bluuebunny/crossref_metadata_2025 huggingface dataset:
Imaging of Postoperative Infection at the Knee Joint
Authors: Gimber Lana , Omar Imran , Klauser Andrea , Miller Michael , Wild Jason , Chadaz Tyson , Taljanovic Mihra
Published: August 2018

Postoperative infections of the knee are uncommon but may occur with joint arthroplasties, fracture fixation, or after arthroscopic procedures. The ultimate diagnosis is made by joint aspiration or tissue sampling. Joint aspiration and tissue sampling can be performed under imaging guidance or intraoperatively. Imaging is an important adjunct to clinical and laboratory findings and should start with radiographs. Cross-sectional imaging including magnetic resonance (MR) imaging, computed tomography (CT), nuclear studies, and ultrasound (US) are frequently used if the diagnosis is in doubt and to evaluate the extent of disease. We discuss the current algorithm in the diagnosis of various postoperative infections of the knee joint. The article addresses the utility of radiography, MR imaging, CT, US, and the most commonly used nuclear studies in the diagnosis of various postoperative knee infections and the imaging appearances of these infections on each of these diagnostic modalities.
Mapping the Flow of Pediatric Trauma Patients Using Process Mining
Authors: Durojaiye Ashimiyu , McGeorge Nicolette , Puett Lisa , Stewart Dylan , Fackler James , Hoonakker Peter , Lehmann Harold , Gurses Ayse
Published: August 2018

Background Inhospital pediatric trauma care typically spans multiple locations, which influences the use of resources, that could be improved by gaining a better understanding of the inhospital flow of patients and identifying opportunities for improvement.

Objectives To describe a process mining approach for mapping the inhospital flow of pediatric trauma patients, to identify and characterize the major patient pathways and care transitions, and to identify opportunities for patient flow and triage improvement.

Methods From the trauma registry of a level I pediatric trauma center, data were extracted regarding the two highest trauma activation levels, Alpha (n = 228) and Bravo (n = 1,713). An event log was generated from the admission, discharge, and transfer data from which patient pathways and care transitions were identified and described. The Flexible Heuristics Miner algorithm was used to generate a process map for the cohort, and separate process maps for Alpha and Bravo encounters, which were assessed for conformance when fitness value was less than 0.950, with the identification and comparison of conforming and nonconforming encounters.

Results The process map for the cohort was similar to a validated process map derived through qualitative methods. The process map for Bravo encounters had a relatively low fitness of 0.887, and 96 (5.6%) encounters were identified as nonconforming with characteristics comparable to Alpha encounters. In total, 28 patient pathways and 20 care transitions were identified. The top five patient pathways were traversed by 92.1% of patients, whereas the top five care transitions accounted for 87.5% of all care transitions. A larger-than-expected number of discharges from the pediatric intensive care unit (PICU) were identified, with 84.2% involving discharge to home without the need for home care services.

Conclusion Process mining was successfully applied to derive process maps from trauma registry data and to identify opportunities for trauma triage improvement and optimization of PICU use.
Chronische Schmerzerkrankung und Bewegung/Aktivität/Sport
Authors: Pfingsten M.
Published: August 2018

Patienten mit Schmerzen zeigen oftmals ein bestimmtes Verhalten, das sich vorrangig durch Inaktivität, Schonung und Vermeidung auszeichnet. Dieses Verhalten wird als ein aufrechterhaltender Mechanismus in der Chronifizierung von Schmerzerkrankungen angesehen. Im Rahmen des sogenannten Angst-Vermeidungs-Modells sind die kognitiven, emotionalen und verhaltensmäßigen Zusammenhänge dieses Verhaltens dargestellt, das durch Lernprinzipien der operanten Konditionierung erklärbar wird. Dieses gelernte Verhalten ist sehr löschungsresistent und Patienten finden selbstständig oftmals keinen Ausweg mehr daraus. Die oftmals zu beobachtende Inaktivität von Menschen mit Schmerzerkrankungen hat damit einen psychologischen Hintergrund, der nicht im direkten bzw. bewussten Einfluss der Betroffenen selbst steht. Für das Ablegen dieses Vermeidungsverhaltens und für die Wiederaufnahme normalen körperlich aktiven Verhaltens können verhaltenstherapeutische Prinzipien hilf-reich sein, die in Patienteninformationen bzw. der Ausgestaltung körperlicher Aktivierungsprogramme Berücksichtigung finden. Derartige Mechanismen scheinen auch bei Rheumapatienten Relevanz zu haben.
High-solids fermentation of food wastes for biogas recovery by using horizontal anaerobic reactor
Authors: Zhao Mingxing , Yang Lili , Guo Miao , Huang Zhenxing , Shi Wansheng , Wang Tao , Ruan Wenquan
Published: August 2018

The biogas recovery from food wastes by anaerobic digestion was considered to be a feasible way for waste treatment. The system performance of high-solid anaerobic digestion of canteen food wastes by a horizontal reactor (8l) was investigated in this study. The TS of the reaction system was kept at 15%. The results indicated that biogas remained stable at about 650 ml/gTS when the volumetric loading rate (VLR) increased from 2 gTS/l.d to 8 gTS/l.d; however, it decreased at the VLR of 11 gTS/l.d. It suggested that VLR of 8 gTS/l.d was the optimal rate for this horizontal anaerobic reactor. After the adjustment of the running operation, the reactor remained stable with the accumulative biogas yield of 484 ml/gTS. The concentration of soluble chemical oxygen demand, ammonia nitrogen, volatile fatty acid, and alkalinity sharply increased to 41 024 mg/l, 2711 mg/l, 16 366 mg/l, and 14 250 mg/l at day 65 which reflected at the instable stage of the reactor, respectively. The maximum values of amylase and protease enzyme occurred at the initial stage of the reaction system with 1.42 U/ml (day 10) and 1.53 × 10−3 U/ml (day 17), respectively. After that, the two enzymes remained stable.
Estimating complete band diagrams of non-ideal heterointerfaces by combining ellipsometry and photoemission spectroscopy
Authors: Crovetto Andrea
Published: August 2018

