bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth-temperature-dependent coalescence determines structural phase of mist-chemical-vapor-deposition-grown SnO2 thin films
Authors: Kan Daisuke , Niwa Yasuyuki , Koganezawa Tomoyuki , Shimakawa Yuichi
Published: September 2018

We grew SnO2 thin films on (001) YSZ substrates by a mist chemical vapor deposition (mist CVD) method and investigated their structural properties by measuring synchrotron x-ray diffraction. We found that the structural phases of the films depend on the growth temperature. SnO2 deposited at 400 °C was found to be epitaxially grown on the substrate and to have the high-pressure-stabilized structure [i.e., columbite structure with the (100)-orientation]. On the other hand, films deposited at 700 °C have a mixture of the epitaxially grown columbite structure and a polycrystalline rutile structure. We also found that while films deposited at both temperatures are grown in island-growth manners, the size of the islands in the initial stage of growth depends on the growth temperature. The islands of the films grown at 400 °C have diameters of 59 nm ± 10 nm, while the islands of the films grown at 700 °C have diameters 2 times larger (110 nm ± 16 nm). These observations indicate that the coalescence of the deposited mist particles resulting from the higher temperature growth, which makes the island larger, leads to partial relaxation of the substrate-induced strain. This explains why the films deposited at 700 °C consist of a mixture of the columbite and rutile structures. Our results highlight the significance of the growth-temperature-dependent coalescence and its induced strain relaxation as the factor determining the structural phase of mist-CVD-grown films.
Towards hybrid density functional calculations of molecular crystals via fragment-based methods
Authors: Loboda Oleksandr A. , Dolgonos Grygoriy A. , Boese A. Daniel
Published: September 2018

We introduce and employ two QM:QM schemes (a quantum mechanical method embedded into another quantum mechanical method) and report their performance for the X23 set of molecular crystals. We furthermore present the theory to calculate the stress tensors necessary for the computation of optimized cell volumes of molecular crystals and compare all results to those obtained with various density functionals and more approximate methods. Our QM:QM calculations with PBE0:PBE+D3, PBE0:PBE+MBD, and B3LYP:BLYP+D3 yield at a reduced computational cost lattice energy errors close to the ones of the parent hybrid density functional method, whereas for cell volumes, the errors of the QM:QM scheme methods are in between the generalized gradient approximation and hybrid functionals.
Focal spot characteristics of Thomson scattering x-ray sources
Authors: Chi Zhijun , Du Yingchao , Huang Wenhui , Tang Chuanxiang
Published: September 2018

With the recent rapid development of x-ray imaging using Thomson scattering x-ray sources, there is an increasing demand for knowledge of the focal spot characteristics of this type of light source. This is because imaging quality is closely related to focal spot characteristics. In this paper, an analytical expression of the focal spot size and beam parameters at arbitrary interaction angles is derived. Based on this, the focal spot can be optimized in a straightforward manner by adjusting the laser and electron focusing at a fixed interaction geometry. As the beam focusing increases, a smaller focal spot and a higher photon yield are obtained, while the bandwidth of scattered x rays deteriorates, leading to a compromise of the above three physical parameters. Considering the beam position and time fluctuations, the focal spot will be broadened and the photon yield will be reduced. Using typical beam parameters at the Tsinghua Thomson scattering x-ray source, it is shown that a micrometer-sized focal spot can be easily achieved. The results will help one to develop the x-ray imaging field, especially in micro-computed tomography applications based on Thomson light sources.
Effects of weak planetary rotation on the stability and dynamics of internal stratified jets
Authors: Radko Timour , Lorfeld David
Published: September 2018

This study explores the stability characteristics and nonlinear evolution of internal jets in rotating stratified fluids using a combination of direct numerical simulations and linear instability analyses. Our ultimate goal is the assessment of the potential impact of the Earth’s rotation on relatively small-scale structures, exemplified by turbulent wakes generated by propagating bluff objects in the ocean. We question the popular notion that ascribes a secondary role to the Coriolis effects in large Rossby number (Ro) systems. It is shown that the Earth’s rotation can substantially influence circulation patterns with Rossby numbers as high as Ro ∼ 103. Therefore, such effects must be taken into account in the numerical and theoretical models of finescale (∼10–100 m) processes in the ocean. We present a series of examples in which planetary rotation controls flows with large but finite values of Ro through centrifugal destabilization. These calculations reveal that centrifugal instabilities can affect fluid motion either directly, by modifying the basic state, or indirectly, by preferentially eliminating anticyclonic coherent vortices that form in the course of dynamic destabilization of jets. The results of this study have potentially significant geophysical implications in terms of elucidating mechanisms of energy cascade to progressively smaller scales. In the naval context, we anticipate that our investigation could influence the development of algorithms for detection and analysis of late wakes, generated by propagating submersibles in the ocean.
Letter: Hydroelastic interactions between water waves and floating freshwater ice
Authors: Dolatshah A. , Nelli F. , Bennetts L. G. , Alberello A. , Meylan M. H. , Monty J. P. , Toffoli A.
Published: September 2018

