bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress modulation in desiccating crack networks for producing effective templates for patterning metal network based transparent conductors
Authors: Kumar Ankush , Pujar Rajashekhar , Gupta Nikita , Tarafdar Sujata , Kulkarni Giridhar U.
Published: July 2017

A drying layer of a colloidal dispersion tends to produce cracks, often in a network, due to internal stress arising from the rearrangement of particles while the substrate adhesion resists such movements. The stress can be modulated using experimental agents such as electric field, humidity, and surface structuring. In this work, repeated wet-drying cycles of the cracking layer have been used as stress modulating agents taking an aqueous dispersion of acrylic resin nanoparticles as the colloidal layer, offering cracks with widths in the sub-ten micrometer range. With increasing wet-drying cycles, the colloidal layer is seen to develop higher crack density and connectivity, as well as a well-defined hierarchy of formation. Thus developed crack layers have been used as templates for depositing metals (Cu and Au) to realize fine metal wire meshes. The latter serve as transparent conductors with excellent optoelectronic properties.
Ab initio lifetime correction to scattering states for time-dependent electronic-structure calculations with incomplete basis sets
Authors: Coccia Emanuele , Assaraf Roland , Luppi Eleonora , Toulouse Julien
Published: July 2017

We propose a method for obtaining effective lifetimes of scattering electronic states for avoiding the artificial confinement of the wave function due to the use of incomplete basis sets in time-dependent electronic-structure calculations of atoms and molecules. In this method, using a fitting procedure, the lifetimes are extracted from the spatial asymptotic decay of the approximate scattering wave functions obtained with a given basis set. The method is based on a rigorous analysis of the complex-energy solutions of the Schrödinger equation. It gives lifetimes adapted to any given basis set without using any empirical parameters. The method can be considered as an ab initio version of the heuristic lifetime model of Klinkusch et al. [J. Chem. Phys. 131, 114304 (2009)]. The method is validated on H and He atoms using Gaussian-type basis sets for the calculation of high-harmonic-generation spectra.
Accurate acoustic power measurement for low-intensity focused ultrasound using focal axial vibration velocity
Authors: Tao Chenyang , Guo Gepu , Ma Qingyu , Tu Juan , Zhang Dong , Hu Jimin
Published: July 2017

Low-intensity focused ultrasound is a form of therapy that can have reversible acoustothermal effects on biological tissue, depending on the exposure parameters. The acoustic power (AP) should be chosen with caution for the sake of safety. To recover the energy of counteracted radial vibrations at the focal point, an accurate AP measurement method using the focal axial vibration velocity (FAVV) is proposed in explicit formulae and is demonstrated experimentally using a laser vibrometer. The experimental APs for two transducers agree well with theoretical calculations and numerical simulations, showing that AP is proportional to the square of the FAVV, with a fixed power gain determined by the physical parameters of the transducers. The favorable results suggest that the FAVV can be used as a valuable parameter for non-contact AP measurement, providing a new strategy for accurate power control for low-intensity focused ultrasound in biomedical engineering.
An energy harvesting bracelet
Authors: Wu Zhiyi , Tang Jianhong , Zhang Xin , Yu Zhicheng
Published: July 2017

An energy harvesting bracelet (EHB) based on two mutually exclusive circular motion permanent magnetic movers is demonstrated, which is able to capture energy through the natural motions of the wearer's wrist. The EHB can transform the translational motion in any orientation except the axial into the rotational motion of the movers, which passes through four coil transducers and induces significantly large electro-motive forces across the coils. A prototype EHB is shown to produce power that can charge a capacitor with 470 μF 25 V up to more than 0.81 V during at most 132 ms from any single excitations.
Mini-beam modes on standard MX beamline BL17U at SSRF
Authors: Wang Qisheng , Yu Feng , Cui Ying , Zhang Kunhao , Pan Qiangyan , Zhong Changyou , Liu Ke , Zhou Huan , Sun Bo , He Jianhua
Published: July 2017