In this work, we show that spectroscopic ellipsometry can be combined with photoemission spectroscopy to obtain complete interface band diagrams of non-ideal semiconductor heterointerfaces, such as interfaces between thin-film polycrystalline materials. The non-destructive ellipsometry measurement probes the near-interface bandgap of the two semiconductors (including the buried semiconductor) after the interface has formed. This is important in the non-ideal case where chemical processes during interface growth modify the electronic properties of the two separated surfaces. Knowledge of near-interface bandgaps improves accuracy in conduction band offset measurements of non-ideal interfaces, and it sheds light on their device physics. Both of those positive outcomes are demonstrated in the Cu2ZnSnS4/CdS interface used here as a case study, where the bandgap of both materials decreases by up to 200 meV from the bulk to the near-interface region. This finding reveals a preferential electron-hole recombination channel near the interface, and it yields corrected values for the interfacial conduction band offset.
Probabilistic multi-objective arbitrage of dispersed energy storage systems for optimal congestion management of active distribution networks including solar/wind/CHP hybrid energy system
Authors: Abdolahi Arya , Salehi Javad , Samadi Gazijahani Farhad , Safari Amin
Published: August 2018

Nowadays, dispersed storage systems (DSSs) have an irrefutable role in creating the favourable substrates for optimal management of active distribution networks (ADNs). Actually, they are capable of managing the congestion of ADNs by providing feasible solution that can dramatically improve the system reliability and resiliency against contingencies that threaten the network security. To this end, this paper deals with optimal arbitrage of DSSs in ADNs including the solar/wind/CHP hybrid energy system aiming at finding the optimal trade-off between congestion and economic targets by defining a novel probabilistic risk-based multi-objective model. In particular, the proposed method is fulfilled considering (1) feeders/line congestions, (2) network voltage deviations, (3) power losses, (4) operating cost of distributed generation associated with the cost of DSS charging/discharging, and (5) uncertainty pertaining to renewable generation. The two conflicting objectives consisting of congestion alleviation and procurement cost minimization are optimized simultaneously by multiobjective particle swarm optimization to purvey the Pareto-optimal curve, and subsequently, fuzzy decision-making is executed to extract the best solution from the Pareto curve obtained with respect to defined risk-based strategies. Finally, a case study referring to the modified IEEE 33-bus distribution system is utilized to evidence the efficiency and proficiency of the proposed congestion relief approach.
Localization of nonlinear spin waves in magnetic multilayers
Authors: Gerasimchuk Igor V. , Gerasimchuk Victor S.
Published: August 2018

For a description of the dynamics of a wide range of nonlinear multilayered magnetic media, we derive the nonlinear Schrödinger equation containing both linear and nonlinear δ-functional spatial perturbations. In the case of a system with one narrow magnetic layer having different values of single-ion anisotropy from that one of the matrix, within the long-wave approximation, we obtain the corresponding boundary conditions and find the solution localized near the layer. The regions of existence of this localized soliton state are determined, its properties are investigated, and the quasi-classical quantization of the soliton state is carried out. Finally, we conclude about the stability of the obtained localized solution with respect to small perturbations of the amplitude and phase.
Novel frequency stability measurement method with whole sample time range
Authors: Qu Bayi , Xue Fanxin , Yu Dongsong , Xu Longfei , Zhou Wei
Published: August 2018

A method to measure the frequency stabilities with a nearly whole range of sample time is presented. Precision as high as 10−5/100 ns has been obtained by it when measuring transient stability with 100 ns sample time, 10−12/s has been obtained toward short-term stability with 1 s sample time, and 10−16/day has been obtained with regard to long-term stability with 1 day sample time. In addition, because the frequency stabilities in a wider range of sample time can correspond to the phase noise index more accurately, the phenomena which are difficult to be observed in a phase noise curve can be detected through this measurement.
Lipids with bulky head groups generate large membrane curvatures by small compositional asymmetries
Authors: Sreekumari Aparna , Lipowsky Reinhard
Published: August 2018

