bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arsenate Respiratory Reductase
Authors: Stolz John F , Basu Partha 
Published: June 2020

AbstractThe arsenate respiratory reductase serves as the terminal electron acceptor in dissimilatory arsenate reduction. The enzyme, Arr, is a heterodimer with a large catalytic subunit, ArrA, and a smaller electron transfer subunit, ArrB. It was initially purified fromChrysiogenes arsenatisand subsequently from the FirmicuteBacillus selenitireducens, and genetically characterized fromShewanellasp. strain ANA‐3. The crystal structure of ArrAB has been determined for the enzyme from ANA‐3 as the complex (1.6 Å resolution), bound to arsenate (1.8 Å resolution), bound to arsenite (1.8 Å resolution), and bound to an inhibitor, phosphate (1.7 Å resolution). ArrA has two metal binding domains, the molybdopterin binding domain, which contains a cysteine residue that coordinates to the Mo, and a [4Fe–4S] cluster binding domain. ArrB has four [4Fe–4S] cluster binding domains. The rapid turnover exhibited by Arr fromShewanellasp. ANA‐3 (kcat of 9810 s−1) suggest it is an efficient enzyme limited by diffusion.
Protein Metalation by Inorganic Anticancer Drugs
Authors: Marzo Tiziano , Ferraro Giarita , Merlino Antonello , Messori Luigi 
Published: June 2020

AbstractToday, there is a growing awareness that proteins, beyond nucleic acids, represent primary druggable targets for anticancer metal‐based agents. Indeed, it has been unambiguously ascertained that the coordinative binding of metal‐based drugs to selected proteins (the so‐called protein metalation process) plays a key role in the mechanism of action of a variety of inorganic anticancer agents, for example, some gold‐ and ruthenium‐based drugs. Through an innovative investigation strategy, developed in our laboratories, that is mostly based on the combined use of electrospray ionization mass spectrometry (ESI MS) and X‐ray crystallography on the same metallodrug/protein system, it is now possible to elucidate in depth the metalation process of a variety of proteins; a few instructive examples of metallodrug–protein adducts are herein provided. In turn, metalation may result in protein loss of function and may initiate a cascade of cellular processes eventually leading to cancer cell death. Trends and regularities observed in the protein modification process are highlighted, and their possible biological implications are considered. The perspectives for future work aimed at elucidating the actual molecular mechanisms of innovative metal‐based agents, their interactions with proteins, and the actual patterns of protein metalation are critically discussed in the frame of the emerging omics sciences and technologies.
A collision prediction framework for noncoplanar radiotherapy planning and delivery
Authors: Islam Naveed , Kilian‐Meneghin Josh , deBoer Steven , Podgorsak Matthew 
Published: June 2020

AbstractPurposeNoncoplanar radiotherapy can provide significant dosimetric benefits. However, clinical implementation of such techniques is not fully realized, partially due to the absence of a collision prediction tool integrated into the clinical workflow. In this work, the feasibility of developing a collision prediction system (CPS) suitable for integration into clinical practice has been investigated.MethodsThe CPS is based on a geometric model of the Linear Accelerator (Linac), and patient morphology acquired at the simulator using a combination of the planning CT scan and 3‐D vision camera (Microsoft, Kinect) data. Physical dimensions of Linac components were taken to construct a geometric model. The Linac components include the treatment couch, gantry, and imaging devices. The treatment couch coordinates were determined based on a correspondence among the CT couch top, Linac couch, and the treatment isocenter location. A collision is predicted based on dot products between vectors denoting points in Linac components and patient morphology. Collision test cases were simulated with the CPS and experimentally verified using ArcCheck and Rando phantoms to simulate a patient.ResultsFor 111 collision test cases, the sensitivity and specificity of the CPS model were calculated to be 0.95 and 1.00, respectively. The CPS predicted collision states that left conservative margins, as designed, relative to actual collision locations. The average difference between the predicted and measured collision states was 2.3 cm for lateral couch movements. The predicted couch rotational position for a collision between the gantry and a patient analog differed from actual values on average by 3.8°. The magnitude of these differences is sufficient to account for interfractional patient positioning variations during treatment.ConclusionThe feasibility of developing a CPS using geometric models and standard vector algebra has been investigated. This study outlines a framework for potential clinical implementation of a CPS for noncoplanar radiotherapy.
Actigraphy‐estimated sleep and 24‐hour activity rhythms and the risk of dementia
Authors: Lysen Thom S. , Luik Annemarie I. , Ikram M. Kamran , Tiemeier Henning , Ikram M. Arfan 
Published: June 2020