The macromolecular crystallography beamlines at third-generation synchrotron facilities play a central role in solving macromolecular crystal structures and also in understanding the biological function at molecular levels. The MX beamline BL17U at Shanghai Synchrotron Radiation Facility is a typical standard MX beamline with a focused beam size (H × V) of FWHM around 80 μm × 45 μm. However the protein samples brought to the beamline are down to 5-10 m from the important and challenging science project now. These samples require smaller size beam. In order to achieve the mini-size beamline, two mini-beam modes have been developed on BL17U: the pinhole-based mini-beam and the focused mini-beam by compound refractive lens (CRL). Compared to the pinhole-based mode, three times increase in flux is obtained by the CRL mode at a similar beam size. The flux gain obtained by the CRL needs to be considered for data collection strategies. It takes few minutes to switch the beamline from the normal to CRL mini-beam mode.
Note: A high count rate real-time digital processing method for PGNAA data acquisition system
Authors: Liu Yuzhe , Chen Lian , Li Feng , Liang Futian , Jin Ge
Published: July 2017

The prompt gamma neutron activation analysis (PGNAA) technique is a real-time online method to analyze the composition of industrial materials. This paper presents a data acquisition system with a high count rate and real-time digital processing method for PGNAA. Limited by the decay time of the detector, the ORTEC multi-channel analyzer (MCA) can normally achieve an average count rate of 100 kcps. However, this system uses an electrical technique to increase the average count rate and reduce dead time, and guarantees good accuracy. Since the measuring time is usually limited to about 120 s, in order to accelerate the accumulation rate of spectrum and reduce the statistical error, the average count rate is expected to reach more than 500 kcps.
Bulk-mediated surface transport in the presence of bias
Authors: Berezhkovskii Alexander M. , Dagdug Leonardo , Bezrukov Sergey M.
Published: July 2017

Surface transport, when the particle is allowed to leave the surface, travel in the bulk for some time, and then return to the surface, is referred to as bulk-mediated surface transport. Recently, we proposed a formalism that significantly simplifies analysis of bulk-mediated surface diffusion [A. M. Berezhkovskii, L. Dagdug, and S. M. Bezrukov, J. Chem. Phys. 143, 084103 (2015)]. Here this formalism is extended to bulk-mediated surface transport in the presence of bias, i.e., when the particle has arbitrary drift velocities on the surface and in the bulk. A key advantage of our approach is that the transport problem reduces to that of a two-state problem of the particle transitions between the surface and the bulk. The latter can be solved with relative ease. The formalism is used to find the Laplace transforms of the first two moments of the particle displacement over the surface in time t at arbitrary values of the particle drift velocities and diffusivities on the surface and in the bulk. This allows us to analyze in detail the time dependence of the effective drift velocity of the particle on the surface, which can be highly nontrivial.
Effect of microwave annealing on electrical characteristics of TiN/Al/TiN/HfO2/Si MOS capacitors
Authors: Shih Tzu-Lang , Su Yin-Hsien , Kuo Tai-Chen , Lee Wen-Hsi , Current Michael Ira
Published: July 2017

In this letter, microwave annealing over a wide range of power (300–2700 W) in nitrogen ambient was performed on TiN/Al/TiN/HfO2/Si metal-oxide-semiconductor capacitors. Capacitors with rapid thermal annealing at 500 °C were also fabricated for comparison at the same wafer temperature measured during microwave annealing at 2700 W. For microwave annealed capacitors, key parameters such as equivalent oxide thickness, interface state density, oxide trapped charge, leakage current density, and breakdown voltage were all improved with increasing microwave annealing power. For the capacitor with rapid thermal annealing at 500 °C, diffusion of Al into TiN and growth of the interfacial oxide layer are detected, leading to the shift in flat-band voltage and increase in equivalent oxide thickness, respectively. The results further indicate that it is more effective to remove the charged traps by microwave annealing than by rapid thermal annealing, and the reduction in leakage current density after microwave annealing corresponds to the reduction in charge traps based on a trap-assisted tunneling model. With no trade-off relationship between the electrical characteristics and no undesired effect such as diffusion of species, microwave annealing demonstrates great potential for the post-metallization annealing process for the high-k/metal gate structure.
Imaging of potential gradient on platinum induced by hydrogen adsorption
Authors: Takahashi Yoshio , Kasai Hiroto , Usagawa Toshiyuki
Published: July 2017

