bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast and accurate view classification of echocardiograms using deep learning
Authors: Madani Ali , Arnaout Ramy , Mofrad Mohammad , Arnaout Rima
Published: January 2018

Echocardiography is essential to cardiology. However, the need for human interpretation has limited echocardiography’s full potential for precision medicine. Deep learning is an emerging tool for analyzing images but has not yet been widely applied to echocardiograms, partly due to their complex multi-view format. The essential first step toward comprehensive computer-assisted echocardiographic interpretation is determining whether computers can learn to recognize these views. We trained a convolutional neural network to simultaneously classify 15 standard views (12 video, 3 still), based on labeled still images and videos from 267 transthoracic echocardiograms that captured a range of real-world clinical variation. Our model classified among 12 video views with 97.8% overall test accuracy without overfitting. Even on single low-resolution images, accuracy among 15 views was 91.7% vs. 70.2–84.0% for board-certified echocardiographers. Data visualization experiments showed that the model recognizes similarities among related views and classifies using clinically relevant image features. Our results provide a foundation for artificial intelligence-assisted echocardiographic interpretation.
Inhibitor-assisted synthesis of molecularly imprinted microbeads for protein recognition
Authors: Basan Hasan , Dinc Mehmet , Mizaikoff Boris
Published: January 2018

Synergistic effect of inhibitor assisted affinity and surface molecular imprinting strategy on pepsin imprinting.
A near-infrared fluorescent probe for sensitive detection and imaging of sulfane sulfur in living cells and in vivo
Authors: Han Xiaoyue , Song Xinyu , Li Bowei , Yu Fabiao , Chen Lingxin
Published: January 2018

A near-infrared fluorescent probe was fabricated for the sensitive detection and imaging of sulfane sulfur in living cells and in vivo.
Chiral triazolylidene-Pd-PEPPSI: synthesis, characterization, and application in asymmetric Suzuki–Miyaura cross-coupling
Authors: Haraguchi Ryosuke , Hoshino Shun , Yamazaki Tatsuro , Fukuzawa Shin-ichi
Published: January 2018

A novel triazolylidene-Pd-PEPPSI with ferrocene-based planar chirality has been synthesized, characterized, and applied to the asymmetric Suzuki–Miyaura cross-coupling.
The influence of like-charge attraction on the structure and dynamics of ionic liquids: NMR chemical shifts, quadrupole coupling constants, rotational correlation times and failure of Stokes–Einstein–Debye
Authors: Strate Anne , Overbeck Viviane , Lehde Viktoria , Neumann Jan , Bonsa Anne-Marie , Niemann Thomas , Paschek Dietmar , Michalik Dirk , Ludwig Ralf
Published: January 2018

The formation of clusters of like-charge influences the structure and dynamics of ionic liquids.
Estimating the mean first passage time of protein misfolding
Authors: Singh Vishal , Biswas Parbati
Published: January 2018

MFPT of the misfolded protein is directly correlated to the age of onset and appearance of misfolding diseases in humans.
Collisions of noble gas atoms with graphene and a graphene nanodome
Authors: Zhang Xin , Cao Shiwei , Li Zhan , Zhang Ning , Chen Ximeng
Published: January 2018

The graphene nanodome exhibits some novel mechanical properties and it is probably an excellent shield.
Novel two-dimensional ferromagnetic semiconductors: Ga-based transition-metal trichalcogenide monolayers
Authors: Yu Maolin , Liu Xiaofei , Guo Wanlin
Published: January 2018

Ga-based two-dimensional transition-metal trichalcogenides with tunable ferromagnetic semiconducting properties are explored by first-principles calculations.
A theoretical study of the confinement effects on the energetics and vibrational properties of 4,4′-bipyridine adsorption on H-ZSM-5 zeolite
Authors: Castellà-Ventura M. , Moissette A. , Kassab E.
Published: January 2018

Confinement effects of H-ZSM-5 on the adsorption of bidentate 4,4′-bipyridine, wherein each ring is surrounded by a different zeolite environment.
Intelligent environmental nanomaterials
Authors: Chang Jian , Zhang Lianbin , Wang Peng
Published: January 2018

We offer a comprehensive overview for the design concepts and latest progresses on the intelligent environmental nanomaterials.
Renewable atom-efficient polyesters and thermosetting resins derived from high oleic soybean oil
Authors: Xu Shichao , Lamm Meghan E. , Rahman Md Anisur , Zhang Xinzhou , Zhu Tianyu , Zhao Zhendong , Tang Chuanbing
Published: January 2018

We report an atom-efficient approach to the preparation of sustainable polyesters and their corresponding thermosetting resins (RESINs) from renewable plant oils.
Pneumatically actuated cell-stretching array platform for engineering cell patterns in vitro
Authors: Kamble Harshad , Vadivelu Raja , Barton Matthew , Shiddiky Muhammad J. A. , Nguyen Nam-Trung
Published: January 2018

We report a pneumatically actuated cell-stretching well array to engineer cell patterns in vitro.
Solar-driven photothermal nanostructured materials designs and prerequisites for evaporation and catalysis applications
Authors: Zhu Liangliang , Gao Minmin , Peh Connor Kang Nuo , Ho Ghim Wei
Published: January 2018

Solar-driven photothermal conversion by nanostructured materials is a direct solar energy conversion process that has been used as a novel strategy to augment vaporization and catalysis performance.
Single crystal diamond membranes for nanoelectronics
Authors: Bray Kerem , Kato Hiromitsu , Previdi Rodolfo , Sandstrom Russell , Ganesan Kumaravelu , Ogura Masahiko , Makino Toshiharu , Yamasaki Satoshi , Magyar Andrew P. , Toth Milos , Aharonovich Igor
Published: January 2018