Hydroelastic interactions between regular water waves and floating freshwater ice are investigated using laboratory experiments for a range of incident wave periods and steepnesses. It is shown that only incident waves with sufficiently long period and large steepness break up the ice cover and that the extent of breakup increases with increasing period and steepness. Furthermore, it is shown that an increasing proportion of the incident wave propagates through the ice-covered water as the period and steepness increase, indicating the existence of a positive feedback loop between the ice breakup and increased wave propagation.
Zn-doped PbO nanoparticles (NPs)/fluorine-doped tin oxide (FTO) as photoanode for enhancement of visible-near-infrared (NIR) broad spectral photocurrent application of narrow bandgap nanostructures: SnSe NPs as a case study
Authors: Azarang Majid , Aliahmad Mousa , Ghorban Shiravizadeh A. , Azimi H. R. , Yousefi Ramin
Published: September 2018

The capability of undoped and Zn-doped PbO nanoparticles (NPs) with different Zn concentrations, which were deposited on fluorine-doped tin oxide (FTO) glass, as a photoanode of the photocurrent device based on SnSe NPs, was investigated. An X-ray diffraction pattern of undoped PbO NPs indicated a mixture phase of orthorhombic, tetragonal phases of PbO, and a monoclinic phase of Pb2O3, while Zn-doped PbO NP samples showed a single orthorhombic phase of PbO, and these results were confirmed by Raman spectra results. Room temperature photoluminescence (PL) spectroscopy results of undoped and Zn(2%)-doped PbO NPs showed two emissions in the violet and red regions that belonged to the bandgap and defect, respectively. In addition, PL results indicated an extra emission for the Zn-doped PbO NPs in the green region by increasing Zn concentrations up to 4% and 6%. However, the red emission intensity was reduced by increasing Zn concentrations. Finally, undoped and Zn-doped PbO NPs with FTO glasses were used as photoanodes to measure the photocurrent response of SnSe NPs in the visible and near-infrared (NIR) regions, and the results were compared with FTO/TiO2 as a photoanode, which has been typically used as photoanodes in quantum dot solar cells and dye-sensitized solar cells. It was observed that undoped and Zn-doped PbO NPs caused enhancement of photocurrent performance of the device. However, the responsivity of the device with FTO/Zn(2%)-doped PbO/ under NIR illumination source was higher than the responsivity of other devices under the same illumination source.
Hardware approach enables significantly faster training of deep neural networks
Authors: DeJarnette Drew
Published: September 2018

Phase change memory is used in cross-bar arrays to massively parallelize the computation required to train fully connected, multinode neural networks, by encoding the weights into multiple resistive memory devices.
Intraparticle charge delocalization through conjugated metal-ligand interfacial bonds: Effects of metal d electrons
Authors: Peng Yi , Hirata Eduardo Y. , Pan Wanzhang , Chen Limei , Lu Jia En , Chen Shaowei
Published: September 2018

Intraparticle charge delocalization occurs when metal nanoparticles are functionalized with organic capping ligands through conjugated metal-ligand interfacial bonds. In this study, metal nanoparticles of 5d metals (Ir, Pt, and Au) and 4d metals (Ru, Rh, and Pd) were prepared and capped with ethynylphenylacetylene and the impacts of the number of metal d electrons on the nanoparticle optoelectronic properties were examined. Both FTIR and photoluminescence measurements indicate that intraparticle charge delocalization was enhanced with the increase of the number of d electrons in the same period with palladium being an exception.
H2 dissociation by Au1-doped closed-shell titanium oxide cluster anions
Authors: Jiang Li-xue , Li Xiao-na , Li Zi-yu , Li Hai-fang , He Sheng-gui
Published: September 2018

Dissociation of molecular hydrogen (H2) is extensively studied to understand the mechanism of hydrogenation reactions. In this study, H2 dissociation by Au1-doped closed-shell titanium oxide cluster anions AuTi3O7− and AuTi3O8− has been identified by mass spectrometry and quantum chemistry calculations. The clusters were generated by laser ablation and mass-selected to react with H2 in an ion trap reactor. In the reaction of AuTi3O8− with H2, the ion pair Au+−O22− rather than Au+−O2− is the active site to promote H2 dissociation. This finding is in contrast with the previous result that the lattice oxygen is usually the reactive oxygen species in H2 dissociation. The higher reactivity of the peroxide species is further supported by frontier molecular orbital analysis. This study provides new insights into gold catalysis involving H2 activation and dissociation.
High-Order harmonic generation of aligned acetylene in elliptically polarized strong laser fields
Authors: Liang Hong-jing , Wang Qiao-xia , Fan Xin , Shan Li-yu , Feng Shuang , Yan Bing , Ma Ri , Xu Hai-feng
Published: September 2018

