bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D adiabatic T1ρ prepared ultrashort echo time cones sequence for whole knee imaging
Authors: Ma Ya‐Jun , Carl Michael , Searleman Adam , Lu Xing , Chang Eric Y. , Du Jiang 
Published: March 2018

PurposeTo develop a 3D adiabatic T1ρ prepared ultrashort echo time cones (3D AdiabT1ρ UTE‐Cones) sequence for whole knee imaging on a clinical 3T scanner.MethodsA train of adiabatic full passage pulses were used for spin locking, followed by time‐efficient multispoke UTE acquisition to detect signals from both short and long T2 tissues in the whole knee joint. A modified signal model was proposed for multispoke UTE data fitting. The feasibility of this 3D AdiabT1ρ UTE‐Cones technique was demonstrated through numerical simulation, phantom, and ex vivo knee sample studies. The 3D AdiabT1ρ UTE‐Cones technique was then applied to 6 in vivo knee joints of healthy volunteers to measure T1ρ values of quadriceps tendon, patellar tendon, anterior cruciate ligament (ACL), posterior cruciate ligament (PCL), meniscus, patellar cartilage, and muscle.ResultsNumerical simulation, phantom and ex vivo knee sample studies demonstrated the feasibility of whole knee imaging using the proposed multispoke 3D AdiabT1ρ UTE‐Cones sequence. The healthy volunteer knee study demonstrated an averaged T1ρ of 13.9 ± 0.7 ms for the quadriceps tendon, 9.7 ± 0.8 ms for the patellar tendon, 34.9 ± 2.8 ms for the ACL, 21.6 ± 1.4 ms for the PCL, 22.5 ± 1.9 ms for the meniscus, 44.5 ± 2.4 ms for the patellar cartilage, and 43.2 ± 1.1 ms for the muscle.ConclusionThe 3D AdiabT1ρ UTE‐Cones sequence allows volumetric T1ρ assessment of both short and long T2 tissues in the knee joint on a clinical 3T scanner.
Trendbericht Organische Chemie 2017
Authors: Straub Bernd , Andexer Jennifer N. , Arenz Christoph , Beifuss Uwe , Beuerle Florian , Brasholz Malte , Breinbauer Rolf , Ditrich Klaus , Ernst Martin , Gulder Tobias A. M. , Kordes Markus , Krueger Anke , Lehmann Matthias , Lindel Thomas , Lüdeke Steffen , Luy Burkhard , Meier Michael A. R. , Mück‐Lichtenfeld Christian , Muhle‐Goll Claudia , Narine Arun , Paradies Jan , Pfau Roland , Pietruszka Jörg , Schaschke Norbert , Senge Mathias O. , Werner Thomas , Werz Daniel B. , Winter Christian , Worgull Dennis 
Published: March 2018

AbstractMolekularer Knoten mit topologischer Chiralität – Strukturaufklärung des Polyol‐Makrolids Deplelid A – Totalsynthese von Crocagin A – Organokatalyse in supramolekularen Aggregaten – nachhaltige Oxidation an Oxymorphon – eisenkatalysierte enantioselektive C‐H‐Aktivierung‐ und Alkylierung – fluoreszierendes künstliches DNA‐Basenpaar
Distributed estimation for spatial rigid motion based on dual quaternions
Authors: Zu Yue , Lee Unsik , Dai Ran 
Published: March 2018

SummaryThis paper proposes 2 distributed optimization algorithms for the estimation of spatial rigid motion using multiple image sensors in a connected network. The objective is to increase the estimation precision of translational and rotational motion based on dual quaternion models and the cooperation between connected sensors. The dual decomposition subgradient method and distributed Newton optimization method are applied to decompose the filtering task into a series of suboptimal problems and then solve them individually to achieve the global optimality. Our approach assumes that each sensor can communicate with its neighboring sensors to update the individual estimates. Discussion on converging speed of both methods are provided. Simulation examples are demonstrated to compare the 2 distributed algorithms with the traditional extended Kalman filter in terms of estimation accuracy and converging rate.
Stimmgabeln – einfach und verästelt
Authors: Mathelitsch Leopold , Granitzer Petra , Rumpf Klemens , Verovnik Ivo 
Published: March 2018