Single crystal, nanoscale diamond membranes are highly sought after for a variety of applications including nanophotonics, nanoelectronics and quantum information science.
Hierarchically ZnIn2S4 nanosheet-constructed microwire arrays: template-free synthesis and excellent photocatalytic performances
Authors: Tu Xinglong , Lu Jing , Li Ming , Su Yanjie , Yin Guilin , He Dannong
Published: January 2018

ZnIn2S4 NCMAs are successfully synthesized on a zinc substrate without any template or surfactant for the first time.
Palladium-polymer nanoreactors for the aqueous asymmetric synthesis of therapeutic flavonoids
Authors: Lestini E. , Blackman L. D. , Zammit C. M. , Chen T. , Williams R. J. , Inam M. , Couturaud B. , O'Reilly R. K.
Published: January 2018

Polymeric core–shell micelles incorporating a chiral palladium pyridinooxazoline catalyst are presented as nanoreactors for the aqueous asymmetric synthesis of flavanones, a class of flavonoids, with therapeutic properties.
Cp2TiCl2-catalyzed highly regioselective hydroamination of styrenes with hydroxylamines
Authors: Luo Xuewei , Wang Sheng , Xi Chanjuan
Published: January 2018

An efficient Cp2TiCl2-catalyzed one-pot two-step hydroamination procedure that allows the direct formation of tertiary amines from styrenes and an electrophilic nitrogen source has been reported with high regioselectivity.
Cotton-like micro- and nanoscale poly(lactic acid) nonwoven fibers fabricated by centrifugal melt-spinning for tissue engineering
Authors: Zhou Hongli , Tang Yufeng , Wang Zongliang , Zhang Peibiao , Zhu Qingsan
Published: January 2018

Schematic of the centrifugal melt spinning apparatus, consisting of (a) a rotary disk, (b) heating circuit, (c) electromotor, (d) filling inlet and (e) rotary collector on a drum.
Metabonomic strategy for the detection of metabolic effects of probiotics combined with prebiotic supplementation in weaned rats
Authors: Wang Mengxia , Zhang Xiaojun , Wang Yuanyuan , Li Yuan , Chen Yongxiong , Zheng Haihui , Ma Fangli , Ma Chung Wah , Lu Biyu , Xie Zhiyong , Liao Qiongfeng
Published: January 2018

Dietary probiotic supplementation is beneficial to the growth of weaned rats by regulating the metabolism.
Development of immunoassays for detecting oxyfluorfen residue in agricultural and environmental samples
Authors: Sheng Enze , Du Mei , Yang Jiachuan , Hua Xiude , Wang Minghua
Published: January 2018

An enzyme-linked immunosorbent assay (ELISA) and chemiluminescent immunoassays (CLEIA) were developed to detect oxyfluorfen in agricultural and environmental samples.
Sensitive determination of trace Cd(ii) and Pb(ii) in soil by an improved stripping voltammetry method using two differentin situplated bismuth-film electrodes based on a novel electrochemical measurement system
Authors: Zhao Guo , Wang Hui , Liu Gang
Published: January 2018

A double-stripping voltammetry method was designed and developed to improve the sensitivity and anti-interference ability for detection of heavy metals.
Synthesis and application of pillared clay heterogeneous catalysts for wastewater treatment: a review
Authors: Baloyi Jeffrey , Ntho Thabang , Moma John
Published: January 2018

The use of pillared interlayered clays (PILCs) as heterogenous catalysts in wastewater treatment technologies, particularly advanced oxidation processes (AOPs), is gaining popularity for the treatment of refractory wastewater effluents.
Ahmpatinin iBu, a new HIV-1 protease inhibitor, from Streptomyces sp. CPCC 202950
Authors: Chen Ming-Hua , Chang Shan-Shan , Dong Biao , Yu Li-Yan , Wu Ye-Xiang , Wang Ren-Zhong , Jiang Wei , Gao Zeng-Ping , Si Shu-Yi
Published: January 2018

Ahmpatinin iBu and statinin iBu, two new linear peptides, were isolated from Streptomyces sp. CPCC 202950. Ahmpatinin iBu exhibited significant inhibitory activity against HIV-1 protease with an IC50 value of 1.79 nM.
Evolution of entrained water film thickness and dynamics of Marangoni flow in Marangoni drying
Authors: Li Changkun , Zhao Dewen , Wen Jialin , Cheng Jie , Lu Xinchun
Published: January 2018

The receding contact line driven by Marangoni flow induces an immersed pressure gradient, and thus a sudden increase of tangential velocity in dynamic meniscus.
Influence of iron precursor hydration state on performance of non-precious metal fuel cell catalysts
Authors: Janson C. , Dombrovskis J. K. , Palmqvist A. E. C.
Published: January 2018

Performance of Fe-OMC fuel cell catalysts depends on type of iron–nitrogen complex formed using different iron chloride precursor hydration states.
A highly polarization sensitive antimonene photodetector with a broadband photoresponse and strong anisotropy
Authors: Chu Feihong , Chen Mingyan , Wang Yin , Xie Yiqun , Liu Beiyun , Yang Yanhan , An Xingtao , Zhang Yongzhe
Published: January 2018

Photodetectors based on two-dimensional materials have shown impressive performance including fast and broadband photoresponse and high responsivity.
K2NaAlF6:Mn4+red phosphor: room-temperature synthesis and electronic/vibronic structures
Authors: Yi Xiaodong , Li Renfu , Zhu Haomiao , Gao Jun , You Wenwu , Gong Zhongliang , Guo Wang , Chen Xueyuan
Published: January 2018