AbstractIntroductionWe investigated and compared associations of objective estimates of sleep and 24‐hour activity rhythms using actigraphy with risk of dementia.MethodsWe included 1322 non‐demented participants from the prospective, population‐based Rotterdam Study cohort with valid actigraphy data (mean age 66 ± 8 years, 53% women), and followed them for up to 11.2 years to determine incident dementia.ResultsDuring follow‐up, 60 individuals developed dementia, of which 49 had Alzheimer's disease (AD). Poor sleep as indicated by longer sleep latency, wake after sleep onset, and time in bed and lower sleep efficiency, as well as an earlier “lights out” time, were associated with increased risk of dementia, especially AD. We found no associations of 24‐hour activity rhythms with dementia risk.DiscussionPoor sleep, but not 24‐hour activity rhythm disturbance, is associated with increased risk of dementia. Actigraphy‐estimated nighttime wakefulness may be further targeted in etiologic or risk prediction studies.
Untersuchung der Mineral‐Wasser‐Grenzschicht mit nicht‐linearer optischer Spektroskopie
Authors: Backus Ellen H. G. , Schaefer Jan , Bonn Mischa 
Published: June 2020

AbstractDie Wechselwirkung zwischen Mineralen und Wasser ist vielschichtig und komplex. Die Mineraloberfläche kann durch Wasser (de)protoniert werden und hierdurch ihre Ladung ändern. Die Oberflächenladungen werden zusätzlich von den in der wässrigen Phase gelösten Mineralionen abgeschirmt. Beides beeinflusst die Interaktion der Oberfläche mit Wasser. Prozesse und Wechselwirkungen auf molekularer Ebene bestimmen daher an sich makroskopische Phänomene wie flussinduzierte Auflösung, Benetzung und Ladung. Aufgrund dieser Erkenntnis werden Mineral‐Wasser‐Grenzschichten auf molekularer Ebene untersucht. In diesem Zusammenhang prüfen wir hier neue Entwicklungen oberflächenspezifischer nicht‐linearer Spektroskopietechniken wie Summenfrequenzerzeugung und Frequenzverdopplung (SFG/SHG), die Auskunft über die molekulare Anordnung der Wassermoleküle an den ersten Schichten Nahe der Mineraloberfläche geben können. Die Ergebnisse illustrieren die Feinheiten der chemischen und physikalischen Interaktionen zwischen Wasser und dem Mineral sowie die entscheidende Rolle der Mineralauflösung und anderer Ionen in der Lösung bei der Bestimmung dieser Interaktionen.
Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles
Authors: Schäfer Ken , Kolli Hima Bindu , Killingmoe Christensen Mikkel , Bore Sigbjørn Løland , Diezemann Gregor , Gauss Jürgen , Milano Giuseppe , Lund Reidar , Cascella Michele 
Published: June 2020

AbstractThe shape and size of self‐assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long‐range interactions. Combining small‐angle X‐ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry breaking of the irreducible building blocks, with the formation of transient surfactant dimers mediated by the counterions that promote the stabilization of cylindrical instead of spherical micelles. The present model is of general applicability and can be extended to all systems controlled by the presence of mobile charges.
Mechanische Verzahnung von einwandigen Kohlenstoffnanoröhren durch dynamisch‐kovalente Bildung von konkaven Disulfidmakrozyklen
Authors: Balakrishna Bugga , Menon Arjun , Cao Kecheng , Gsänger Sebastian , Beil Sebastian B. , Villalva Julia , Shyshov Oleksandr , Martin Oliver , Hirsch Andreas , Meyer Bernd , Kaiser Ute , Guldi Dirk M. , von Delius Max 
Published: June 2020