ZusammenfassungDas Schwingen von Stimmgabeln lässt sich grundsätzlich durch eine Balkenschwingung beschreiben. Ein schwingender Zinken entspricht einem Dipolstrahler. Beide Zinken zusammen ergeben einen Quadrupolstrahler. Die Zinken sind in der Regel schmal im Vergleich zur abgestrahlten Wellenlänge. Das sorgt für einen akustischen Kurzschluss, der erklärt, warum Stimmgabeln so leise sind. Im Fundus der Universität Graz befinden sich vierzinkige Stimmgabeln. Konstruiert wurden sie im 19. Jahrhundert von einem österreichischen Professor. Nach einer zeitgenössischen Notiz wollte er damit menschliche Vokallaute nachbilden.
Semen‐derived amyloidogenic peptides—Key players of HIV infection
Authors: Lee Young‐Ho , Ramamoorthy Ayyalusamy 
Published: March 2018

AbstractMisfolding and amyloid aggregation of intrinsically disordered proteins (IDPs) are implicated in a variety of diseases. Studies have shown that membrane plays important roles on the formation of intermediate structures of IDPs that can initiate (and/or speed‐up) amyloid aggregation to form fibers. The process of amyloid aggregation also disrupts membrane to cause cell death in amyloid diseases like Alzheimer's disease and type‐2 diabetes. On the other hand, recent studies reported the membrane fusion properties of amyloid fibers. Remarkably, amyloid‐fibril formation by short peptide fragments of highly abundant prostatic acidic‐phosphatase (PAP) in human semen and are capable of boosting the rate of HIV infection up to 400,000‐fold during sexual contact. Unlike the least toxic fully matured fibers of most amyloid proteins, the semen‐derived enhancer of virus infection (SEVI) amyloid‐fibrils of PAP peptide fragments are highly potent in rendering the maximum rate of HIV infection. This unusual property of amyloid fibers has witnessed increasing number of studies on the biophysical aspects of fiber formation and fiber‐membrane interactions. NMR studies have reported a highly disordered partial helical structure in a membrane environment for the intrinsically disordered PAP peptide that promotes the fusion of the viral membrane with that of host cells. The purpose of this review article is to unify and integrate biophysical and immunological research reported in the previous studies on SEVI. Specifically, amyloid aggregation, dramatic HIV infection enhancing properties, membrane fusion properties, high resolution NMR structure, and approaches to eliminate the enhancement of HIV infection of SEVI peptides are discussed.
Crystal structure of B‐cell co‐receptor CD19 in complex with antibody B43 reveals an unexpected fold
Authors: Teplyakov Alexey , Obmolova Galina , Luo Jinquan , Gilliland Gary L. 
Published: March 2018

AbstractCD19 is a transmembrane protein expressed on malignant B cells, but not in other lineages or other tissues, which makes it an attractive target for monoclonal antibody‐mediated immunotherapy. Anti‐CD19 antibody B43 was utilized in a bispecific T‐cell engager (BiTE) blinatumomab that demonstrated potency for the treatment of relapsed acute lymphoblastic leukemia. To gain insight into the mechanism of action of the antibody, the crystal structure of B43 Fab was determined in complex with CD19 and in the unbound form. The structure revealed the binding epitope, explained the lack of cross‐reactivity toward non‐human species, and suggested the key‐and‐lock mechanism of antigen recognition. Most unexpectedly, the structure revealed a unique molecular topology of CD19. Rather than a tandem of c‐type immunoglobulin folds predicted from the amino acid sequence, the extracellular domain of CD19 exhibits an elongated β‐sandwich formed by two immunoglobulin folds by swapping their C‐terminal halves. This is the first structure of CD19, which has no sequence homologs.
Phylogenetic spread of sequence data affects fitness of SOD1 consensus enzymes: Insights from sequence statistics and structural analyses
Authors: Goyal Venuka Durani , Magliery Thomas J. 
Published: March 2018

AbstractNon‐natural protein sequences with native‐like structures and functions can be constructed successfully using consensus design. This design strategy is relatively well understood in repeat proteins with simple binding function, however detailed studies are lacking in globular enzymes. The SOD1 family is a good model for such studies due to the availability of large amount of sequence and structure data motivated by involvement of human SOD1 in the fatal motor neuron disease amyotrophic lateral sclerosis (ALS). We constructed two consensus SOD1 enzymes from multiple sequence alignments from all organisms and eukaryotic organisms. A significant difference in their catalytic activities shows that the phylogenetic spread of the sequences used affects the fitness of the construct obtained. A mutation in an electrostatic loop and overall design incompatibilities between bacterial and eukaryotic sequences were implicated in this disparity. Based on this analysis, a bioinformatics approach was used to classify mutations thought to cause familial ALS providing a unique high level view of the physical basis of disease‐causing aggregation of human SOD1.
MUFOLD‐SS: New deep inception‐inside‐inception networks for protein secondary structure prediction
Authors: Fang Chao , Shang Yi , Xu Dong 
Published: March 2018