K2NaAlF6:Mn4+red phosphor was synthesizedviathe co-precipitation approach at room-temperature and its fine electronic/vibronic structures were revealed.
Goodbye to S2−in aqueous solution
Authors: May P. M. , Batka D. , Hefter G. , Königsberger E. , Rowland D.
Published: January 2018

S2−(aq) is a widespread but deleterious artefact which needs to be eliminated by the chemical community.
Decarbonylative thioetherification by nickel catalysis using air- and moisture-stable nickel precatalysts
Authors: Liu Chengwei , Szostak Michal
Published: January 2018

A general, highly selective method for decarbonylative thioetherification of aryl thioesters by C–S cleavage using inexpensive, air- and moisture-stable nickel precatalyst is reported.
Syntheses and evaluation of new acridone derivatives for selective binding of oncogene c-myc promoter i-motifs in gene transcriptional regulation
Authors: Shu Bing , Cao Jiaojiao , Kuang Guotao , Qiu Jun , Zhang Meiling , Zhang Yan , Wang Mingxue , Li Xiaoya , Kang Shuangshuang , Ou Tian-Miao , Tan Jia-Heng , Huang Zhi-Shu , Li Ding
Published: January 2018

We synthesized a series of acridone derivatives for specific binding ligands of i-motifs.
Correction: Cationic phthalocyanine dendrimers as potential antimicrobial photosensitisers
Authors: Ruiz-González Rubén , Setaro Francesca , Gulías Òscar , Agut Montserrat , Hahn Uwe , Torres Tomás , Nonell Santi
Published: January 2018

Correction for ‘Cationic phthalocyanine dendrimers as potential antimicrobial photosensitisers’ by Rubén Ruiz-González et al., Org. Biomol. Chem., 2017, 15, 9008–9017.
Scalable synthesis of wrinkled mesoporous titania microspheres with uniform large micron sizes for efficient removal of Cr(vi)
Authors: Yu Zhikai , Gao Xingmin , Yao Yan , Zhang Xiangcheng , Bian Guo-Qing , Wu Winston Duo , Chen Xiao Dong , Li Wei , Selomulya Cordelia , Wu Zhangxiong , Zhao Dongyuan
Published: January 2018

Scalable synthesis of wrinkled mesoporous TiO2 microspheres with uniform large micron sizes is achieved. They show excellent performance for removal of Cr(vi).
Two novel rhodamine-based molecules with different mechanochromic and photochromic properties in solid state
Authors: Ma Zhiyong , Ji Yajian , Lan Youshi , Kuang Gui-Chao , Jia Xinru
Published: January 2018

Two novel molecules (AnRhB-1 and AnRhB-2) were synthesized using Rhodamine B and anthracene as building units via Schiff base chemistry with different spacers.
The co-existence of hot and cold gas in debris discs
Authors: Rebollido I. , Eiroa C. , Montesinos B. , Maldonado J. , Villaver E. , Absil O. , Bayo A. , Canovas H. , Carmona A. , Chen Ch. , Ertel S. , Garufi A. , Henning Th. , Iglesias D. P. , Launhardt R. , Liseau R. , Meeus G. , Moór A. , Mora A. , Olofsson J. , Rauw G. , Riviere-Marichalar P.
Published: January 2018

Context. Debris discs have often been described as gas-poor discs as the gas-to-dust ratio is expected to be considerably lower than in primordial, protoplanetary discs. However, recent observations have confirmed the presence of a non-negligible amount of cold gas in the circumstellar (CS) debris discs around young main-sequence stars. This cold gas has been suggested to be related to the outgassing of planetesimals and cometary-like objects. Aims. The goal of this paper is to investigate the presence of hot gas in the immediate surroundings of the cold-gas-bearing debris-disc central stars.

Methods. High-resolution optical spectra of all currently known cold-gas-bearing debris-disc systems, with the exception of β Pic and Fomalhaut, have been obtained from La Palma (Spain), La Silla (Chile), and La Luz (Mexico) observatories. To verify the presence of hot gas around the sample of stars, we have analysed the Ca II H&K and the Na I D lines searching for non-photospheric absorptions of CS origin, usually attributed to cometary-like activity.

Results. Narrow, stable Ca II and/or Na I absorption features have been detected superimposed to the photospheric lines in 10 out of the 15 observed cold-gas-bearing debris-disc stars. Features are found at the radial velocity of the stars, or slightly blue- or red-shifted, and/or at the velocity of the local interstellar medium (ISM). Some stars also present transient variable events or absorptions extended towards red wavelengths (red wings). These are the first detections of such Ca II features in 7 out of the 15 observed stars. Although an ISM origin cannot categorically be excluded, the results suggest that the stable and variable absorptions arise from relatively hot gas located in the CS close-in environment of the stars. This hot gas is detected in at least ~80%, of edge-on cold-gas-bearing debris discs, while in only ~10% of the discs seen close to face-on. We interpret this result as a geometrical effect, and suggest that the non-detection of hot gas absorptions in some face-on systems is due to the disc inclination and likely not to the absence of the hot-gas component. This gas is likely released in physical processes related in some way to the evaporation of exocomets, evaporation of dust grains, or grain-grain collisions close to the central star.
On the consistency of Sobol indices with respect to stochastic ordering of model parameters
Authors: Cousin A. , Janon A. , Maume-Deschamps V. , Niang I.
Published: January 2018