AbstractDie Bildung von diskreten Makrozyklen, die sich um einwandige Kohlenstoffnanoröhren (SWCNTs) bilden, hat sich kürzlich als eine vielversprechende Strategie zur Funktionalisierung dieser Kohlenstoffnanomaterialien und der Modifizierung ihrer Eigenschaften herausgestellt. Hier zeigen wir, dass der reversible Disulfidaustausch, der unter milden Bedingungen abläuft, ideal geeignet ist, um relativ große Mengen mechanisch verzahnter Disulfidmakrozyklen auf den eindimensionalen Nanoröhren zu platzieren. Vermutlich als Folge der Fehlerkorrektur und der Anwesenheit von relativ starren, gebogenen π‐Systemen in unseren Schlüsselbausteinen, konnten wir Beweise für die größenselektive Funktionalisierung von SWCNTs mit unterschiedlichem Durchmesser beobachten. Eine Kombination aus UV/vis/NIR, Raman, Photolumineszenz‐Anregung (PLE) und transienten Absorptionsspektroskopien zeigte, dass die kleinen (6,4)‐SWCNTs überwiegend von den kleinen Makrozyklen 12 umschlossen wurden, wohingegen die größeren (6,5)‐SWCNTs ideal für die größeren Makrozyklen 22 schienen. Die Beobachtung der Größenselektivität, die computerchemisch rationalisiert wurde, könnte sich für die Reinigung von Nanoröhrengemischen als nützlich erweisen, da wir in der Lage waren, die Disulfidmakrozyklen quantitativ unter milden Reduktionsbedingungen zu entfernen.
Divergent Synthesis of Monosubstituted and Unsymmetrical 3,6‐Disubstituted Tetrazines from Carboxylic Ester Precursors
Authors: Xie Yixin , Fang Yinzhi , Huang Zhen , Tallon Amanda M. , am Ende Christopher W. , Fox Joseph M. 
Published: June 2020

AbstractSince tetrazines are important tools to the field of bioorthogonal chemistry, there is a need for new approaches to synthesize unsymmetrical and 3‐monosubstituted tetrazines. Described here is a general, one‐pot method for converting (3‐methyloxetan‐3‐yl)methyl carboxylic esters into 3‐thiomethyltetrazines. These versatile intermediates were applied to the synthesis of unsymmetrical tetrazines through Pd‐catalyzed cross‐coupling and in the first catalytic thioether reduction to access monosubstituted tetrazines. This method enables the development of new tetrazine compounds possessing a favorable combination of kinetics, small size, and hydrophilicity. It was applied to a broad range of aliphatic and aromatic ester precursors and to the synthesis of heterocycles including BODIPY fluorophores and biotin. In addition, a series of tetrazine probes for monoacylglycerol lipase (MAGL) were synthesized and the most reactive one was applied to the labeling of endogenous MAGL in live cells.
Two Pyrophosphates with Large Birefringences and Second‐Harmonic Responses as Ultraviolet Nonlinear Optical Materials
Authors: Lu Xuefang , Chen Zhaohui , Shi Xuerui , Jing Qun , Lee Ming‐Hsien 
Published: June 2020

AbstractTwo new pyrophosphates nonlinear optical (NLO) materials, Rb3PbBi(P2O7)2 (I) and Cs3PbBi(P2O7)2 (II), were successfully designed and synthesized. Both compounds exhibit large NLO effects and birefringences. Material I presents the scarce case of possessing the coexistence of large birefringence (0.031 at 1064 nm and 0.037 at 532 nm) and second harmonic generation (SHG) response (2.8× potassium dihydrogen phosphate (KDP)) in ultraviolet NLO phosphates and its SHG is the largest in the phase‐matching (PM) pyrophosphates. Both I and II have three‐dimensional (3D) crystal structures composed of corner‐shared RbO12 (CsO11), RbO10 (CsO10), BiO6, PbO7 (PbO6) and P2O7 groups, in which P2O7 and PbO7 (PbO6) units form an alveolate [PbPO]∞ skeleton frame. Theoretical calculations reveal that the P−O, Bi−O and Pb−O units are mainly responsible for the moderate birefringence and large SHG efficiency of I.
An Atomic View of Cation Diffusion Pathways from Single‐Crystal Topochemical Transformations
Authors: Handy Joseph V. , Luo Yuting , Andrews Justin L. , Bhuvanesh Nattamai , Banerjee Sarbajit 
Published: June 2020