Glycolipids such as GM1 have bulky head groups consisting of several monosaccharides. When these lipids are added to phospholipid bilayers, they generate large membrane curvatures even for small compositional asymmetries between the two leaflets of the bilayers. On the micrometer scale, these bilayer asymmetries lead to the spontaneous tubulation of giant vesicles as recently observed by optical microscopy. Here, we study these mixed membranes on the nanometer scale using coarse-grained molecular simulations. The membrane composition is defined by the mole fractions ϕ1 and ϕ2 of the large-head lipid in the two leaflets of the bilayer. Symmetric membranes are obtained for ϕ1 = ϕ2 ≡ ϕle, and asymmetric ones for ϕ1 ≠ ϕ2. In both cases, we compute the density and stress profiles across the membranes. The stress profiles are used to identify the tensionless states of the membranes. Symmetric and tensionless bilayers are found to be stable within the whole composition range 0 ≤ ϕle ≤ 1. For these symmetric bilayers, both the area compressibility modulus and the bending rigidity are found to vary non-monotonically with the leaflet mole fraction ϕle. For asymmetric bilayers, we compute the product of bending rigidity and spontaneous curvature from the first moment of the stress profile and determine the bending rigidities of the asymmetric membranes using the ϕle-dependent rigidities of the single leaflets. When we combine these results, the compositional asymmetry ϕ1 − ϕ2 is found to generate the spontaneous curvature (ϕ1 − ϕ2)/(0.63 ℓme) with the membrane thickness ℓme ≃ 4 nm. Therefore, the spontaneous curvature increases linearly with the compositional asymmetry. Furthermore, the small compositional asymmetry ϕ1 − ϕ2 = 0.04 leads to the large spontaneous curvature 1/(63 nm) and the increased asymmetry ϕ1 − ϕ2 = 0.2 generates the huge spontaneous curvature 1/(13 nm). These large values of the spontaneous curvature will facilitate future simulation studies of various membrane processes such as bud formation and nanoparticle engulfment.
Impact of poloxamer 188 (Pluronic F-68) additive on cell mechanical properties, quantification by real-time deformability cytometry
Authors: Guzniczak Ewa , Jimenez Melanie , Irwin Matthew , Otto Oliver , Willoughby Nicholas , Bridle Helen
Published: August 2018

Advances in cellular therapies have led to the development of new approaches for cell product purification and formulation, e.g., utilizing cell endogenous properties such as size and deformability as a basis for separation from potentially harmful undesirable by-products. However, commonly used additives such as Pluronic F-68 and other poloxamer macromolecules can change the mechanical properties of cells and consequently alter their processing. In this paper, we quantified the short-term effect of Pluronic F-68 on the mechanotype of three different cell types (Jurkat cells, red blood cells, and human embryonic kidney cells) using real-time deformability cytometry. The impact of the additive concentration was assessed in terms of cell size and deformability. We observed that cells respond progressively to the presence of Pluronic F-68 within first 3 h of incubation and become significantly stiffer (p-value < 0.001) in comparison to a serum-free control and a control containing serum. We also observed that the short-term response manifested as cell stiffening is true (p-value < 0.001) for the concentration reaching 1% (w/v) of the poloxamer additive in tested buffers. Additionally, using flow cytometry, we assessed that changes in cell deformability triggered by addition of Pluronic F-68 are not accompanied by size or viability alterations.
Tuning the crystallographic orientation and magnetic properties of multiferroic CuO epitaxial film on single crystalline SrTiO3 substrates
Authors: Sil Anomitra , Naik Mit H. , Ranjan Rajeev , Anil Kumar P. S.
Published: August 2018

We report a comparative study between the crystal structure and magnetic properties of multiferroic epitaxial CuO thin films grown on (001) and (110) oriented SrTiO3 substrates. CuO thin films were successfully grown along the [010] direction, which is also the direction of their ferroelectric polarization, on (110) oriented SrTiO3 substrates. We correlate our structural findings with the magnetic properties. It was observed that the heterostructure with the CuO film grown along the [010] direction shows distinct anomalies in the temperature dependent magnetization plot at 213 K and 230 K, whereas no such anomaly was observed in the case of the heterostructure grown on the (001) SrTiO3 substrate with the [111] CuO film. Buffered MgO layers were used between the CuO layer and the substrate to improve the crystalline quality of the CuO film.
Oxygen mediated phase transformation in room temperature grown TiO2 thin films with enhanced photocatalytic activity
Authors: Banerjee D. , Barman A. , Deshmukh S. , Saini C. P. , Maity G. , Pradhan S. K. , Gupta M. , Phase D. M. , Roy S. S. , Kanjilal A.
Published: August 2018

Room temperature transformation from anatase (A-TiO2) to rutile (R-TiO2) thin films through an intermediate mixed phase on stainless steel driven by a controlled oxygen flow rate (OFR) is investigated. Such OFR dependent phase transition is confirmed by X-ray diffraction and also consistent with X-ray absorption spectroscopy at Ti L and O K-edges, showing a long range ordering in TiO6 octahedral symmetry. X-ray photoelectron spectroscopy reveals a gradual reduction in Ti2O3 and/or TiO intermediate phases with increasing OFR. Finally, an enhanced photocatalytic activity is observed in the mixed phase and discussed in terms of photo-generated charge transport in the type-II staggered band structure between A-TiO2 and R-TiO2 phases.
Increased multiplexing of superconducting microresonator arrays by post-characterization adaptation of the on-chip capacitors
Authors: Shu S. , Calvo M. , Goupy J. , Leclercq S. , Catalano A. , Bideaud A. , Monfardini A. , Driessen E. F. C.
Published: August 2018