In the past decade, Sobol’s variance decomposition has been used as a tool to assess how the output of a model is affected by the uncertainty on its input parameters. We show some links between global sensitivity analysis and stochastic ordering theory. More specifically, we study the influence of inputs’ distributions on Sobol indices in relation with stochastic orders. This gives an argument in favor of using Sobol’s indices in uncertainty quantification, as one indicator among others.
Aldol Condensations on a 3-Alkylidene-2,5-diketopiperazine: Synthesis of Two Marine Natural Products
Authors: Fairhurst Magnus , Zeeshan Muhammad , Haug Bengt , Bayer Annette
Published: January 2018

The synthesis of two marine natural products containing a 3-alkylidene-6-arylidene-2,5-diketopiperazine scaffold by employing two consecutive aldol condensations starting with 1,4-diacetyl-2,5-diketopiperazine is reported. The target compounds contain a phenol or an imidazole group as aryl substituents, respectively, and suitable conditions for the aldol condensation of 1-acyl-3-alkylidene-2,5-diketopiperazine with the required functionalised aromatic aldehydes were developed. Provided the optimal base was used, introduction of the phenol group did not require use of a protecting group. Boc-protection was beneficial for introduction of the imidazole group, and conditions for carrying out the aldol condensation and Boc-deprotection in one step were identified. The stereochemistry of the target compounds was confirmed by NMR analysis.
Scapholunate Ligament Internal Brace 360-Degree Tenodesis (SLITT) Procedure
Authors: Greene Ryan , Kakar Sanjeev
Published: January 2018

Background Scapholunate (SL) joint instability is one of the most common injuries of the wrist and may result from a fall or high-energy mechanism on the outstretched hand. The purpose of this case report is to describe the outcome of a 360-degree tenodesis to the SL joint with an internal brace (SLITT) for the treatment of SL instability.

Case Description A 42-year-old male patient underwent SL ligament reconstruction with the SLITT procedure 12 months after injury. Given the intrinsic stability of the reconstruction, Kirschner (K) wires were not used and an early range of motion protocol was initiated. Thirteen months after his reconstruction, he was back at work with maintenance of his carpal alignment.

Discussion Since its initial description, a myriad of different surgical techniques for SL instability have been devised with varied success. These include capsular shrinkage, dorsal capsulodesis, reduction-association with a screw of the scapholunate joint (RASL), scapholunate axis method (SLAM), bone ligament bone grafts, and a variety of tendon reconstructions. Possible explanations for this varied outcome may be related to the use of soft tissue reconstructions for irreducible injuries and reconstruction of only the dorsal SL ligament. In addition, many of these techniques involve prolonged immobilization with the use of K-wires.

Clinical Relevance The SLITT procedure reconstructs both the volar and dorsal SL ligament. Given the added stability afforded by intrinsic bracing, we feel that this reconstruction may permit earlier range of motion without the need for K-wire stabilization.
Osteochondral Injuries of the Knee in Pediatric Patients
Authors: Bauer Kathryn
Published: January 2018

Osteochondral injuries in pediatric patients may occur as a result of a traumatic injury or secondary to an osteochondritis dissecans (OCD) lesion. Lateral patella dislocation is a common traumatic cause of osteochondral injury that typically occurs at the medial facet of the patella or at the lateral aspect of the distal femur. Multiple theories have been proposed for the cause of an OCD lesion in the knee, including trauma or repetitive microtrauma, local vascular insufficiency, and family history. The most “classic” location for OCD lesions of the knee is the lateral aspect of the medial femoral condyle of the distal femur. Multiple treatment options are available for both traumatic osteochondral injuries and OCD lesions, with important determining factors of treatment being skeletal maturity of the patient, instability of the fragment, lesion location, and size of the lesion. Nonsurgical management is appropriate in some situations. Surgical options range from simple fragment excision to internal fixation of the fracture fragment to more complex cartilage restoration or replacement procedures. This special focus section will discuss the diagnosis and treatment options for traumatic osteochondral knee injuries, including the subset secondary to juvenile OCD lesions.
Clinical Use of the Amplatzer Device in the Management of Intracardiac Defects: A Single-Center Experience
Authors: Rao Seema , Scaff Tyler , Gurley John , Saha Sibu
Published: January 2018

Device therapy is a viable alternative to open heart surgery in the management of intracardiac defects. The Amplatzer septal occluder (ASO) is one such device that has been adapted to close a wide variety of cardiac defects with few complications and a high success rate. This is a retrospective review of all the patients who received the ASO between 2012 and 2016 at the University of Kentucky. In total, 169 patients underwent percutaneous closure of a septal defect with Amplatzer during the timeframe studied, and of those, 91% received the device for an atrial septal defect or patent foramen ovale. Patients presented with stroke, transient ischemic attack, migraine, dyspnea or other symptoms and were diagnosed by transesophageal echocardiography and cardiac catheterization. All Amplatzer devices achieved successful closure without requiring a second procedure. Four patients sustained complications of the procedure, with two experiencing tamponade, one with hematoma, and one with cellulitis. The Amplatzer device was not directly implicated in the three fatalities that occurred within 30 days of the septal occlusion procedure. The ASO has performed very well at our institution and we expect it to serve additional functions as the field of transcatheter cardiology develops.
Sprachlokalisation mittels MEG und EEG in der prächirurgischen Epilepsiediagnostik
Authors: Pataraia Ekaterina , Trimmel Karin
Published: January 2018