AbstractProtein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neural network architecture, named the Deep inception‐inside‐inception (Deep3I) network, is proposed for protein secondary structure prediction and implemented as a software tool MUFOLD‐SS. The input to MUFOLD‐SS is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio‐chemical properties of amino acids, PSI‐BLAST profile, and HHBlits profile. MUFOLD‐SS is composed of a sequence of nested inception modules and maps the input matrix to either eight states or three states of secondary structures. The architecture of MUFOLD‐SS enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, MUFOLD‐SS outperformed the best existing methods and other deep neural networks significantly. MUFold‐SS can be downloaded from http://dslsrv8.cs.missouri.edu/~cf797/MUFoldSS/download.html.
Low pressure‐induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time‐resolved infrared spectroscopy
Authors: He Zhipeng , Liu Zhao , Zhou Xiaofeng , Huang He 
Published: March 2018

AbstractThe secondary structure transitions of regenerated silk fibroin (RSF) under different external perturbations have been studied extensively, except for pressure. In this work, time‐resolved infrared spectroscopy with the attenuated total reflectance (ATR) accessory was employed to follow the secondary structure transitions of RSF in its wet film under low pressure. It has been found that pressure alone is favorable only to the formation of β‐sheet structure. Under constant pressure there is an optimum amount of D2O in the wet film (D2O : film = 2:1) so as to provide the optimal condition for the reorganization of the secondary structure and to have the largest formation of β‐sheet structure. Under constant amount of D2O and constant pressure, the secondary structure transitions of RSF in its wet film can be divided into three stages along with time. In the first stage, random coil, α‐helix, and β‐turn were quickly transformed into β‐sheet. In the second stage, random coil and β‐turn were relatively slowly transformed into β‐sheet and α‐helix, and the content of α‐helix was recovered to the value prior to the application of pressure. In the third and final stage, no measurable changes can be found for each secondary structure. This study may be helpful to understand the secondary structure changes of silk fibroin in silkworm's glands under hydrostatic pressure.
Accurate description of excited state intramolecular proton transfer that involves zwitterionic state using optimally tuned range‐separated time‐dependent density functional theory
Authors: Zhou Panwang , Zhao Li 
Published: March 2018

AbstractExcited‐state intramolecular proton transfer (ESIPT) reaction typically involves the excited‐state of charge‐transfer (CT) character. Thus, locating the transition state (TS) and providing an accurate description for the canonical and tautomeric forms play important roles and remain as challenges in the investigation of ESIPT reaction. In this study, the ESIPT reaction of a recently developed ESIPT chromophore (compound 1) (N. Suzuki et al., Angew. Chem. Int. Ed. 2014, 53, 8231) that involves the CT and zwitterionic states has been investigated using the time‐dependent density functional theory (TDDFT) method with different functionals and the second‐order algebraic diagrammatic construction (ADC(2)) method. Theoretical results suggest that the TDDFT method with IP‐tuned range‐separated functional should be applied to investigate ESIPT reaction when the zwitterionic or CT states are involved. In addition, the TS geometries for the ESIPT reaction of compound 1 in three different solvents have been successfully located, and the Gibbs free energies along the reaction path have been provided. The calculated results can clearly explain the experimentally observed solvent‐dependent fluorescence of compound 1.
Organocatalyzed Synthesis of Medicinally Important Chromeno[2, 3‐d]pyrimidine‐triones in Biodegradable Reaction Medium
Authors: Rai Pragati , Sagir Hozeyfa , Kumar Akhilesh , B. Yadav Vijay , R. Siddiqui I. 
Published: March 2018