The local gradient of electrostatic potential in the Pt gate of a Si-metal oxide semiconductor field effect transistor has been visualized using a phase reconstruction method with through-focus images of transmission electron microscopy based on the transport-of-intensity equation, which was quantitatively corrected by electron holography. The potential change by hydrogen adsorption in a specimen was detected by taking the difference between H2-adsorbed and H2-not-adsorbed phase images. We found that the potential gradient was localized at Pt interfaces and that the direction of the polarization was Pt inward. The direct visualization suggests that the potential gradient originated from hydrogen dipoles generated and located at the Pt interfaces.
Effects of deposition methods and processing techniques on band gap, interband electronic transitions, and optical absorption in perovskite CH3NH3PbI3 films
Authors: Li Wenwu , Sha Tingting , Wang Yan , Yu Wenlei , Jiang Kai , Zhou Hang , Liu Chuan , Hu Zhigao , Chu Junhao
Published: July 2017

Despite intensive studies on the improvements of conversion efficiencies in solar cells, many questions regarding the effects of deposition techniques on optical properties and electronic band structures of CH3NH3PbI3 (MAPbI3) remain unresolved. Here, perovskite MAPbI3 films were prepared using different deposition methods and processing techniques. The effects of deposition and processing parameters on dielectric functions and optical absorption were investigated by fitting the reflectance spectra in the photon energy range of 0.5–5.16 eV. It is found that the bandgap (Eg) of the films deposited by two-step spinning (1.591 eV) is larger than that prepared by evaporations (1.514 eV), due to different Pb-I orbital hybridization and spin-orbit coupling. Moreover, the Eg value of the films increases from 1.543 eV to 1.591 eV after toluene solution dripping. Five interband electronic transitions (Ep1, Ep2, Ep3, Ep4, and Ep5) are observed, and the origins of Ep2, Ep3, and Ep4 are assigned to the direct transitions between the highest valence band and the lowest lying conduction band at the R, M, and X symmetry points. Further, the transition energies of the films deposited by evaporation are less than those prepared by two-step spinning. The present results shed light on preparing more reliable and reproducible high performance MAPbI3-based solar cells.
Note: Novel trigger pulse feed method for mega-volt gas switch
Authors: Yin Jiahui , Sun Fengju , Jiang Xiaofeng , Wang Zhiguo , Liang Tianxue , Jiang Hongyu , Qiu Aici
Published: July 2017

It is difficult to feed the trigger pulse into an electrically triggered mega-volt switch, and the present note presents a novel trigger pulse feed method. The trigger pulse is introduced via a damping resistor, which is mounted between the inner and outer cylindrical electrodes of the pulse transmission line. The mega-volt pulse is damped because the voltage is resistively divided by the resistor and trigger cable arrangement. Both the complex breakdown processes of the switch and its insulation issues are experimentally studied. The function and the beneficial effects of the damping resistor, installed together with an additional inductor, are discussed. Finally, the parameters of these two damping components are set to 500 Ω and 2 μH values for which the switch has been demonstrated to work successfully at over 2.3 MV.
Carbon nanodots-based nanocomposites with enhanced photocatalytic performance and photothermal effects
Authors: Zhang J. , Tang Y. L. , Hu G. , Gao B. L. , Gan Z. X. , Chu P. K.
Published: July 2017

Carbon nanomaterials with variable bandgaps exhibit wide spectral absorption, and photoluminescent nanodots have attracted much interest. In this work, carbon nanodots (CNDs) are grafted onto the surface of TiO2 nanotubes to enhance the photocatalytic properties. The CNDs increase light absorption, trap and shuttle photo-generated electrons, and enhance the pollutant adsorptivity. In addition, the synergistic photothermal effect of the CNDs-based nanocomposite facilitates photocatalysis. The CNDs-based nanocomposites with improved photothermal performance and efficient photocatalytic characteristics have large potential in environment and energy applications.
Expanded equine cumulus–oocyte complexes exhibit higher meiotic competence and lower glucose consumption than compact cumulus–oocyte complexes
Authors: González-Fernández L. , Sánchez-Calabuig M. J. , Alves M. G. , Oliveira P. F. , Macedo S. , Gutiérrez-Adán A. , Rocha A. , Macías-García B.
Published: July 2017