We present an interdigitated capacitor trimming technique for fine-tuning the resonance frequency of superconducting microresonators and increasing the multiplexing factor. We first measure the optical response of the array with a beam mapping system to link all resonances to their physical resonators. Then, a new set of resonance frequencies with uniform spacing and higher multiplexing factor is designed. We use simulations to deduce the lengths that we should trim from the capacitor fingers in order to shift the resonances to the desired frequencies. The sample is then modified using contact lithography and re-measured using the same setup. We demonstrate this technique on a 112-pixel aluminum lumped-element kinetic-inductance detector array. Before trimming, the resonance frequency deviation of this array is investigated. The variation of the inductor width plays the main role for the deviation. After trimming, the mean fractional frequency error for identified resonators is −6.4 × 10−4, with a standard deviation of 1.8 × 10−4. The final optical yield is increased from 70.5% to 96.7% with no observable crosstalk beyond −15 dB during mapping. This technique could be applied to other photon-sensitive superconducting microresonator arrays for increasing the yield and multiplexing factor.
Properties of AlN single crystals doped with Beryllium via high temperature diffusion
Authors: Soltamov V. A. , Rabchinskii M. K. , Yavkin B. V. , Kazarova O. P. , Nagalyuk S. S. , Davydov V. Yu. , Smirnov A. N. , Lebedev V. F. , Mokhov E. N. , Orlinskii S. B. , Baranov P. G.
Published: August 2018

We report on co-doping of high-quality AlN single crystals by group II Beryllium acceptors by means of diffusion from the vapour phase at a temperature of 1850 °C. We discovered that Be is characterized by the high diffusion length, allowing one to produce Be co-doping of sub-mm-thick AlN wafers. We show that Be diffusion led to the quenching of the visible (VIS) 450 nm (2.75 eV) and deep ultraviolet (UV) 265 nm (4.7 eV) optical absorption bands with simultaneous induction of the absorption band peaked at 248 nm (5 eV). By means of electron paramagnetic resonance (EPR), we also found that the presence of Be impurities compensated the donor type paramagnetic centers. Correlation of the EPR data with the optical absorption allowed us to conclude that Be produced in the AlN via diffusion acted predominantly as an acceptor, inducing the shift of the Fermi level to the lower part of the AlN bandgap. This shift of the Fermi level results in recharging of the deep level defects in the AlN bandgap, which explains the observed quenching of the VIS and UV absorption bands.
Study of 3D sloshing in a vertical cylindrical tank
Authors: Caron P. A. , Cruchaga M. A. , Larreteguy A. E.
Published: August 2018

Moving liquid-gas interfaces appear frequently in both natural processes and engineering applications. In the case of partially filled tanks, for instance, the accurate description of the free surface transient behavior during transportation or earthquakes is of paramount importance for structural stability analyses. This work presents new experimental data of sloshing at laboratory scale in a vertical cylindrical tank with different filling levels, along with numerical simulations of selected cases using an open source finite volume application. Maximum and minimum experimental wave heights, measured with ultrasonic sensors, are reported for several non-resonant cases during the periodic steady state regime, along with snapshots of a video recorded near-resonance case. For the numerical simulations, a suitable mesh was designed based on a mesh convergence analysis focused on the simulated velocity profiles at the tank wall. A slight nonlinear behavior is detected in the experimental wave patterns, expressed as non-symmetrical minimum and maximum wave heights. The near-resonance case, in turn, shows a highly three-dimensional behavior of the free surface and a rotational effect. The numerical results obtained for the non-resonant cases show good overall agreement with the experiments, although the non-linear behavior is not accurately modelled. The evolution of the highly distorted free surface in the near-resonance case is well captured by the simulation, along with the observed rotational effect.
Letter: Does flame-generated vorticity increase turbulent burning velocity?
Authors: Lipatnikov A. N. , Sabelnikov V. A. , Nishiki S. , Hasegawa T.
Published: August 2018

Direct numerical simulation data obtained from a statistically stationary, 1D, planar, weakly turbulent, premixed flame, which is associated with the flamelet combustion regime, are analyzed in order to show that generation of vorticity due to baroclinic torque within flamelets can impede wrinkling the reaction surface, reduce its area, and decrease the burning rate. These data call for revisiting the widely accepted concept of combustion acceleration due to flame-generated turbulence.
Nonequilibrium steady-state discharge in the focused wave beam
Authors: Gildenburg V. B. , Pavlichenko I. A. , Smirnova D. A.
Published: August 2018

The steady-state structure of a nonequilibrium discharge maintained in the medium by a focused electromagnetic wave beam is determined based on the physical model treating the discharge as a distributed nonlinear system with a given level of the electric field amplitude self-limitation. In this model, finding the self-consistent spatial distributions of the plasma density and the electric field phase in the ionized region is reduced to some inverse electrodynamic problem, whose solution is found in application to the axially symmetric geometry. The electromagnetic field outside the discharge plasma is found in the approximation of geometric optics with the ray reflection and refraction at the boundary being taken into account. The differential equations determining the form of the plasma-vacuum interface are derived and integrated numerically and the distributions of the plasma density and the electric field within and around the discharge are calculated as applied to the conditions of interest for the microwave and optical discharges in gases and solids.
Structural, magnetic, and transport properties of Fe1−xRhx/MgO(001) films grown by molecular-beam epitaxy
Authors: Mei Antonio B. , Tang Yongjian , Grab Jennifer L. , Schubert Jürgen , Ralph Daniel C. , Schlom Darrell G.
Published: August 2018

Fe1−xRhx layers are grown with varying rhodium fraction x on (001)-oriented MgO substrates by molecular-beam epitaxy. Film structural, morphological, magnetic, and transport properties are investigated. At room temperature, layers are ferromagnetic (FM) for x < 0.48 and antiferromagnetic (AF) for x > 0.48. Separating the two magnetically ordered phases at x = 0.48 is an abrupt change in the Fe1−xRhx lattice parameter of Δa = 0.0028 nm (Δa/a = −0.9%). For AF layers, the FM state is recovered by heating across a first-order phase transition. The transition leads to a large resistivity modulation, Δρ/ρ  = 80%, over a narrow temperature range, ΔT = 3 K, in stoichiometric Fe0.50Rh0.50/MgO(001). For samples with compositions deviating from x = 0.50, fluctuations broaden ΔT and defect scattering reduces Δρ/ρ.
One-minute nano-tomography using hard X-ray full-field transmission microscope
Authors: Ge Mingyuan , Coburn David Scott , Nazaretski Evgeny , Xu Weihe , Gofron Kazimierz , Xu Huijuan , Yin Zhijian , Lee Wah-Keat
Published: August 2018