We perform an experimental study on high-order harmonic generation (HHG) of aligned acetylene molecules induced by a 35-fs 800-nm strong laser field, by using a home-built HHG spectrometer. It is observed that the molecular HHG probability declines with increasing the laser ellipticity, which is in consistence with the deduction from the well-known tunneling-plus-rescattering scenario. By introducing a weak femtosecond laser pulse to non-adiabatically align the molecules, we investigated the molecular orbital effect on the HHG in both linearly and elliptically polarized driving laser fields. The results show that the harmonic intensity is maximum for the molecular axis aligned perpendicularly to the laser electric field. It indicates that both the highest occupied molecular orbitals (HOMO) and HOMO-1 contribute to the strong-field HHG of acetylene molecules. Our study should pave the way for understanding the interaction of molecules with ultrafast strong laser fields.
Average arrival time: An alternative approach for studying fluorescent behavior of single quantum dots
Authors: Sun Yong-lei , Zhao Jing
Published: September 2018

Due to photoluminescence intermittency of single colloidal quantum dots (QDs), the traditional exponential fluorescence lifetime analysis is not perfect to characterize QDs’ fluorescent emission behavior. In this work we used the time-tagged time-resolved (TTTR) mode to record the fluorescent photons from single QDs. We showed that this method is compatible with the traditional lifetime analysis. In addition, by constructing the trajectory over time and the distribution of average arrival time (AAT) of the fluorescent photons, more details about the emission behavior of QDs were revealed.
A hierarchical-equation-of-motion based semiclassical approach to quantum dissipation
Authors: Xu Rui-xue , Tao Xue-cheng , Wang Yao , Liu Yang , Zhang Hou-dao , Yan YiJing
Published: September 2018

We present a semiclassical (SC) approach for quantum dissipative dynamics, constructed on basis of the hierarchical-equation-of-motion (HEOM) formalism. The dynamical components considered in the developed SC-HEOM are wavepackets’ phase-space moments of not only the primary reduced system density operator but also the auxiliary density operators (ADOs) of HEOM. It is a highly numerically efficient method, meanwhile taking into account the high-order effects of system-bath couplings. The SC-HEOM methodology is exemplified in this work on the hierarchical quantum master equation [J. Chem. Phys. 131, 214111 (2009)] and numerically demonstrated on linear spectra of anharmonic oscillators.
Effect of Lactobacillus plantarum and Lactobacillus buchneri addition on fermentation, bacterial community and aerobic stability in lucerne silage
Authors: Si Huazhe , Liu Hanlu , Li Zhipeng , Nan Weixiao , Jin Chunai , Sui Yutong , Li Guangyu
Published: September 2018

Changes in the microbial community are closely related to the fermentation of silage. However, how host genetic variation shapes the community structure of the silage microbiota and its metabolic phenotype is poorly understood. The objective of present study was to evaluate the effects of the application of the homo-fermentative Lactobacillus plantarum and hetero-fermentative Lactobacillus buchneri strains to lucerne silage on the fermentation characteristics, aerobic stability, and microbial community and their correlations. The three silages treated with L. plantarum or L. buchneri were well preserved and had significantly lower pH values, butyric acid, propionic acid, and ammonia-N concentrations, and significantly higher residual water-soluble carbohydrate, dry matter and lactic acid contents than the controls. The treated groups had more lactic acid bacteria and lower quantities of other bacteria in their microbial communities. Inoculation of lactic acid bacteria influenced the abundances of other bacteria and controlled the silage fermentation characteristics. L. buchneri inhibited the abundance of Enterobacter_ludwigii to increase the crude protein content, L. plantarum improve the neutral detergent fibre content by affecting the abundance of Arthrobacter_sp._Ens13. In conclusion, the application of L. plantarum and L. buchneri improved the quality of lucerne silage fermentation, and L. buchneri resulted in greater improvements after aerobic exposure.
Reservoir provides cool-water refuge for adult Chinook salmon in a trap-and-haul reintroduction program
Authors: Naughton George P. , Keefer Matthew L. , Clabough Tami S. , Knoff Matthew J. , Blubaugh Timothy J. , Sharpe Cameron , Caudill Christopher C.
Published: September 2018

Trap-and-haul is a mitigation strategy at many hydropower dams lacking upstream fish-passage facilities, and protocols are needed to maximise its effectiveness. We used biotelemetry to assess the potential benefits of releasing transported adult Chinook salmon (Oncorhynchus tshawytscha) into a cold-water reservoir v. a relatively warm-water tributary before spawning. Over 5 years, we released 160 salmon into Foster Reservoir (Oregon, USA) and another 102 into the South Santiam River near historical salmon spawning areas further upstream. In total, 70% of reservoir-released salmon entered an upriver tributary after spending a median of 3–95 days annually in the reservoir. Data recovered from 61 archival temperature loggers indicated that salmon were ~3–6°C cooler per day in the reservoir than in the river. We estimated that cumulative exposure of reservoir-released fish was reduced by 64 degree days, on average (range=–129 to 392), relative to river-released fish. Release into the reservoir was not risk free; 14% of all reservoir-released fish fell back downstream v. 1% of river-released fish. We conclude that reduced transport distance, reduced thermal exposure and potential survival benefits of releasing salmon into reservoirs should be weighed against risks of factors such as fallback and homing errors.
Evolution of a pre-exposure prophylaxis (PrEP) service in a community-located sexual health clinic: concise report of the PrEPxpress
Authors: Girometti Nicolo , McCormack Sheena , Devitt Emma , Gedela Keerti , Nwokolo Nneka , Patel Sheel , Suchak Tara , McOwan Alan , Whitlock Gary
Published: September 2018