AbstractThe diffusion pathways of Li‐ions as they traverse cathode structures in the course of insertion reactions underpin many questions fundamental to the functionality of Li‐ion batteries. Much current knowledge derives from computational models or the imaging of lithiation behavior at larger length scales; however, it remains difficult to experimentally image Li‐ion diffusion at the atomistic level. Here, by using topochemical Li‐ion insertion and extraction to induce single‐crystal‐to‐single‐crystal transformations in a tunnel‐structured V2O5 polymorph, coupled with operando powder X‐ray diffraction, we leverage single‐crystal X‐ray diffraction to identify the sequence of lattice interstitial sites preferred by Li‐ions to high depths of discharge, and use electron density maps to create a snapshot of ion diffusion in a metastable phase. Our methods enable the atomistic imaging of Li‐ions in this cathode material in kinetic states and provide an experimentally validated angstrom‐level 3D picture of atomic pathways thus far only conjectured through DFT calculations.
Variability in the number of infraorbital foramina in rhesus macaques (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis)
Authors: Marchewka Justyna , Mrożek Kamil , Leszczyński Bartosz , Wróbel Andrzej , Głąb Henryk 
Published: June 2020

AbstractThis study aimed to determine the number of infraorbital foramina in monkeys of the Papionini tribe. The authors performed a μCT analysis of the morphology of the infraorbital foramina. A total number of 52 simian skulls belonged to two macaque species: Macaca mulatta and Macaca fascicularis were used in the study. The number of infraorbital foramina was counted macroscopically and with the use of a magnifying glass. Next, the skull representing the most common morphological type was selected and scanned by micro‐computed tomography (μCT). The Shapiro–Wilk normality test was used in the study. To compare the differences in the number of infraorbital foramen between species, sex and sides, the Mann–Whitney U test was applied. Three infraorbital foramina were present in most individuals from the test group. The Mann–Whitney test revealed no statistically significant difference between the number of foramina on the right‐ and left‐hand side. Likewise, no statistically significant differences between the numbers of infraorbital foramina across sexes were observed. Volumetric reconstructions revealed the presence of separate infraorbital canals for each infraorbital foramen. Craniofacial innervation in macaques is formed by complex branching patterns of cranial nerves. Variability in the number of infraorbital foramina suggests a variable maxillary innervation pattern in these animals. Based on the analysis of volumetric projections, the presence of two labial branches and a single nasal branch of the infraorbital nerve is suggested. Detailed descriptions are supported by quantitative data and μCT evidence.
Nickel Alloying Significantly Enhances the Power Density of Ruthenium‐Based Supercapacitors
Authors: Morag Ahiud , Shauloff Nitzan , Maman Nitzan , Froumin Natalya , Ezersky Vladimir , Jelinek Raz 
Published: June 2020

AbstractSupercapacitors operating at high frequencies while exhibiting high capacitance have been challenging to fabricate due to high resistance and constrained ion diffusion in the active layers. To overcome these limitations, thin layers of pseudocapacitive materials with high theoretical capacitance can be used. Still, construction of such electrodes exhibiting effective ion diffusion, sufficient electrochemically‐active surface area, and high conductivity has encountered significant difficulties. Here, we integrated nickel atoms into a ruthenium layer through a simple electrochemical deposition method, producing a thin electrode comprising hexagonal nickel ruthenium (NiRu) nanodendrites. Further oxidation of the NiRu alloy generated a thin surface layer of pseudocapacitive RuO2 exhibiting significant areal capacitance. A symmetric device from two NiRu/RuO2 electrodes displayed an energy density of 0.714 μWh cm−2 with a remarkable power density of 1500 mW cm−2, ∼250 W cm−3 for a full device. The NiRu/RuO2 supercapacitor outperforms commercial capacitors in both energy and power densities and may replace bulky capacitors in microelectronic devices.
Spy chemistry‐enabled protein directional immobilization and protein purification
Authors: Lin Zhanglin , Lin Qiao , Li Jiahui , Pistolozzi Marco , Zhao Lei , Yang Xiaofeng , Ye Yanrui 
Published: June 2020

AbstractSite‐directed protein immobilization allows the homogeneous orientation of proteins with high retention of activity, which is advantageous for many applications. Here, we report a facile, specific, and efficient strategy based on the SpyTag‐SpyCatcher chemistry. Two SpyTag‐fused model proteins, that is, the monomeric red fluorescent protein (RFP) and the oligomeric glutaryl‐7‐aminocephalosporanic acid acylase, were easily immobilized onto a SpyCatcher‐modified resin directly from cell lysates, with activity recoveries in the range of 85–91%. This strategy was further adapted to protein purification, which proceeded through the selective capture of the SpyCatcher‐fused target proteins by a SpyTag‐modified resin, with the aid of an intein to generate authentic N‐termini. For two model proteins, that is, RFP and a variable domain of a heavy chain antibody, the yields were ∼3–7 mg/L culture with >90% purities. This approach could provide a versatile tool for producing high‐performance immobilized protein devices and proteins for industrial and therapeutic uses.
CLIK: Cloud‐based Linux kernel practice environment and judgment system
Authors: Park Hyunchan , Kim Youngpil 
Published: June 2020