Full field transmission X-ray microscopy (TXM) is a powerful technique for non-destructive 3D imaging with nanometer-scale spatial resolution. However, to date, the typical acquisition time with the hard X-ray TXM at a synchrotron facility is >10 min for a 3D nano-tomography dataset with sub-50 nm spatial resolution. This is a significant limit on the types of 3D dynamics that can be investigated using this technique. Here, we present a demonstration of one-minute nano-tomography with sub-50 nm spatial resolution. This achievement is made possible with an in-house designed and commissioned TXM instrument at the Full-field X-ray Imaging beamline at the National Synchrotron Light Source-II at Brookhaven National Laboratory. This capability represents an order of magnitude decrease in the time required for studying sample dynamics with 10 s of nm spatial resolution.
Local field potentials of subthalamic nucleus contain electrophysiological footprints of motor subtypes of Parkinson’s disease
Authors: Telkes Ilknur , Viswanathan Ashwin , Jimenez-Shahed Joohi , Abosch Aviva , Ozturk Musa , Gupte Akshay , Jankovic Joseph , Ince Nuri F.
Published: August 2018

Significance

Despite the fact that deep-brain stimulation (DBS) of the subthalamic nucleus (STN) has emerged as an effective surgical treatment for Parkinson’s disease (PD), there is no available neurobiomarker providing information about the symptoms of PD subtypes in STN. In this paper, we report the finding of neural correlates of two motor phenotypes of PD in the territories of STN. Despite advances in imaging, microelectrode recording continues to be best practice and the dominant method for STN localization during DBS surgery [Abosch A, et al. (2013)
Stereotact Funct Neurosurg
91:1–11]. Hence, we anticipate our findings will provide possibilities for the intraoperative interpretation of oscillatory dynamics of STN and that these well-localized patterns can be used as objective tools for future neuromodulation technologies.
N-glycanase NGLY1 regulates mitochondrial homeostasis and inflammation through NRF1
Authors: Yang Kun , Huang Ryan , Fujihira Haruhiko , Suzuki Tadashi , Yan Nan
Published: August 2018

Mutations in the NGLY1 (N-glycanase 1) gene, encoding an evolutionarily conserved deglycosylation enzyme, are associated with a rare congenital disorder leading to global developmental delay and neurological abnormalities. The molecular mechanism of the NGLY1 disease and its function in tissue and immune homeostasis remain unknown. Here, we find that NGLY1-deficient human and mouse cells chronically activate cytosolic nucleic acid–sensing pathways, leading to elevated interferon gene signature. We also find that cellular clearance of damaged mitochondria by mitophagy is impaired in the absence of NGLY1, resulting in severely fragmented mitochondria and activation of cGAS–STING as well as MDA5–MAVS pathways. Furthermore, we show that NGLY1 regulates mitochondrial homeostasis through transcriptional factor NRF1. Remarkably, pharmacological activation of a homologous but nonglycosylated transcriptional factor NRF2 restores mitochondrial homeostasis and suppresses immune gene activation in NGLY1-deficient cells. Together, our findings reveal novel functions of the NGLY1–NRF1 pathway in mitochondrial homeostasis and inflammation and uncover an unexpected therapeutic strategy using pharmacological activators of NRF2 for treating mitochondrial and immune dysregulation.
Spatial regulation of the actin cytoskeleton by HSF-1 during aging
Authors: Higuchi-Sanabria Ryo , Paul Joseph W. , Durieux Jenni , Benitez Camila , Frankino Phillip A. , Tronnes Sarah U. , Garcia Gilberto , Daniele Joseph R. , Monshietehadi Samira , Dillin Andrew
Published: August 2018

There are many studies suggesting an age-associated decline in the actin cytoskeleton, and this has been adopted as common knowledge in the field of aging biology. However, a direct identification of this phenomenon in aging multicellular organisms has not been performed. Here, we express LifeAct::mRuby in a tissue-specific manner to interrogate cytoskeletal organization as a function of age. We show for the first time in Caenorhabditis elegans that the organization and morphology of the actin cytoskeleton deteriorate at advanced age in the muscles, intestine, and hypodermis. Moreover, hsf-1 is essential for regulating cytoskeletal integrity during aging, so that knockdown of hsf-1 results in premature aging of actin and its overexpression protects actin cytoskeletal integrity in the muscles, the intestine, and the hypodermis. Finally, hsf-1 overexpression in neurons alone is sufficient to protect cytoskeletal integrity in nonneuronal cells.
Adjutant: an R-based tool to support topic discovery for systematic and literature reviews
Authors: Crisan Anamaria , Munzner Tamara , Gardy Jennifer L
Published: August 2018

Adjutant is an open-source, interactive and R-based application to support mining PubMed for literature reviews. Given a PubMed-compatible search query, Adjutant downloads the relevant articles and allows the user to perform an unsupervised clustering analysis to identify data-driven topic clusters. Following clustering, users can also sample documents using different strategies to obtain a more manageable dataset for further analysis. Adjutant makes explicit trade-offs between speed and accuracy, which are modifiable by the user, such that a complete analysis of several thousand documents can take a few minutes. All analytic datasets generated by Adjutant are saved, allowing users to easily conduct other downstream analyses that Adjutant does not explicitly support.