Screening and treatment of sexually transmissible infections, including HIV, are free in the UK nations; pre-exposure prophylaxis (PrEP) became free in England in October 2017 through the PrEP Impact trial. Doctor-led PrEP clinics started at 56 Dean Street in September 2015, with the drug purchased privately at full price. The service was expanded to other staff to support initiation and monitoring of increasing numbers of attendees purchasing PrEP from online pharmacies. Nonetheless, when the clinic was given a target of 1700 for the PrEP Impact trial, it was clear this could not be achieved in a timely manner through 56 Dean Street alone. To prepare for the trial, all staff with HIV testing competencies were trained in good clinical practice and trial-specific procedures, and a patient group directive was approved to facilitate nurse prescribing and dispensing. Electronic pro formas to capture eligibility for starting or continuing PrEP were adapted for the Dean Street Express clinic, with some information collected directly from service users using touch screens. These interventions, together with an update to the 2016 information leaflet developed by the community, enabled enrolment and follow-up of 1700 participants in 4 months. PrEP advice and monitoring were easily accommodated in the 56 Dean Street sexual health service, but did require additional training and approval for nurse prescribing and dispensing drug in order to achieve the target, which still fell short of the demand.
Cost and anonymity as factors for the effective implementation of pre-exposure prophylaxis: an observational study among gay, bisexual and other men who have sex with men in Singapore
Authors: Tan Rayner Kay Jin , Teo Alvin Kuo Jing , Kaur Nashwinder , Harrison-Quintana Jack , I-Cheng Chen Mark , Wong Chen Seong
Published: September 2018

Background
HIV pre-exposure prophylaxis (PrEP) is currently offered by several public and private clinics at unsubsidised prices in Singapore, but to date, no information is available on the effect of these services. This study sought to assess the knowledge and uptake of, and willingness to use PrEP among gay, bisexual and other men who have sex with men (GBMSM) in Singapore. Methods: Recruitment was conducted through Grindr®, a geosocial networking application for GBMSM. Results were quantitatively analysed through descriptive statistics and multivariate Poisson regression models, while open-ended responses were qualitatively coded and categorised. Results: Of the 1339 participants who responded, 1098 participants who indicated their knowledge and use of PrEP were included in the analytic sample. Overall, 15.0% (n=154) had taken PrEP, 66.2% (n=678) had heard of but not taken PrEP, while 18.8% (n=193) had never heard of PrEP. Of those who had ever taken PrEP, 59.6% (n=90) had obtained PrEP from overseas or other unofficial sources. Of those who had heard of but never taken PrEP, 73.3% (n=486) reported that they would consider taking PrEP. Those who had taken PrEP were older and had higher educational attainment. Conclusions: The gap between the willingness to use PrEP and its uptake may be attributed to the cost of PrEP and issues of anonymity at healthcare settings in Singapore. National financing schemes are needed to expand access to PrEP if it is to make a meaningful effect to the Singapore HIV/AIDS response.
Environmental catastrophes and mitigation policies in a multiregion world
Authors: Besley Timothy , Dixit Avinash
Published: September 2018

In this paper we present a simple model for assessing the willingness to pay for reductions in the risk associated with catastrophic climate change. The model is extremely tractable and applies to a multiregion world but with global externalities and has five key features: (
i
) Neither the occurrence nor the costs of a catastrophic event in any one year are precisely predictable; (
ii
) the probability of a catastrophe occurring in any one year increases as the levels of greenhouse gases in the atmosphere increase; (
iii
) greenhouse gases are a worldwide public bad with emissions from any one country or region increasing the risks for all; (
iv
) there is two-sided irreversibility; if nothing is done and the problem proves serious, the climate, economic activity, and human life will suffer permanent damage, but if we spend large sums on countermeasures and the problem turns out to be minor or even nonexistent, we will have wasted resources unnecessarily; and (
v
) technological progress may yield partial or even complete solutions. The framework that we propose can give a sense of the quantitative significance of mitigation strategies. We illustrate these for a core set of parameter values.
Structural evidence for the roles of divalent cations in actin polymerization and activation of ATP hydrolysis
Authors: Scipion Clement P. M. , Ghoshdastider Umesh , Ferrer Fernando J. , Yuen Tsz-Ying , Wongsantichon Jantana , Robinson Robert C.
Published: September 2018

Significance

Actin polymerization is a divalent cation-dependent process. Here we identify a cation binding site on the surface of actin in a 2.0-Å resolution X-ray structure of actin and find evidence of three additional sites in published high-resolution structures. These cations are stable in molecular dynamics (MD) simulations of the filament, suggesting a functional role in polymerization or filament rigidity. Polymerization activates the ATPase activity of the incorporating actin protomers. Careful analysis of water molecules that approach the ATP in the MD simulations revealed Gln137-activated water to be in a suitable position in F-actin, to initiate attack for ATP hydrolysis, and its occupancy was dependent on bound cations.
RMTL: an R library for multi-task learning
Authors: Cao Han , Zhou Jiayu , Schwarz Emanuel
Published: September 2018

Motivation

Multi-task learning (MTL) is a machine learning technique for simultaneous learning of multiple related classification or regression tasks. Despite its increasing popularity, MTL algorithms are currently not available in the widely used software environment R, creating a bottleneck for their application in biomedical research.

