF4A. To shut‐off host–cell protein synthesis, eIF4G is cleaved during picornaviral infection by a virally encoded proteinase; the structural basis of this reaction and its stimulation by eIF4E is unclear. We have structurally and biochemically investigated the interaction of purified foot‐and‐mouth disease virus (FMDV) leader proteinase (Lbpro), human rhinovirus 2 (HRV2) 2A proteinase (2Apro) and coxsackievirus B4 (CVB4) 2Apro with purified eIF4GII, eIF4E and the eIF4GII/eIF4E complex. Using nuclear magnetic resonance (NMR), we completed 13C/15N sequential backbone assignment of human eIF4GII residues 551–745 and examined their binding to murine eIF4E. eIF4GII551–745 is intrinsically unstructured and remains so when bound to eIF4E. NMR and biophysical techniques for determining stoichiometry and binding constants revealed that the papain‐like Lbpro only forms a stable complex with eIF4GII551–745 in the presence of eIF4E, with KD values in the low nanomolar range; Lbpro contacts both eIF4GII and eIF4E. Furthermore, the unrelated chymotrypsin‐like 2Apro from HRV2 and CVB4 also build a stable complex with eIF4GII/eIF4E, but with KD values in the low micromolar range. The HRV2 enzyme also forms a stable complex with eIF4E; however, none of the proteinases tested complex stably with eIF4GII alone. Thus, these three picornaviral proteinases have independently evolved to establish distinct triangular heterotrimeric protein complexes that may actively target ribosomes involved in mRNA recruitment to ensure efficient host cell shut‐off.
Characterization of the internal properties of InGaN/GaN core–shell LEDs
Authors: Ledig Johannes , Wang Xue , Fündling Sönke , Schuhmann Henning , Seibt Michael , Jahn Uwe , Wehmann Hergo‐Heinrich , Waag Andreas 
Published: September 2015

In this paper, we present the structural, optical, and electrical characterization of InGaN/GaN core‐shell micro‐LED structures selectively grown by metal organic vapor phase epitaxy (MOVPE) in arranged arrays. In particular we analyze the core‐shell geometry of the pillars, consisting of a fivefold InGaN/GaN multiple quantum well and a p‐type layer on all sidewall and top facets. Additionally we analyze the optical properties of the structure and the active region with high spatial resolution by cathodoluminescence. Electron beam induced current measurements (EBIC) are performed using an SEM based manipulator setup, giving proof of the presence of a depletion region as well as the intended doping polarity of the n‐type core and a p‐type shell wrapped around the whole structure. Using a p–n–p configuration also current crowding is discussed by EBIC and electroluminescence is demonstrated by measuring emission patterns from single core–shell structures.Color overlay of SE image (grey, FOV = 12.7 μm) and EBIC image (red) of a cleaved core–shell LED pillar contacted by two probe tips at a substrate tilt of 30°.
Impact of a Standard Rodent Chow Diet on Tissue n‐6 Fatty Acids, Δ9‐Desaturation Index, and Plasmalogen Mass in Rats Fed for One Year
Authors: Pédrono F. , Boulier‐Monthéan N. , Catheline D. , Legrand P. 
Published: September 2015

AbstractAlthough many studies focus on senescence mechanisms, few habitually consider age as a biological parameter. Considering the effect of interactions between food and age on metabolism, here we depict the lipid framework of 12 tissues isolated from Sprague–Dawley rats fed standard rodent chow over 1 year, an age below which animals are commonly studied. The aim is to define relevant markers of lipid metabolism influenced by age in performing a fatty acid (FA) and dimethylacetal profile from total lipids. First, our results confirm impregnation of adipose and muscular tissues with medium‐chain FA derived from maternal milk during early infancy. Secondly, when animals were switched to standard croquettes, tissues were remarkably enriched in n‐6 FA and especially 18:2n‐6. This impregnation over time was coupled with a decrease of the desaturation index and correlated with lower activities of hepatic Δ5‐ and Δ6‐desaturases. In parallel, we emphasize the singular status of testis, where 22:5n‐6, 24:4n‐6, and 24:5n‐6 were exceptionally accumulated with growth. Thirdly, 18:1n‐7, usually found as a discrete FA, greatly accrued over the course of time, mostly in liver and coupled with Δ9‐desaturase expression. Fourthly, skeletal muscle was characterized by a surprising enrichment of 22:6n‐3 in adults, which tended to decline in older rats. Finally, plasmalogen‐derived dimethylacetals were specifically abundant in brain, erythrocytes, lung, and heart. Most notably, a shift in the fatty aldehyde moiety was observed, especially in brain and erythrocytes, implying that red blood cell analysis could be a good indicator of brain plasmalogens.
The trimeric serine protease HtrA1 forms a cage-like inhibition complex with an anti-HtrA1 antibody
Authors: Ciferri Claudio , Lipari Michael T. , Liang Wei-Ching , Estevez Alberto , Hang Julie , Stawicki Scott , Wu Yan , Moran Paul , Elliott Mike , Eigenbrot Charles , Katschke Kenneth J. , van Lookeren Campagne Menno , Kirchhofer Daniel 
Published: September 2015