Availability and implementation

Adjutant is implemented in R, using Shiny, and is available at https://github.com/amcrisan/Adjutant.

Supplementary information

Supplementary data are available at Bioinformatics online.
SpaRC: scalable sequence clustering using Apache Spark
Authors: Shi Lizhen , Meng Xiandong , Tseng Elizabeth , Mascagni Michael , Wang Zhong
Published: August 2018

Motivation

Whole genome shotgun based next-generation transcriptomics and metagenomics studies often generate 100–1000 GB sequence data derived from tens of thousands of different genes or microbial species. Assembly of these data sets requires tradeoffs between scalability and accuracy. Current assembly methods optimized for scalability often sacrifice accuracy and vice versa. An ideal solution would both scale and produce optimal accuracy for individual genes or genomes.

Results

Here we describe an Apache Spark-based scalable sequence clustering application, SparkReadClust (SpaRC), that partitions reads based on their molecule of origin to enable downstream assembly optimization. SpaRC produces high clustering performance on transcriptomes and metagenomes from both short and long read sequencing technologies. It achieves near-linear scalability with input data size and number of compute nodes. SpaRC can run on both cloud computing and HPC environments without modification while delivering similar performance. Our results demonstrate that SpaRC provides a scalable solution for clustering billions of reads from next-generation sequencing experiments, and Apache Spark represents a cost-effective solution with rapid development/deployment cycles for similar large-scale sequence data analysis problems.

Availability and implementation

https://bitbucket.org/berkeleylab/jgi-sparc
The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models
Authors: Zhang Yuqing , Bernau Christoph , Parmigiani Giovanni , Waldron Levi
Published: August 2018

Cross-study validation (CSV) of prediction models is an alternative to traditional cross-validation (CV) in domains where multiple comparable datasets are available. Although many studies have noted potential sources of heterogeneity in genomic studies, to our knowledge none have systematically investigated their intertwined impacts on prediction accuracy across studies. We employ a hybrid parametric/non-parametric bootstrap method to realistically simulate publicly available compendia of microarray, RNA-seq, and whole metagenome shotgun microbiome studies of health outcomes. Three types of heterogeneity between studies are manipulated and studied: (i) imbalances in the prevalence of clinical and pathological covariates, (ii) differences in gene covariance that could be caused by batch, platform, or tumor purity effects, and (iii) differences in the “true” model that associates gene expression and clinical factors to outcome. We assess model accuracy, while altering these factors. Lower accuracy is seen in CSV than in CV. Surprisingly, heterogeneity in known clinical covariates and differences in gene covariance structure have very limited contributions in the loss of accuracy when validating in new studies. However, forcing identical generative models greatly reduces the within/across study difference. These results, observed consistently for multiple disease outcomes and omics platforms, suggest that the most easily identifiable sources of study heterogeneity are not necessarily the primary ones that undermine the ability to accurately replicate the accuracy of omics prediction models in new studies. Unidentified heterogeneity, such as could arise from unmeasured confounding, may be more important.
Iron overload is accompanied by mitochondrial and lysosomal dysfunction in WDR45 mutant cells
Authors: Seibler Philip , Burbulla Lena F , Dulovic Marija , Zittel Simone , Heine Johanne , Schmidt Thomas , Rudolph Franziska , Westenberger Ana , Rakovic Aleksandar , Münchau Alexander , Krainc Dimitri , Klein Christine
Published: August 2018

Beta-propeller protein-associated neurodegeneration is a subtype of monogenic neurodegeneration with brain iron accumulation caused by de novo mutations in WDR45. The WDR45 protein functions as a beta-propeller scaffold and plays a putative role in autophagy through its interaction with phospholipids and autophagy-related proteins. Loss of WDR45 function due to disease-causing mutations has been linked to defects in autophagic flux in patient and animal cells. However, the role of WDR45 in iron homeostasis remains elusive. Here we studied patient-specific WDR45 mutant fibroblasts and induced pluripotent stem cell-derived midbrain neurons. Our data demonstrated that loss of WDR45 increased cellular iron levels and oxidative stress, accompanied by mitochondrial abnormalities, autophagic defects, and diminished lysosomal function. Restoring WDR45 levels partially rescued oxidative stress and the susceptibility to iron treatment, and activation of autophagy reduced the observed iron overload in WDR45 mutant cells. Our data suggest that iron-containing macromolecules and organelles cannot effectively be degraded through the lysosomal pathway due to loss of WDR45 function.
Expression of Transcripts Selective for GABA Neuron Subpopulations across the Cortical Visuospatial Working Memory Network in the Healthy State and Schizophrenia
Authors: Tsubomoto Makoto , Kawabata Rika , Zhu Xiaonan , Minabe Yoshio , Chen Kehui , Lewis David A , Hashimoto Takanori
Published: August 2018