Results

We developed an efficient, easy-to-use R library for MTL (www.r-project.org) comprising 10 algorithms applicable for regression, classification, joint predictor selection, task clustering, low-rank learning and incorporation of biological networks. We demonstrate the utility of the algorithms using simulated data.

Availability and implementation

The RMTL package is an open source R package and is freely available at https://github.com/transbioZI/RMTL. RMTL will also be available on cran.r-project.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT
Authors: Crisan Anamaria , Gardy Jennifer L , Munzner Tamara
Published: September 2018

Motivation

Data visualization is an important tool for exploring and communicating findings from genomic and healthcare datasets. Yet, without a systematic way of organizing and describing the design space of data visualizations, researchers may not be aware of the breadth of possible visualization design choices or how to distinguish between good and bad options.

Results

We have developed a method that systematically surveys data visualizations using the analysis of both text and images. Our method supports the construction of a visualization design space that is explorable along two axes: why the visualization was created and how it was constructed. We applied our method to a corpus of scientific research articles from infectious disease genomic epidemiology and derived a Genomic Epidemiology Visualization Typology (GEViT) that describes how visualizations were created from a series of chart types, combinations and enhancements. We have also implemented an online gallery that allows others to explore our resulting design space of visualizations. Our results have important implications for visualization design and for researchers intending to develop or use data visualization tools. Finally, the method that we introduce is extensible to constructing visualizations design spaces across other research areas.

Availability and implementation

Our browsable gallery is available at http://gevit.net and all project code can be found at https://github.com/amcrisan/gevitAnalysisRelease.

Supplementary information

Supplementary data are available at Bioinformatics online.
Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis
Authors: Gong Gaorui , Dan Cheng , Xiao Shijun , Guo Wenjie , Huang Peipei , Xiong Yang , Wu Junjie , He Yan , Zhang Jicheng , Li Xiaohui , Chen Nansheng , Gui Jian-Fang , Mei Jie
Published: September 2018

Background

The yellow catfish, Pelteobagrus fulvidraco, belonging to the Siluriformes order, is an economically important freshwater aquaculture fish species in Asia, especially in Southern China. The aquaculture industry has recently been facing tremendous challenges in germplasm degeneration and poor disease resistance. As the yellow catfish exhibits notable sex dimorphism in growth, with adult males about two- to three-fold bigger than females, the way in which the aquaculture industry takes advantage of such sex dimorphism is another challenge. To address these issues, a high-quality reference genome of the yellow catfish would be a very useful resource.

Findings

To construct a high-quality reference genome for the yellow catfish, we generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and Pacific Biosciences (PacBio) sequencing platforms, respectively. The sequencing data were assembled into a 732.8 Mb genome assembly with a contig N50 length of 1.1 Mb. Additionally, we applied Hi-C technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with 26 chromosomes and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding genes annotated in the yellow catfish genome, the phylogenetic relationships of the yellow catfish with other teleosts showed that yellow catfish separated from the common ancestor of channel catfish ~81.9 million years ago. We identified 1,717 gene families to be expanded in the yellow catfish, and those gene families are mainly enriched in the immune system, signal transduction, glycosphingolipid biosynthesis, and fatty acid biosynthesis.

Conclusions

Taking advantage of Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level genome assembly for the yellow catfish P. fulvidraco. The genomic resources generated in this work not only offer a valuable reference genome for functional genomics studies of yellow catfish to decipher the economic traits and sex determination but also provide important chromosome information for genome comparisons in the wider evolutionary research community.
Cardiomyopathy and altered integrin-actin signaling in Fhl1 mutant female mice
Authors: Kubota Akatsuki , Juanola-Falgarona Martí , Emmanuele Valentina , Sanchez-Quintero Maria Jose , Kariya Shingo , Sera Fusako , Homma Shunichi , Tanji Kurenai , Quinzii Catarina M , Hirano Michio
Published: September 2018