Ziel der Epilepsiechirurgie ist die Entfernung des epileptogenen Gewebes, dabei darf kein neurologisches oder neuropsychologisches Defizit verursacht werden. Aus diesem Grund ist die möglichst genaue Abgrenzung des sprachspezifischen Kortex von großer Bedeutung. In der folgenden narrativen Übersicht werden die methodischen Grundlagen und klinischen Anwendungen der Magnetoenzephalografie (MEG) und der hochauflösenden Skalp-Elektroenzephalografie (EEG) diskutiert. Es wird eine kurze Übersicht zu diversen Verfahren gegeben, die zur Lateralisation und Lokalisation der Sprachfunktionen in der MEG und bei Quellenanalysemethoden in der EEG benützt werden. Darüber hinaus werden die Möglichkeiten und Grenzen beider Methoden zur Erfassung der Organisation und Reorganisation der Sprachfunktionen des Kortex bei Epilepsieerkrankten besprochen.
Cylindrical and spherical Akhmediev breather and freak waves in ultracold neutral plasmas
Authors: El-Tantawy S. A. , El-Awady E. I.
Published: January 2018

The properties of cylindrical and spherical ion-acoustic breathers Akhmediev breather and freak waves in strongly coupled ultracold neutral plasmas (UNPs), whose constituents are inertial strongly coupled ions and weakly coupled Maxwellian electrons, are investigated numerically. Using the derivative expansion method, the basic set of fluid equations is reduced to a nonplanar (cylindrical and spherical)/modified nonlinear Schrödinger equation (mNLSE). The analytical solutions of the mNLSE were not possible until now, so their numerical solutions are obtained using the finite difference scheme with the help of the Dirichlet boundary conditions. Moreover, the criteria for the existence and propagation of breathers are discussed in detail. The geometrical effects due to the cylindrical and spherical geometries on the breather profile are studied numerically. It is found that the propagation of the ion-acoustic breathers in one-dimensional planar and nonplanar geometries is very different. Finally, our results may help to manipulate matter breathers experimentally in UNPs.
Dynamical heterogeneities of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations
Authors: Usui Kota , Hunger Johannes , Bonn Mischa , Sulpizi Marialore
Published: January 2018

Room temperature ionic liquids (RTILs) have been shown to exhibit spatial heterogeneity or structural heterogeneity in the sense that they form hydrophobic and ionic domains. Yet studies of the relationship between this structural heterogeneity and the ∼picosecond motion of the molecular constituents remain limited. In order to obtain insight into the time scales relevant to this structural heterogeneity, we perform molecular dynamics simulations of a series of RTILs. To investigate the relationship between the structures, i.e., the presence of hydrophobic and ionic domains, and the dynamics, we gradually increase the size of the hydrophobic part of the cation from ethylammonium nitrate (EAN), via propylammonium nitrate (PAN), to butylammonium nitrate (BAN). The two ends of the organic cation, namely, the charged Nhead–H group and the hydrophobic Ctail–H group, exhibit rotational dynamics on different time scales, evidencing dynamical heterogeneity. The dynamics of the Nhead–H group is slower because of the strong coulombic interaction with the nitrate counter-ionic anions, while the dynamics of the Ctail–H group is faster because of the weaker van der Waals interaction with the surrounding atoms. In particular, the rotation of the Nhead–H group slows down with increasing cationic chain length, while the rotation of the Ctail–H group shows little dependence on the cationic chain length, manifesting that the dynamical heterogeneity is enhanced with a longer cationic chain. The slowdown of the Nhead–H group with increasing cationic chain length is associated with a lower number of nitrate anions near the Nhead–H group, which presumably results in the increase of the energy barrier for the rotation. The sensitivity of the Nhead–H rotation to the number of surrounding nitrate anions, in conjunction with the varying number of nitrate anions, gives rise to a broad distribution of Nhead–H reorientation times. Our results suggest that the asymmetry of the cations and the larger excluded volume for longer cationic chain are important for both the structural heterogeneity and the dynamical heterogeneities. The observed dynamical heterogeneities may affect the rates of chemical reactions depending on where the reactants are solvated in ionic liquids and provide an additional guideline for the design of RTILs as solvents.
Rapid sampling of stochastic displacements in Brownian dynamics simulations with stresslet constraints
Authors: Fiore Andrew M. , Swan James W.
Published: January 2018

Brownian Dynamics simulations are an important tool for modeling the dynamics of soft matter. However, accurate and rapid computations of the hydrodynamic interactions between suspended, microscopic components in a soft material are a significant computational challenge. Here, we present a new method for Brownian dynamics simulations of suspended colloidal scale particles such as colloids, polymers, surfactants, and proteins subject to a particular and important class of hydrodynamic constraints. The total computational cost of the algorithm is practically linear with the number of particles modeled and can be further optimized when the characteristic mass fractal dimension of the suspended particles is known. Specifically, we consider the so-called “stresslet” constraint for which suspended particles resist local deformation. This acts to produce a symmetric force dipole in the fluid and imparts rigidity to the particles. The presented method is an extension of the recently reported positively split formulation for Ewald summation of the Rotne-Prager-Yamakawa mobility tensor to higher order terms in the hydrodynamic scattering series accounting for force dipoles [A. M. Fiore et al., J. Chem. Phys. 146(12), 124116 (2017)]. The hydrodynamic mobility tensor, which is proportional to the covariance of particle Brownian displacements, is constructed as an Ewald sum in a novel way which guarantees that the real-space and wave-space contributions to the sum are independently symmetric and positive-definite for all possible particle configurations. This property of the Ewald sum is leveraged to rapidly sample the Brownian displacements from a superposition of statistically independent processes with the wave-space and real-space contributions as respective covariances. The cost of computing the Brownian displacements in this way is comparable to the cost of computing the deterministic displacements. The addition of a stresslet constraint to the over-damped particle equations of motion leads to a stochastic differential algebraic equation (SDAE) of index 1, which is integrated forward in time using a mid-point integration scheme that implicitly produces stochastic displacements consistent with the fluctuation-dissipation theorem for the constrained system. Calculations for hard sphere dispersions are illustrated and used to explore the performance of the algorithm. An open source, high-performance implementation on graphics processing units capable of dynamic simulations of millions of particles and integrated with the software package HOOMD-blue is used for benchmarking and made freely available in the supplementary material.
Generation of attosecond electron bunches by the relativistic Weibel instability
Authors: Khodadadi Azadboni F. , Sadighi-Bonabi R.
Published: January 2018