AbstractA convenient and simple approach for the synthesis of medicinally important chromeno[2, 3‐d]pyrimidine‐triones has been disclosed under metal‐free conditions. Glycerol as biodegradable reaction medium in combination with organocatalyst has been used which facilitates the formation of the desired product. Absence of side‐products as well as non‐hazardous reaction conditions are another green attributes of our described protocol. A broad range of substrates were well tolerated in this reaction system.
High‐Potential Metalless Nanocarbon Foam Supercapacitors Operating in Aqueous Electrolyte
Authors: Liu Chueh , Li Changling , Ahmed Kazi , Mutlu Zafer , Lee Ilkeun , Zaera Francisco , Ozkan Cengiz S. , Ozkan Mihrimah 
Published: March 2018

AbstractLight‐weight graphite foam decorated with carbon nanotubes (dia. 20–50 nm) is utilized as an effective electrode without binders, conductive additives, or metallic current collectors for supercapacitors in aqueous electrolyte. Facile nitric acid treatment renders wide operating potentials, high specific capacitances and energy densities, and long lifespan over 10 000 cycles manifested as 164.5 and 111.8 F g−1, 22.85 and 12.58 Wh kg−1, 74.6% and 95.6% capacitance retention for 2 and 1.8 V, respectively. Overcharge protection is demonstrated by repetitive cycling between 2 and 2.5 V for 2000 cycles without catastrophic structural demolition or severe capacity fading. Graphite foam without metallic strut possessing low density (≈0.4–0.45 g cm−3) further reduces the total weight of the electrode. The thorough investigation of the specific capacitances and coulombic efficiencies versus potential windows and current densities provides insights into the selection of operation conditions for future practical devices.
Rapid Detection of Copper in Biological Systems Using Click Chemistry
Authors: Zheng Wenshu , Li Huiling , Chen Wenwen , Zhang Jiangjiang , Wang Nuoxin , Guo Xuefeng , Jiang Xingyu 
Published: March 2018

AbstractA fast (1 min), straightforward but efficient, click chemistry‐based system that enables the rapid detection of free copper (Cu) ions in either biological fluids or living cells without tedious pretreatment is provided. Cu can quickly induce the conjugation between graphene oxide (GO) and a fluorescent dye via click reaction. On the basis of the high specificity of bioorthogonal reaction and the effective quenching ability of GO, the assay studied in this paper can respond to Cu ions in less than 1 min with excellent selectivity and sensitivity, which is the fastest sensor for Cu as far as it is known. In addition, the application of this system is verified by performing assays in living cells and untreated urine samples from patients suffering from Wilson's Disease. Such a Cu detection system shows great promises in both fundamental research and routine clinical diagnostics.
Monitoring the Dynamic Process of Formation of Plasmonic Molecular Junctions during Single Nanoparticle Collisions
Authors: Guo Jing , Pan Jie , Chang Shuai , Wang Xuewen , Kong Na , Yang Wenrong , He Jin 
Published: March 2018

AbstractThe capability to study the dynamic formation of plasmonic molecular junction is of fundamental importance, and it will provide new insights into molecular electronics/plasmonics, single‐entity electrochemistry, and nanooptoelectronics. Here, a facile method to form plasmonic molecular junctions is reported by utilizing single gold nanoparticle (NP) collision events at a highly curved gold nanoelectrode modified with a self‐assembled monolayer. By using time‐resolved electrochemical current measurement and surface‐enhanced Raman scattering spectroscopy, the current changes and the evolution of interfacial chemical bonding are successfully observed in the newly formed molecular tunnel junctions during and after the gold NP “hit‐n‐stay” and “hit‐n‐run” collision events. The results lead to an in‐depth understanding of the single NP motion and the associated molecular level changes during the formation of the plasmonic molecular junctions in a single NP collision event. This method also provides a new platform to study molecular changes at the single molecule level during electron transport in a dynamic molecular tunnel junction.
Immobilization of Nanoparticles on Fibrous Clay Surfaces: Towards Promising Nanoplatforms for Advanced Functional Applications
Authors: Aranda Pilar , Ruiz‐Hitzky Eduardo 
Published: March 2018

AbstractThis account discusses on diverse general approaches employed for the preparation of heterostructured materials based on the immobilization of metal oxides and other nanoparticles on sepiolite and palygorskite fibrous clay minerals, showing the many opportunities of application offered by the resulting materials. Various examples from our own experience have been selected to show how sepiolite acts as a convenient nanoplatform for immobilization of diverse type of nanoparticles, such as TiO2, Fe3O4, Prussian blue, zeolites, layered double hydroxides, carbon nanotubes and graphenes, etc., to produce functional materials for applications in catalysis, environmental remediation, sensing devices, energy production, and others.
Why Patients Decline Genomic Sequencing Studies: Experiences from the CSER Consortium
Authors: Amendola Laura M. , Robinson Jill O. , Hart Ragan , Biswas Sawona , Lee Kaitlyn , Bernhardt Barbara A. , East Kelly , Gilmore Marian J. , Kauffman Tia L. , Lewis Katie L. , Roche Myra , Scollon Sarah , Wynn Julia , Blout Carrie 
Published: March 2018