X-linked scapuloperoneal myopathy (X-SM), one of Four-and-a-half LIM 1 (FHL1) related diseases, is an adult-onset slowly progressive myopathy, often associated with cardiomyopathy. We previously generated a knock-in mouse model that has the same mutation (c.365 G > C, p.W122S) as human X-SM patients. The mutant male mouse developed late-onset slowly progressive myopathy without cardiomyopathy. In this study, we observed that heterozygous (Het) and homozygous (Homo) female mice did not show alterations of skeletal muscle function or histology. In contrast, 20-month-old mutant female mice showed signs of cardiomyopathy on echocardiograms with increased systolic diameter [wild-type (WT): 2.74 ± 0.22 mm, mean ± standard deviation (SD); Het: 3.13 ± 0.11 mm, P < 0.01; Homo: 3.08 ± 0.37 mm, P < 0.05) and lower fractional shortening (WT: 31.1 ± 4.4%, mean ± SD; Het: 22.7 ± 2.5%, P < 0.01; Homo: 22.4 ± 6.9%, P < 0.01]. Histological analysis of cardiac muscle revealed frequent extraordinarily large rectangular nuclei in mutant female mice that were also observed in human cardiac muscle from X-SM patients. Western blot demonstrated decreased Fhl1 protein levels in cardiac muscle, but not in skeletal muscle, of Homo mutant female mice. Proteomic analysis of cardiac muscle from 20-month-old Homo mutant female mice indicated abnormalities of the integrin signaling pathway (ISP) in association with cardiac dysfunction. The ISP dysregulation was further supported by altered levels of a subunit of the ISP downstream effectors Arpc1a in Fhl1 mutant mice and ARPC1A in X-SM patient muscles. This study reveals the first mouse model of FHL1-related cardiomyopathy and implicates ISP dysregulation in the pathogenesis of FHL1 myopathy.
Extended experimental study on PSO with partial population restart based on complex network analysis
Authors: Pluhacek Michal , Viktorin Adam , Senkerik Roman , Kadavy Tomas , Zelinka Ivan
Published: September 2018

This extended study presents a hybridization of particle swarm optimization (PSO) with complex network construction and analysis. A partial population restart is performed in certain moments of the run of the algorithm based on the information obtained from a complex network analysis. The complex network structure represents the communication in the population. We present experimental results of the method alongside with statistical evaluation and discuss future possibilities of this approach. The main goal of the work is not to propose a new highly competitive PSO variant but to present the possibility of using the unconventional tool as an alternative to conventional diversity measures. The main benefit of the network analysis is that it has same-time requirements regardless of the dimension of the problem.
Margaret Cavendish
Authors: Boyle Deborah
Published: September 2018

Margaret Cavendish, Duchess of Newcastle (b.1623–d. 1673), published at least six works of natural philosophy under her own name (the number depends on how one counts various second editions she published). Her prolific output also included poems, plays, essays, speeches, stories, science fiction, and letters to fictional correspondents. Despite Cavendish’s own desire for fame, her reputation suffered at the hands of readers and biographers who dismissed her philosophical writings without giving them any serious consideration. However, interest in Cavendish’s philosophical theories has increased exponentially since the 1980s. Much of the secondary literature published in the 1980s and 1990s aimed to dispel the idea that Cavendish is not worthy of study and to establish both that Cavendish’s writings were informed by her careful readings of the work of her contemporaries and that Cavendish’s own philosophical thinking consisted of a detailed, internally consistent alternative to the mechanistic natural philosophy embraced by many of those contemporaries. Now, fortunately, scholars do not feel the need to justify their study of Cavendish. Secondary literature published since the early 2000s on Cavendish’s philosophical work starts from the assumptions that studying Cavendish’s works enriches our understanding of the landscape of 17th-century philosophy and that the details of Cavendish’s views are inherently worth analyzing. The secondary literature on Cavendish is now extensive and comes from many disciplines—English literature, philosophy, history, history of science, political science, and cultural studies, among others—and, accordingly, draws on a variety of methodological approaches. This article focuses on Cavendish’s philosophical views and includes secondary literature that is based on close textual analysis and sensitivity to the historical and philosophical contexts in which Cavendish was writing. Works are divided into the following sections: Primary Sources, Modern Editions, Digital Scholarship, Biographies, Overviews, Anthologies, Epistemology, Mathematics, Medicine, Natural Philosophy, Political and Social Philosophy, Religion and Theology, and Rhetorical Style.
Pastoralism in the Andes
Authors: Dransart Penelope
Published: September 2018