The relativistic Weibel instability and temperature anisotropy can generate electron bunches of attosecond duration which makes it an attractive method for the generation and amplification of tunable ultrashort pulses. In this paper, the effect of the relativistic Weibel instability and temperature anisotropy on generating attosecond electron bunches is investigated. Calculations show that with the reduction relativistic parameter, γ, by a factor of 2, increasing 14.6% of the relativistic Weibel instability leads to about 62% reduction of the nanobunching gain saturation time and the density perturbation generated by the temperature anisotropy and the relativistic Weibel instability. The nanobunching density perturbation has a maximum value corresponding to 2.12 × 1037 for wavenumber kc/ωpe = 1.33 and γ  =  3. Evidence of ultrashort electron bunches could be applied to attosecond electron and coherent x-ray production.
A photoemission moments model using density functional and transfer matrix methods applied to coating layers on surfaces: Theory
Authors: Jensen Kevin L. , Finkenstadt Daniel , Shabaev Andrew , Lambrakos Samuel G. , Moody Nathan A. , Petillo John J. , Yamaguchi Hisato , Liu Fangze
Published: January 2018

Recent experimental measurements of a bulk material covered with a small number of graphene layers reported by Yamaguchi et al. [NPJ 2D Mater. Appl. 1, 12 (2017)] (on bialkali) and Liu et al. [Appl. Phys. Lett. 110, 041607 (2017)] (on copper) and the needs of emission models in beam optics codes have lead to substantial changes in a Moments model of photoemission. The changes account for (i) a barrier profile and density of states factor based on density functional theory (DFT) evaluations, (ii) a Drude-Lorentz model of the optical constants and laser penetration depth, and (iii) a transmission probability evaluated by an Airy Transfer Matrix Approach. Importantly, the DFT results lead to a surface barrier profile of a shape similar to both resonant barriers and reflectionless wells: the associated quantum mechanical transmission probabilities are shown to be comparable to those recently required to enable the Moments (and Three Step) model to match experimental data but for reasons very different than the assumption by conventional wisdom that a barrier is responsible. The substantial modifications of the Moments model components, motivated by computational materials methods, are developed. The results prepare the Moments model for use in treating heterostructures and discrete energy level systems (e.g., quantum dots) proposed for decoupling the opposing metrics of performance that undermine the performance of advanced light sources like the x-ray Free Electron Laser. The consequences of the modified components on quantum yield, emittance, and emission models needed by beam optics codes are discussed.
Substrate thermal conductivity controls the ability to manufacture microstructures via laser-induced direct write
Authors: Tomko John A. , Olson David H. , Braun Jeffrey L. , Kelliher Andrew P. , Kaehr Bryan , Hopkins Patrick E.
Published: January 2018

In controlling the thermal properties of the surrounding environment, we provide insight into the underlying mechanisms driving the widely used laser direct write method for additive manufacturing. We find that the onset of silver nitrate reduction for the formation of direct write structures directly corresponds to the calculated steady-state temperature rises associated with both continuous wave and high-repetition rate, ultrafast pulsed laser systems. Furthermore, varying the geometry of the heat affected zone, which is controllable based on in-plane thermal diffusion in the substrate, and laser power, allows for control of the written geometries without any prior substrate preparation. These findings allow for the advance of rapid manufacturing of micro- and nanoscale structures with minimal material constraints through consideration of the laser-controllable thermal transport in ionic liquid/substrate media.
Induced waveform transitions of dissipative solitons
Authors: Kochetov Bogdan A. , Tuz Vladimir R.
Published: January 2018

The effect of an externally applied force upon the dynamics of dissipative solitons is analyzed in the framework of the one-dimensional cubic-quintic complex Ginzburg-Landau equation supplemented by a potential term with an explicit coordinate dependence. The potential accounts for the external force manipulations and consists of three symmetrically arranged potential wells whose depth varies along the longitudinal coordinate. It is found out that under an influence of such potential a transition between different soliton waveforms coexisting under the same physical conditions can be achieved. A low-dimensional phase-space analysis is applied in order to demonstrate that by only changing the potential profile, transitions between different soliton waveforms can be performed in a controllable way. In particular, it is shown that by means of a selected potential, stationary dissipative soliton can be transformed into another stationary soliton as well as into periodic, quasi-periodic, and chaotic spatiotemporal dissipative structures.
In- and out-of-plane longitudinal acoustic-wave velocities and elastic moduli in h-BN from Brillouin scattering measurements
Authors: Jiménez-Riobóo R. J. , Artús L. , Cuscó R. , Taniguchi T. , Cassabois G. , Gil B.
Published: January 2018

The elastic constants of high-quality, single-crystal hexagonal boron nitride (h-BN) have been measured by means of high resolution Brillouin spectroscopy using a modified reflected light microscope. The sound propagation velocity in the c-axis direction and perpendicular to the c-axis have been obtained from the Brillouin frequency shift, with a proper account taken of the vast difference between the ordinary and extraordinary refractive indices recently reported in the highly anisotropic layered h-BN crystal. The elastic constants c11 and c33 obtained from the Brillouin experiments are somewhat lower than previous determinations based on inelastic x-ray measurements and confirm the overestimation of the h-BN elastic constants by ab initio calculations based on density functional perturbation theory in the local density approximation.
Pulsatile pipe flow transition: Flow waveform effects
Authors: Brindise Melissa C. , Vlachos Pavlos P.
Published: January 2018