AbstractClinical and research settings are increasingly incorporating genomic sequencing (GS) technologies. Previous research has explored reasons for declining genetic testing and participation in genetic studies; however, there is a dearth of literature regarding why potential participants decline participation in GS research, and if any of these reasons are unique to GS. This knowledge is essential to promote informed decision‐making and identify potential barriers to research participation and clinical implementation. We aggregated data from seven sites across the National Institutes of Health's Clinical Sequencing Exploratory Research (CSER) consortium on each project's procedures for recruitment, and rates of and reasons for decline. Data were analyzed using descriptive statistics. The decline rate for enrollment at the seven CSER sites ranged from 12 to 64% (median 28%) and varied based on age and disease status. Projects differed in their protocols for approaching potential participants and obtaining informed consent. Reasons for declining GS research were reported for 1088 potential participants. Commonly cited reasons were similar to those reported for clinical single gene testing and non‐GS genetic research. The most frequently cited reason for decline was study logistics (35%); thus, addressing logistical barriers to enrollment may positively impact GS study recruitment. Privacy and discrimination concerns were cited by 13% of decliners, highlighting the need for researchers and providers to focus educational efforts in this area. The potential psychological burden of pursuing and receiving results from GS and not wanting to receive secondary findings, a concern specific to GS, have been cited as concerns in the literature. A minority of potential participants cited psychological impact (8%) or not wanting to receive secondary findings (2%) as reasons for decline, suggesting that these concerns were not major barriers to participation in these GS studies. Further research is necessary to explore the impact, if any, of different participant groups or study protocols on rates of decline for GS studies. Future studies exploring GS implementation should consider using standardized collection methods to examine reasons for decline in larger populations and more diverse healthcare settings.
Disentangling the biological pathways involved in early features of Alzheimer's disease in the Rotterdam Study
Authors: Ahmad Shahzad , Bannister Christian , van der Lee Sven J. , Vojinovic Dina , Adams Hieab H.H. , Ramirez Alfredo , Escott‐Price Valentina , Sims Rebecca , Baker Emily , Williams Julie , Holmans Peter , Vernooij Meike W. , Ikram M. Arfan , Amin Najaf , van Duijn Cornelia M. 
Published: March 2018

AbstractIntroductionExploring the role of Alzheimer's disease (AD) implicated pathways in the predementia phase may provide new insight for preventive and clinical trials targeting disease specific pathways.MethodsWe constructed weighted Genetic risk scores, first based on 20 genome‐wide significant AD risk variants and second clustering these variants within pathways. Risk scores were investigated for their association with AD, mild cognitive impairment, and brain magnetic resonance imaging phenotypes including white matter lesions, hippocampal volume, and brain volume.ResultsThe risk score capturing endocytosis pathway was significantly associated with mild cognitive impairment (P = 1.44 × 10−4). Immune response (P = .016) and clathrin/AP2 adaptor complex pathway (P = 3.55 × 10−3) excluding apolipoprotein E also showed modest association with white matter lesions but did not sustain Bonferroni correction (P = 9.09 × 10−4).DiscussionOur study suggests that the clinical spectrum of early AD pathology is explained by different biological pathways, in particular, the endocytosis, clathrin/AP2 adaptor complex, and immune response pathways, that are independent of apolipoprotein E (APOE).
Reuse Remix Recycle
Authors: Huggett Jeremy 
Published: March 2018

ABSTRACTPreservation of digital data is predicated on the expectation of its reuse, yet that expectation has never been examined within archaeology. While we have extensive digital archives equipped to share data, evidence of reuse seems paradoxically limited. Most archaeological discussions have focused on data management and preservation and on disciplinary practices surrounding archiving and sharing data. This article addresses the reuse side of the data equation through a series of linked questions: What is the evidence for reuse, what constitutes reuse, what are the motivations for reuse, and what makes some data more suitable for reuse than others? It concludes by posing a series of questions aimed at better understanding our digital engagement with archaeological data.