The topic considered in this bibliography has emerged fairly recently. Pastoralism is a subsistence economy in which people keep large herds of animals, and it is based on the extensive use of pasture grounds. Instead of growing fodder to feed their herds, pastoralists usually take them to different pastures to which they have access. Seasonal mobility is a fundamental aspect of most pastoralist societies. For much of the 20th century, some authors dogmatically proclaimed that pastoralism existed in Eurasia, in various parts of the African continent, and in the sub-Arctic, but not in the Americas. They argued that the introduction of sheep to the Navajo in North America enabled some native people to become pastoralists. In 1908 Éric Boman mentioned herding communities at high altitude in Argentina and, in 1946 Bernard Mishkin remarked on herding communities in Peru, but these notices went unheeded (see Webster 1973, cited under Defining Pastoralism as a Way of Life in the Andes). These mentions acquired significance in the 1960s, when Jorge Flores Ochoa (originally publishing in Spanish) and Horst Nachtigall (originally publishing in German) challenged the view that pastoralism was absent in the Andes. In a series of influential articles, the historian John V. Murra argued that independent pastoralist communities did not exist in the pre-Hispanic past because such communities would have formed part of a greater agrarian economy. Yet the emerging ethnographic evidence suggested there were people who had been specialist herders for considerable periods of time. Researchers therefore started to question how pastoralism arose. Did it have ancient, pre-Hispanic roots, or was the phenomenon recent, postdating the 16th-century arrival of Europeans? In the 1960s, authors did not have access to the findings more recently reported by archaeologists and archaeozoologists. The theme of “production pastorale et société” drew scholars together in France to tackle social aspects of pastoralist production, and some of them turned their attention toward the Andes. By 1969 French researchers had begun to collaborate on interdisciplinary field projects undertaken with counterparts from the United States, focusing on the Ayacucho basin and the Puna de Junín in Peru. From the 1970s onward, the study of pastoralism in the Andes rapidly acquired the multi- and interdisciplinary characteristics on which the selection of publications chosen for this bibliography is based. There is still a shortage of general overviews on pastoralism in the Andes; many of the publications included here restrict their coverage to a particular region and/or to specific aspects of pastoralism. The sections are therefore organized on a thematic basis. These themes intersect, however, and are not mutually exclusive.
Rithy Panh
Authors: Polmuk Chairat
Published: September 2018

Rithy Panh (b. 1964) is an internationally and critically acclaimed Cambodian filmmaker and screenwriter. A survivor of the genocidal Khmer Rouge regime (1975–1979), Panh spent a year at a refugee camp in Thailand and another ten years in France, where he attended the prestigious Institut des Hautes Études Cinématographiques (Institute for advanced cinematographic studies). Panh’s first documentary film Site 2 (1989) documents lives of his compatriots at the refugee camp at a Cambodian-Thai border area; it also marks the filmmaker’s return to Cambodia to confront the country’s past violence and its continuing impact on the present. The cinema of Rithy Panh is thus well known for its thematic emphasis on the traumatic experience of genocide, displacement, and exploitation. His fiction films such as Rice People (1994) and One Evening After the War (1998), as well as documentaries such as The Land of the Wandering Souls (2000) and People of Angkor (2003), showcase Pan’s sustained meditations on socioeconomic struggles in post-genocide Cambodia. During the past decades, Panh’s documentary practices and experimental aesthetics have rekindled critical attention to the complex relations between film and memory, visual representation and ethics, and media testimony and justice. His 2003 documentary film S–21: The Khmer Rouge Killing Machine, in which Khmer Rouge survivors reenact their memories at the notorious Tuol Sleng prison center (known by its code name S–21), has sparked scholarly debates regarding the method of reenactment in relation to trauma. The use of hand-carved clay figurines in his 2013 film The Missing Picture demonstrates another inventive feature of Panh’s documentary aesthetics. The film won Cannes’ Un Certain Regard award and was nominated for the Academy Award for Best Foreign Language Film. Panh’s transnational trajectory sheds light on the general context of postcolonial Southeast Asian cinema as well as the particular situation of the contemporary Cambodian film industry. In 2006, Panh co-founded the Bophana Audiovisual Resource Center in Phnom Penh, an archive of records from the Khmer Rouge period and beyond and a training center for a new generation of Cambodian filmmakers. The Bophana Center is named after Hout Bophana, a woman who was executed under the Pol Pot regime and who inspired Panh’s 1996 film Bophana: A Cambodian Tragedy. Panh has recently expanded his cinematic practices, serving as a co-producer of the Netflix adaptation of Loung Ung’s memoir about the Cambodian genocide, First They Killed My Father (dir. Angelina Jolie, 2017). Panh also curated the multimedia installation Exile, which accompanied his 2017 film by the same name, and directed a stage production, Bangsokol: A Requiem for Cambodia (2018).
Financial Markets in Organization Theory and Economic Sociology
Authors: Ferraro Fabrizio , Casasnovas Guillermo
Published: September 2018

As the organization theory field shifted its attention toward organizational relationships with the environment and market processes, scholars started to study directly financial markets and financial processes, leveraging existing theories (institutional theory, embeddedness, culture, status, social influence) and developing novel ones (categories, performativity). In doing so, their work increasingly converged with the theoretical and empirical interests of economic sociologists, and thus the following bibliography cover studies in both organization theory and economic sociology. Many of the studies listed below were primarily concerned with advancing a specific theoretical agenda, rather than explaining financial markets per se, but in this bibliography we organized them to better appreciate how these findings can collectively further our understanding of financial markets, and their impact on corporations and society. In defining the scope of this bibliography, we included articles published both in sociology and management journals but did not review the vast literature published in economics, finance, and accounting. In terms of topics, we included studies focused on the financial sector, but excluded studies of bank lending, venture capital, and IPOs, as they were mostly focused on understanding these processes from the corporate perspective, rather than from the one of the financial sector and financial markets.
Local Elites in Song-Yuan China
Authors: Ong Chang Woei
Published: September 2018