Although transition is known to exist in various hemodynamic environments, the mechanisms that govern this flow regime and their subsequent effects on biological parameters are not well understood. Previous studies have investigated transition in pulsatile pipe flow using non-physiological sinusoidal waveforms at various Womersley numbers but have produced conflicting results, and multiple input waveform shapes have yet to be explored. In this work, we investigate the effect of the input pulsatile waveform shape on the mechanisms that drive the onset and development of transition using particle image velocimetry, three pulsatile waveforms, and six mean Reynolds numbers. The turbulent kinetic energy budget including dissipation rate, production, and pressure diffusion was computed. The results show that the waveform with a longer deceleration phase duration induced the earliest onset of transition, while the waveform with a longer acceleration period delayed the onset of transition. In accord with the findings of prior studies, for all test cases, turbulence was observed to be produced at the wall and either dissipated or redistributed into the core flow by pressure waves, depending on the mean Reynolds number. Turbulent production increased with increasing temporal velocity gradients until an asymptotic limit was reached. The turbulence dissipation rate was shown to be independent of mean Reynolds number, but a relationship between the temporal gradients of the input velocity waveform and the rate of turbulence dissipation was found. In general, these results demonstrated that the shape of the input pulsatile waveform directly affected the onset and development of transition.
Recent and emerging reproductive biology research in Australia and New Zealand: highlights from the Society for Reproductive Biology Annual Meeting, 2017
Authors: Bertoldo M. J. , Andraweera P. H. , Bromfield E. G. , Cousins F. L. , Lindsay L. A. , Paiva P. , Regan S. L. , Rose R. D. , Akison L. K.
Published: January 2018

Research in reproductive science is essential to promote new developments in reproductive health and medicine, agriculture and conservation. The Society for Reproductive Biology (SRB) 2017 conference held in Perth (WA, Australia) provided a valuable update on current research programs in Australia and New Zealand. This conference review delivers a dedicated summary of significant questions, emerging concepts and innovative technologies presented in the symposia. This research demonstrates significant advances in the identification of precursors for a healthy pregnancy, birth and child, and discusses how these factors can influence disease risk. A key theme included preconception parental health and its effect on gametogenesis, embryo and fetal development and placental function. In addition, the perturbation of key developmental checkpoints was shown to contribute to a variety of pathological states that have the capacity to affect health and fertility. Importantly, the symposia discussed in this review emphasised the role of reproductive biology as a conduit for understanding the transmission of non-communicable diseases, such as metabolic disorders and cancers. The research presented at SRB 2017 has revealed key findings that have the prospect to change not only the fertility of the present generation, but also the health and reproductive capacity of future generations.
Brain-state dependent astrocytic Ca
2+
signals are coupled to both positive and negative BOLD-fMRI signals
Authors: Wang Maosen , He Yi , Sejnowski Terrence J. , Yu Xin
Published: January 2018

Significance

The role of astrocytes on brain function is controversial in many aspects. It remains challenging to specify the in vivo functional impact of astrocytic calcium signal when mediating vasodilation/constriction at varied physiological or pathophysiological conditions. Here, we applied simultaneous fMRI and GCaMP-mediated Ca
2+
optical fiber recording to detect distinct astrocytic Ca
2+
signals (evoked vs. intrinsic) coupled to positive and negative blood-oxygen-level-dependent signals, respectively and concurrently, with unique spatial and temporal patterns. Not only did we demonstrate the distinct neurovascular coupling events coupled to the evoked and intrinsic astrocytic calcium signals, but also revealed the thalamic regulation mechanism underlying the astrocytic calcium-mediated brain state switch. This astrocytic-relevant regulatory mechanism could underlie numerous brain disorder and injury models relevant to gliovascular disruption.
Endoplasmic reticulum acyltransferase with prokaryotic substrate preference contributes to triacylglycerol assembly in
Chlamydomonas
Authors: Kim Yeongho , Terng Ee Leng , Riekhof Wayne R. , Cahoon Edgar B. , Cerutti Heriberto
Published: January 2018

Significance

The acyl chain composition of
Chlamydomonas
triacylglycerols (TAGs) suggests that they are assembled from prokaryotic precursors, proposed to be synthesized in the chloroplast. However, in most eukaryotes, the endoplasmic reticulum (ER) appears to be the main organelle for storage TAG biosynthesis. Interestingly,
Chlamydomonas reinhardtii
has a distinct lysophosphatidic acid acyltransferase that localizes to the ER but resembles prokaryotic lysophosphatidic acid acyltransferases (LPAATs) in its substrate preference. Thus,
Chlamydomonas
and related green algae, unlike land plants, can synthesize “prokaryotic” acyl-lipids in the ER, with intriguing implications for biotechnological applications.
Auxetic metamaterials from disordered networks
Authors: Reid Daniel R. , Pashine Nidhi , Wozniak Justin M. , Jaeger Heinrich M. , Liu Andrea J. , Nagel Sidney R. , de Pablo Juan J.
Published: January 2018

Significance

Recent work indicates that selective pruning of disordered networks of nodes connected by bonds can generate materials with nontrivial mechanical properties, including auxetic networks having a negative Poisson’s ratio