Visuospatial working memory (WM), which is impaired in schizophrenia, depends on a distributed network including visual, posterior parietal, and dorsolateral prefrontal cortical regions. Within each region, information processing is differentially regulated by subsets of γ-aminobutyric acid (GABA) neurons that express parvalbumin (PV), somatostatin (SST), or vasoactive intestinal peptide (VIP). In schizophrenia, WM impairments have been associated with alterations of PV and SST neurons in the dorsolateral prefrontal cortex. Here, we quantified transcripts selectively expressed in GABA neuron subsets across four cortical regions in the WM network from comparison and schizophrenia subjects. In comparison subjects, PV mRNA levels declined and SST mRNA levels increased from posterior to anterior regions, whereas VIP mRNA levels were comparable across regions except for the primary visual cortex (V1). In schizophrenia subjects, each transcript in PV and SST neurons exhibited similar alterations across all regions, whereas transcripts in VIP neurons were unaltered in any region except for V1. These findings suggest that the contribution of each GABA neuron subset to inhibitory regulation of local circuitry normally differs across cortical regions of the visuospatial WM network and that in schizophrenia alterations of PV and SST neurons are a shared feature across these regions, whereas VIP neurons are affected only in V1.
Trends in High-grade Cervical Lesions and Cervical Cancer Screening in 5 States, 2008–2015
Authors: Gargano Julia Warner , Park Ina U , Griffin Marie R , Niccolai Linda M , Powell Melissa , Bennett Nancy M , Johnson Jones Michelle L , Whitney Erin , Pemmaraju Manideepthi , Brackney Monica , Abdullah Nasreen , Scahill Mary , Dahl Rebecca M , Cleveland Angela A , Unger Elizabeth R , Markowitz Lauri E ,   HPV-IMPACT Working Group, Blankenship Sheelah , Allen Stephanie , Meek James , Higgins Kyle , Hadler James , Sosa Lynn , Saadeh Kayla , Williamson Ashley , Fink Deanna , Silverberg Michael J , Laing Robert , Schafer Sean , Oktapodas Marina , Felsen Christina
Published: August 2018

We describe trends in high-grade cervical lesions (CIN2+), identified through population-based surveillance in 2008–2015. In addition to changed screening recommendations, observed CIN2+ declines among screened women aged 18–24 years indicate a population-level impact of human papillomavirus vaccination.
Software application profile: mrrobust—a tool for performing two-sample summary Mendelian randomization analyses
Authors: Spiller Wes , Davies Neil M , Palmer Tom M
Published: August 2018

Motivation

In recent years, Mendelian randomization analysis using summary data from genome-wide association studies has become a popular approach for investigating causal relationships in epidemiology. The mrrobust Stata package implements several of the recently developed methods.

Implementation

mrrobust is freely available as a Stata package.

General features

The package includes inverse variance weighted estimation, as well as a range of median, modal and MR-Egger estimation methods. Using mrrobust, plots can be constructed visualizing each estimate either individually or simultaneously. The package also provides statistics such as IGX2, which are useful in assessing attenuation bias in causal estimates.

Availability

The software is freely available from GitHub [https://raw.github.com/remlapmot/mrrobust/master/].
On Domains Biholomorphic to Teichmüller Spaces
Authors: Gupta Subhojoy , Seshadri Harish
Published: August 2018

We prove that the Teichmüller space $\mathscr{T}$ of a closed surface of genus $g \ge 2$ cannot be biholomorphic to any domain which is locally strictly convex at some boundary point.
Shifted Symplectic Lie Algebroids
Authors: Pym Brent , Safronov Pavel
Published: August 2018

Shifted symplectic Lie and $L_{\infty }$ algebroids model formal neighborhoods of manifolds in shifted symplectic stacks and serve as target spaces for twisted variants of the classical topological field theory defined by Alexandrov--Kontsevich--Schwarz--Zaboronsky. In this paper, we classify zero-, one-, and two-shifted symplectic algebroids and their higher gauge symmetries, in terms of classical geometric “higher structures”, such as Courant algebroids twisted by $\Omega ^{2}$-gerbes. As applications, we produce new examples of twisted Courant algebroids from codimension-two cycles, and we give symplectic interpretations for several well-known features of higher structures (such as twists, Pontryagin classes, and tensor products). The proofs are valid in the $C^{\infty }$, holomorphic, and algebraic settings and are based on a number of technical results on the homotopy theory of $L_{\infty }$ algebroids and their differential forms, which may be of independent interest.
Macrophages in inflammation, repair and regeneration
Authors: Oishi Yumiko , Manabe Ichiro
Published: August 2018

Tissue injury triggers a complex series of cellular responses, starting from inflammation activated by tissue and cell damage and proceeding to healing. By clearing cell debris, activating and resolving inflammation and promoting fibrosis, macrophages play key roles in most, if not all, phases of the response to injury. Recent studies of the mechanisms underlying the initial inflammation and later tissue regeneration and repair revealed that macrophages bridge these processes in part by supporting and activating stem/progenitor cells, clearing damaged tissue, remodeling extracellular matrix to prepare scaffolding for regeneration and promoting angiogenesis. However, macrophages also have a central role in the development of pathology induced by failed resolution (e.g. chronic inflammation) and excessive scarring. In this review, we summarize the activities of macrophages in inflammation and healing in response to acute injury in tissues with differing regenerative capacities. While macrophages lead similar processes in response to tissue injury in these tissues, their priorities and the consequences of their activities differ among tissues. Moreover, the magnitude, nature and duration of injury also greatly affect cellular responses and healing processes. In particular, continuous injury and/or failed resolution of inflammation leads to chronic ailments in which macrophage activities may become detrimental.
Trading Old Masters in Florence 1890–1914: heritage protection and the Florentine art trade in Post-Unification Italy
Authors: Cappellini Patrizia
Published: August 2018