The Song-Yuan period is part of the larger time frame that historians now call the “middle period” (roughly 8th–15th centuries). As compared to the two great and unified dynasties of Han and Tang that came before, the Song dynasty (960–1279) is often perceived to be a militarily weak regime that eventually fell prey to its stronger neighbors, including the Khitan Liao (916–1125), the Tangut Xi Xia (1038–1227), the Jurchen Jin (1115–1234), and finally the Mongol Yuan (1271–1368). We now know that such conventional view of Song military strength is misguided. Yet the Song was unique in its ability to institute a civil order based on the collective visions of the literati (shi士) class. In the Southern Song, the literati were leaders of the local society, often acting as the link between the state and the populace. Even after the establishment of the Yuan, many of these literati families survived and continued to thrive under the new Mongol regime. While new political circumstances may have altered their strategies, their commitments to building a local power base persisted. However, the literati class in the north was weak and local power was concentrated in the hands of non-literati groups, one of which was the religious elites. There, Buddhist monks and Daoist priests took on roles to direct and manage local affairs, tasks typically performed by the literati in the south. Historical sources from the 9th century onward also documented the growing importance of a group of militarized local strongmen known as tuhao土豪. While some of them had converted and assumed literati status and left their power base to pursue an official career, others continued to hold on to their local base. In late 12th and early 13th centuries, many of these local magnates in north China took advantage of the power vacuum at the local level created by the Mongol invasion and established semi-independent political domains that lasted for about half a century. This north-south divide in the elites’ local activism reveals deep-rooted regional variations in the middle period, which continued to shape late imperial Chinese society.
Minimally Invasive Transforaminal Interbody Fusion With Robotically Assisted Bilateral Pedicle Screw Fixation: 2-Dimensional Operative Video
Authors: Godzik Jakub , Walker Corey T , Theodore Nicholas , Uribe Juan S , Chang Steven W , Snyder Laura A
Published: September 2018

Minimally invasive surgery (MIS) techniques may enable faster patient recovery and reduce the incidence of postoperative infections. Image-guided approaches to spinal instrumentation and interbody fusion have gained popularity in MIS, reducing radiation exposure and improving screw placement accuracy. Use of a novel computed tomography (CT) navigation-based robotic arm provides for live image-guided surgery, with the potential for augmenting existing MIS approaches and improving the accuracy of instrumentation placement. We report on the surgical technique of MIS transforaminal lumbar interbody fusion (TLIF) performed with the assistance of a new robotic device (ExcelsiusGPS, Globus Medical Inc, Audubon, Pennsylvania) and intraoperative CT guidance in a patient with single-level lumbar spondylolisthesis. The patient gave written informed consent before treatment. Institutional review board approval was deemed unnecessary. The patient was positioned prone on the operating room table, and an intraoperative CT was obtained with stereotactic arrays placed bilaterally in the posterior superior iliac spine. Screw trajectories were planned using the ExcelsiusGPS software and placed percutaneously with the robotic arm without using a Kirschner wire. Interbody placement was performed via an expandable retractor after muscle dilation. Screw placement accuracy was determined with postoperative CT, which demonstrated good screw positioning without breach. The patient recovered well and was discharged home without complications. The combined use of the new robotic device and intraoperative CT enables accurate and safe fixation for the treatment of symptomatic lumbar spondylolisthesis. The operative video demonstrates the technical nuances of positioning, stereotactic marker placement, work flow, and screw placement.

Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Microsurgical Management of a Spinal Dural Arteriovenous Fistula With Shared Blood Supply to the Artery of Adamkiewicz: 3-Dimensional Operative Video
Authors: Cawley C Michael , Howard Brian M , Barrow Daniel L
Published: September 2018

The presented case is of a 65-yr-old gentleman referred for thoracic myelopathy. He developed bilateral, nondermatomal foot dysesthesia 14 mo prior to presentation, which progressed to numbness below the L3 level. He reported progressive gait instability, bilateral lower extremity weakness, and required a cane for ambulation. He subsequently developed urinary incontinence, while bowel function was spared. The neurological examination upon presentation revealed lower extremity strength was reduced to 4/5 in all major muscle groups bilaterally, while sensation and proprioception were reduced below the L3 level. Patellar and Achilles reflexes were not elicited and clonus was absent. Gait was unsteady and slow. The patient was not able to perform heel, toe and tandem gait. MRI revealed abnormal T2 hyper-intense signal and spinal cord expansion from T6 through the conus medullaris. Angiography revealed a dural arteriovenous fistula (dAVF) originating from the left T9 radicomedullary pedicle, which also supplied the Artery of Adamkiewicz (AoA). The patient underwent T8-10 laminectomies. Prior to disconnection of the fistula, an aneurysm clip was applied to the fistulous point and an indocyanine green video angiogram was completed to show that the fistula no longer opacified, but that the AoA remained patent, which was later confirmed with angiography. As of discharge, the patient's motor exam had improved substantially, though his sensory deficits persisted. This case demonstrates that surgical disconnection is requisite in the treatment of spinal dAVF that have a shared blood supply with the AoA, as embolization risks spinal cord infarction.

 The patient consented to presentation of this case in a de-identified fashion.