ν

. Until now, auxetic networks created based on this strategy have not been successfully realized in experiment. Here a model that includes angle-bending forces and the experimental boundary conditions is introduced for pruning-based design of auxetic materials. By pruning the appropriate bonds,

ν

can be tuned to values approaching the lower mechanical limit of −1, and the corresponding laboratory networks exhibit good agreement with model predictions. Optimization algorithms are then used to show that highly auxetic materials can be engineered from inhomogeneous bonds and nodes that exhibit distinct mechanical characteristics.
Exploring functional pairing between surface glycoconjugates and human galectins using programmable glycodendrimersomes
Authors: Xiao Qi , Ludwig Anna-Kristin , Romanò Cecilia , Buzzacchera Irene , Sherman Samuel E. , Vetro Maria , Vértesy Sabine , Kaltner Herbert , Reed Ellen H. , Möller Martin , Wilson Christopher J. , Hammer Daniel A. , Oscarson Stefan , Klein Michael L. , Gabius Hans-Joachim , Percec Virgil
Published: January 2018

Significance

Cells are decorated with charged and uncharged carbohydrate ligands known as glycans, which are responsible for several key functions, including their interactions with proteins known as lectins. Here, a platform consisting of synthetic nanoscale vesicles, known as glycodendrimersomes, which can be programmed with cell surface-like structural and topological complexity, is employed to dissect design aspects of glycan presentation, with specificity for lectin-mediated bridging. Aggregation assays reveal the extent of cross-linking of these biomimetic nanoscale vesicles—presenting both anionic and neutral ligands in a bioactive manner—with disease-related human and other galectins, thus offering the possibility of unraveling the nature of these fundamental interactions.
Assembly mechanism of the CARMA1–BCL10–MALT1–TRAF6 signalosome
Authors: David Liron , Li Yang , Ma Jun , Garner Ethan , Zhang Xinzheng , Wu Hao
Published: January 2018

The CARMA1–BCL10–MALT1 (CBM) signalosome is a central mediator of T cell receptor and B cell receptor-induced NF-κB signaling that regulates multiple lymphocyte functions. While caspase-recruitment domain (CARD) membrane-associated guanylate kinase (MAGUK) protein 1 (CARMA1) nucleates B cell lymphoma 10 (BCL10) filament formation through interactions between CARDs, mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a paracaspase with structural similarity to caspases, which recruits TNF receptor-associated factor 6 (TRAF6) for K63-linked polyubiquitination. Here we present cryo-electron microscopy (cryo-EM) structure of the BCL10 CARD filament at 4.0-Å resolution. The structure redefines CARD–CARD interactions compared with the previous EM structure determined from a negatively stained sample. Surprisingly, time-lapse confocal imaging shows that BCL10 polymerizes in a unidirectional manner. CARMA1, the BCL10 nucleator, serves as a hub for formation of star-shaped filamentous networks of BCL10 and significantly decreases the lag period of BCL10 polymerization. Cooperative MALT1 interaction with BCL10 filaments observed under EM suggests immediate dimerization of MALT1 in the BCL10 filamentous scaffold. In addition, TRAF6 cooperatively decorates CBM filaments to form higher-order assemblies, likely resulting in all-or-none activation of the downstream pathway. Collectively, these data reveal biophysical mechanisms in the assembly of the CARMA1-BCL10-MALT1-TRAF6 complex for signal transduction.
Tom70 enhances mitochondrial preprotein import efficiency by binding to internal targeting sequences
Authors: Backes Sandra , Hess Steffen , Boos Felix , Woellhaf Michael W. , Gödel Sabrina , Jung Martin , Mühlhaus Timo , Herrmann Johannes M.
Published: January 2018

The biogenesis of mitochondria depends on the import of hundreds of preproteins. N-terminal matrix-targeting signals (MTSs) direct preproteins to the surface receptors Tom20, Tom22, and Tom70. In this study, we show that many preproteins contain additional internal MTS-like signals (iMTS-Ls) in their mature region that share the characteristic properties of presequences. These features allow the in silico prediction of iMTS-Ls. Using Atp1 as model substrate, we show that iMTS-Ls mediate the binding to Tom70 and have the potential to target the protein to mitochondria if they are presented at its N terminus. The import of preproteins with high iMTS-L content is significantly impaired in the absence of Tom70, whereas preproteins with low iMTS-L scores are less dependent on Tom70. We propose a stepping stone model according to which the Tom70-mediated interaction with internal binding sites improves the import competence of preproteins and increases the efficiency of their translocation into the mitochondrial matrix.
pymzML v2.0: introducing a highly compressed and seekable gzip format
Authors: Kösters M , Leufken J , Schulze S , Sugimoto K , Klein J , Zahedi R P , Hippler M , Leidel S A , Fufezan C
Published: January 2018

Motivation

In the new release of pymzML (v2.0), we have optimized the speed of this established tool for mass spectrometry data analysis to adapt to increasing amounts of data in mass spectrometry. Thus, we integrated faster libraries for numerical calculations, improved data retrieving algorithms and have optimized the source code. Importantly, to adapt to rapidly growing file sizes, we developed a generalizable compression scheme for very fast random access and applied this concept to mzML files to retrieve spectral data.

Results

pymzML performs at par with established C programs when it comes to processing times. However, it offers the versatility of a scripting language, while adding unprecedented fast random access to compressed files. Additionally, we designed our compression scheme in such a general way that it can be applied to any field where fast random access to large data blocks in compressed files is desired.

Availability and implementation

pymzML is freely available on https://github.com/pymzML/pymzML under GPL license. pymzML requires Python3.4+ and optionally numpy. Documentation available on http://pymzml.readthedocs.io.