Between 1855 and 1873 many religious orders were abolished in Italy and the contents of convents, monasteries and churches found their way on to the art market. Meanwhile, economic troubles led many noble families to sell their estates, a situation that lasted until World War i. Focusing on the Florentine art market from 1890 to 1914, this paper seeks to shed new light on the roles of some Florentine merchants and their relationships with British antique dealers and German patrons and scholars (such as Wilhelm von Bode). It also reviews the evidence – anecdotal, archival and published – relating to the dealers in question.
Reliability of Oncology Value Framework Outputs: Concordance Between Independent Research Groups
Authors: Del Paggio Joseph C , Cheng Sierra , Booth Christopher M , Cheung Matthew C , Chan Kelvin K W
Published: August 2018

Research groups are increasingly utilizing value frameworks, but little is known of their reliability. To assess framework concordance and interrater reliability between two major value frameworks currently in use, we identified all previously published datasets containing both scores from the American Society of Clinical Oncology Value Framework (ASCO-VF) and grades from the European Society for Medical Oncology-Magnitude of Clinical Benefit Scale (ESMO-MCBS). The intraclass correlation coefficient (ICC) was used to assess interrater reliability. Four eligible studies contained drugs evaluated by both value frameworks, resulting in a dataset of 39 grades/scores for discrete drug indications. ICC was 0.82 (95% confidence interval = 0.70 to 0.90) for ASCO-VF and 0.88 (95% confidence interval = 0.80 to 0.93) for ESMO-MCBS. Absolute concordance was found to be 5% for ASCO-VF and 44% for ESMO-MCBS, increasing to 74% and 80% when deviations within 20 points and 1 grade were considered, respectively. Interrater reliability of ASCO-VF and ESMO-MCBS is, therefore, near perfect, while absolute concordance is poor. This has implications when considering framework outputs in drug funding or treatment decision making.
The black hole fundamental plane in low-excitation radio galaxies
Authors: Li Shuang-Liang , Gu Minfeng
Published: August 2018

The radio–X-ray slope in the fundamental plane of radio-loud active galactic nuclei (AGNs) has been found to be steeper than that of radio-quiet AGNs in previous studies. In this paper, we reinvestigate the fundamental plane in radio-loud AGNs by compiling a sample of 13 low-excitation radio galaxies (LERGs) from the 3CR radio galaxies, for the reason that the accretion mode in LERGs is believed to be a radiatively inefficient accretion flow. All the sources in our sample have data available both at the 5-GHz core radio luminosity as detected by VLA/VLBI/VLBA and at the core X-ray luminosity as detected by Chandra/XMM–Newton. Surprisingly, we find that the slope in the fundamental plane (logLR = 0.52log LX + 0.84log MBH + 10.84) of LERGs is consistent with that reported by Merloni et al. However, the normalization is found to be shifted by about 0.7 dex, which could be due to the difference in the magnetic field strength in different objects. A shallower slope of the LR−LX relationship ($L_{\rm R}\sim L_{\rm X}^{0.63}$) is also found for our sample, which demonstrates that the X-ray emission in LERGs may come from the accretion disc, rather than jets suggested by previous works.
An Experimental Feasibility Study of a Hybrid Telephone Counseling/Text Messaging Intervention for Post-Discharge Cessation Support Among Hospitalized Smokers in Brazil
Authors: Cruvinel Erica , Richter Kimber P , Colugnati Fernando , Ronzani Telmo Mota
Published: August 2018

Objective

Text messaging interventions are effective. Despite high utilization of smartphones, few studies evaluate text messaging for cessation in middle-/lower-income countries. Initiating tobacco treatment in hospitals is an effective but underutilized approach for reaching smokers. We evaluated a hybrid phone counseling/text messaging intervention for supporting cessation among hospitalized smokers in Brazil.

Methods

We used an experimental design to assess the feasibility and potential effect size of the intervention. Participants (N = 66) were recruited from a university hospital and randomized in a 2:1 ratio into TXT (one session of telephone counseling plus 2 weeks of text messaging; N = 44) or Standard Care control group (N = 22). Participants lost to follow-up were counted as smokers.

Results

Counselors sent 1186 texts, of which 924 (77.9%) were received by study participants. Participants rated the TXT content as “helpful” (80.4%) and the phone counseling length to be “just right” (95.1%). Although the study was not powered to evaluate abstinence rates, we did observe a higher prevalence of abstinence in the TXT compared to control group at both 1-month follow-up (25.0% vs. 9.1%) and 3-month follow-up (31.8% vs. 9.1%). Carbon monoxide-verified abstinence at month 3 was also higher in TXT (20.5% vs. 4.5%).

Conclusions

This hybrid telephone/text intervention should progress to full-scale effectiveness testing as it achieved favorable outcomes, was acceptable to participants, and was readily implemented. This type of intervention has strong potential for expanding the reach of hospital-initiated tobacco treatment in middle-/lower-income countries.

Implications

This study extends research on hospital-initiated smoking cessation by establishing the feasibility of a novel text-messaging approach for post-discharge follow-up. Text messaging is a low-cost alternative to proactive telephone counseling that could help overcome resource barriers in middle- and lower-income countries. This hybrid texting/counseling intervention identified smokers in hospitals, established rapport through a single telephone follow-up, and expanded acceptability and reach of later support by using text-messaging, which is free of charge in this and other low-income countries. The favorable cessation outcomes achieved by the hybrid intervention provide support for a fully powered effectiveness trial.