High temperature requirement A1 (HtrA1) is a trypsin-fold serine protease implicated in the progression of age-related macular degeneration (AMD). Our interest in an antibody therapy to neutralize HtrA1 faces the complication that the target adopts a trimeric arrangement, with three active sites in close proximity. In the present study, we describe antibody 94, obtained from a human antibody phage display library, which forms a distinct macromolecular complex with HtrA1 and inhibits the enzymatic activity of recombinant and native HtrA1 forms. Using biochemical methods and negative-staining EM we were able to elucidate the molecular composition of the IgG94 and Fab94 complexes and the associated inhibition mechanism. The 246-kDa complex between the HtrA1 catalytic domain trimer (HtrA1_Cat) and Fab94 had a propeller-like organization with one Fab bound peripherally to each protomer. Low-resolution EM structures and epitope mapping indicated that the antibody binds to the surface-exposed loops B and C of the catalytic domain, suggesting an allosteric inhibition mechanism. The HtrA1_Cat–IgG94 complex (636 kDa) is a cage-like structure with three centrally located IgG94 molecules co-ordinating two HtrA1_Cat trimers and the six active sites pointing into the cavity of the cage. In both complexes, all antigen-recognition regions (paratopes) are found to bind one HtrA1 protomer and all protomers are bound by a paratope, consistent with the complete inhibition of enzyme activity. Therefore, in addition to its potential therapeutic usefulness, antibody 94 establishes a new paradigm of multimeric serine protease inhibition.
Local and global structural drivers for the photoactivation of the orange carotenoid protein
Authors: Gupta Sayan , Guttman Miklos , Leverenz Ryan L. , Zhumadilova Kulyash , Pawlowski Emily G. , Petzold Christopher J. , Lee Kelly K. , Ralston Corie Y. , Kerfeld Cheryl A. 
Published: September 2015

Significance
The orange carotenoid protein (OCP) is critical for the antenna-associated energy-dissipation mechanism of cyanobacteria under high light conditions. We show that light activation causes a global conformation change, the complete separation of the two domains of the OCP. Such a conformational change has been postulated to be a prerequisite for interaction with the antenna. We also identify local structural changes in residue solvent accessibility and roles for structural water molecules in activation of the OCP. By combining small-angle scattering, hydrogen-deuterium exchange, and X-ray hydroxyl radical footprinting studies, we were able to construct a model of the structural changes during the activation of the OCP with an unprecedented level of detail.
Birth of a new gene on the Y chromosome ofDrosophila melanogaster
Authors: Carvalho Antonio Bernardo , Vicoso Beatriz , Russo Claudia A. M. , Swenor Bonnielin , Clark Andrew G. 
Published: September 2015

SignificanceMammalian Y chromosomes are believed to evolve mainly through gene inactivation and loss.DrosophilaY chromosomes seem to not obey this rule, as gene gains are the dominating force in their evolution. Here we describeflagrante delicto Y(FDY), a very young gene that shows how Y-linked genes were acquired.FDYoriginated 2 million years ago from a duplication of a contiguous autosomal segment of 11 kb containing five genes that inserted into the Y chromosome. Four of these autosome-to-Y gene copies became inactivated (“pseudogenes”), lost part of their sequences, and most likely will disappear in the next few million years.FDY, originally a female-biased gene, acquired testis expression and remained functional.
Enhancing burst activation and propagation in cultured neuronal networks by photo-stimulation
Authors: Afshar Ghazaleh , El Hady Ahmed , Geisel Theo , Stuehmer Walter , Wolf Fred 
Published: September 2015

AbstractSpontaneous bursting activity in cultured neuronal networks is initiated by leader neurons, which constitute a small subset of first-to-fire neurons forming a sub-network that recruits follower neurons into the burst. While the existence and stability of leader neurons is well established, the influence of stimulation on the leader-follower dynamics is not sufficiently understood. By combining multi-electrode array recordings with whole field optical stimulation of cultured Channelrhodopsin-2 transduced hippocampal neurons, we show that fade-in photo-stimulation induces a significant shortening of intra-burst firing rate peak delay of follower electrodes after offset of the stimulation compared to unperturbed spontaneous activity. Our study shows that optogenetic stimulation can be used to change the dynamical fine structure of self-organized network bursts.