AbstractAssignments on kernel programming are essential parts of operating system (OS) courses taught to computer science students to provide them a deep understanding of real‐world OSs. However, these assignments require tremendous effort from both students and instructors. Students are routinely flustered by the daunting task of building a practice environment from scratch; instructors are pressurized for time while validating a student's work that requires several kernel installations and reboots. To minimize this effort, we propose CLIK, a cloud‐based Linux kernel practice environment supporting automatic judgment. It provides students with an individual and easy‐to‐use kernel practice environment and instructors with a fast and easy evaluation of students' work with live feedback. Our experiences with two assignments from a real‐world OS course carried out on CLIK show that CLIK can successfully provide Linux kernel environments for 40 students and help instructors greatly by validating their kernels within one minute using parallel and automated judgments. We also describe detailed lessons learned from developing CLIK that will help both researchers and instructors building similar systems.
Extracts and Steroids from the Edible Mushroom Hypholoma lateritium Exhibit Anti‐Inflammatory Properties by Inhibition of COX‐2 and Activation of Nrf2
Authors: Ványolós Attila , Muszyńska Bożena , Chuluunbaatar Bayar , Gdula‐Argasińska Joanna , Kała Katarzyna , Hohmann Judit 
Published: June 2020

AbstractHypholoma lateritium is an edible macrofungus with a common distribution in Europe, North America, and the Far East. The aim of this study was to investigate the potential anti‐inflammatory effects of H. lateritium extracts and its isolated steroids: fasciculic acid B, fasciculol E, fasciculol C, lanosta‐7,9(11)‐diene‐12β,21α‐epoxy‐2α,3β,24β,25‐tetraol, fasciculol F, and demethylincisterol A2. Organic (hexane, chloroform and 50 % methanol) and water extracts of H. lateritium were subjected to in vitro assays to determine pro‐inflammatory protein levels, such as cyclooxygenase‐2 (COX‐2), cytosolic prostaglandin E2 synthase (cPGES), and antioxidant nuclear factor (erythroid‐derived 2)‐like 2 (Nrf2). Fungal extracts demonstrated significant activities on pro‐inflammatory protein levels with minor differences among the activities of the fractions of different polarities. All the compounds proved to exert notable inhibitory properties on COX‐2 and were capable to stimulate the Nrf2 pathway. Fungal extracts and the compounds exerted no cytotoxic activities on RAW 264.7 cells.
Delivery of BR2‐SOX17 fusion protein can inhibit cell survival, proliferation, and invasion in gastric cancer cells through regulating Klotho gene expression
Authors: Yang Lixia , Wu Yue , He Heli , Hu Fan , Li Mei , Mo Li , Xiao You , Wang Xiaoyan , Xie Biao 
Published: June 2020

AbstractThe prognosis of advanced gastric cancer is poor and understanding the biology and subsequent development of new targeting therapy is still an urgent need. This study was conducted to explore the effect of BR2 (a 17‐amino acid peptide)‐SOX17 (human sex determining region Y (SRY)‐related high‐mobility group (HMG) box protein family member 17) fusion protein on Klotho gene expression in gastric cancer cells. The regulatory effects of SOX17 on Klotho gene in gastric cancer cells were tested using dual‐luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay. The therapeutic effects of BR2‐SOX17 were evaluated by proliferation, colony formation, invasion assay, and cell apoptosis analysis. Results showed that SOX17 enhanced Klotho gene expression in gastric adenocarcinoma cells through binding to the promoter of Klotho gene. BR2‐SOX17 fusion protein was effective in delivering SOX17 into gastric cancer cells and subsequently inhibited the cell proliferation, colony formation, and invasion, increased E‐cadherin protein expression, decreased vimentin protein expression, as well as induced apoptosis. Our findings suggested SOX17 can bind to the promoter of Klotho gene to enhance Klotho gene expression in gastric cancer cells. The fused BR2‐SOX17 protein is an effective agent for targeting therapy of gastric cancer.