Equine cumulus–oocyte complexes (COCs) are classified as compact (cCOC) or expanded (eCOC) and vary in their meiotic competence. This difference could be related to divergent glucose metabolism. To test this hypothesis in the present study, eCOCs, cCOCs and expanded or compact mural granulosa cells (EC and CC respectively) were matured in vitro for 30 h, at which time maturation rate, glucose metabolism and the expression of genes involved in glucose transport, glycolysis, apoptosis and meiotic competence were determined. There were significant differences between eCOCs and cCOCs in maturation rate (50% vs 21.7% (n = 192 and 46) respectively; P < 0.001), as well as mean (± s.e.m.) glucose consumption (1.8 ± 0.5 vs 27.9 ± 5.9 nmol per COC respectively) and pyruvate (0.09 ± 0.01 vs 2.4 ± 0.8 nmol per COC respectively) and lactate (4.7 ± 1.3 vs 64.1 ± 20.6 nmol per COC respectively; P < 0.05 for all) production. Glucose consumption in EC and CC did not differ significantly. Expression of hyaluronan-binding protein (tumour necrosis factor alpha induced protein 6; TNFAIP6) was increased in eCOCs and EC, and solute carrier family 2 member 1 (SLC2A1) expression was increased in eCOCs, but there were no differences in the expression of glycolysis-related enzymes and solute carrier family 2 member 3 (SLC2A3) between the COC or mural granulosa cell types. The findings of the present study demonstrate that metabolic and genomic differences exist between eCOCs and cCOCs and mural granulosa cells in the horse.
Myosin-independent cytokinesis in
Giardia
utilizes flagella to coordinate force generation and direct membrane trafficking
Authors: Hardin William R. , Li Renyu , Xu Jason , Shelton Andrew M. , Alas Germain C. M. , Minin Vladimir N. , Paredez Alexander R.
Published: July 2017

Significance

Many protists, including
Giardia
, lack myosin II and thus are unlikely to use the canonical contractile mechanism of cell division.
Giardia
depends solely on its flagella for motility; here, we show that flagella function is also required to drive daughter cells in opposite directions for cytokinesis. Additionally, just before cytokinesis, Rab11 accumulated in the forming furrow and the nascent intracytoplasmic axonemes were oriented to deliver Rab11. This mechanism constitutes a means to mark the center of the cell and guide trafficking to the furrow. These results support an emerging view that flagella play a central role in cell division among protists that lack myosin II.
Identification of pathogenic gene mutations in
LMNA
and
MYBPC3
that alter RNA splicing
Authors: Ito Kaoru , Patel Parth N. , Gorham Joshua M. , McDonough Barbara , DePalma Steven R. , Adler Emily E. , Lam Lien , MacRae Calum A. , Mohiuddin Syed M. , Fatkin Diane , Seidman Christine E. , Seidman J. G.
Published: July 2017

Significance

Sequence variants that create or eliminate splice sites are often clinically classified as variants of unknown significance (VUS) due to imperfect understanding of RNA splice signals and cumbersome functional assays. In autosomal dominant disorders caused by haploinsufficiency, variants that alter normal splicing of one allele are pathogenic. We developed enhanced computational tools to prioritize potential splice-altering VUS and used a minigene assay to functionally confirm splice-altering sequence variants. In studying all reported variants across
LMNA
and
MYBPC3
, two known heart disease genes, we demonstrate that ∼5% of VUS from affected patients alter splicing and are undetected disease-causing variants. This strategy improves clinical detection of pathogenic variants and should be broadly relevant to other human disorders that are caused by haploinsufficiency.
Creative data literacy
Authors: D'Ignazio Catherine
Published: July 2017

Working with data is an increasingly powerful way of making knowledge claims about the world. There is, however, a growing gap between
those who can work effectively with data and those who cannot. Because it is state and corporate actors who possess the resources to
collect, store and analyze data, individuals (e.g., citizens, community members, professionals) are more likely to be the subjects of data
than to use data for civic purposes. There is a strong case to be made for cultivating data literacy for people in non-technical fields as
one way of bridging this gap. Literacy, following the model of popular education proposed by Paulo Freire, requires not only the acquisition
of technical skills but also the emancipation achieved through the literacy process. This article proposes the term creative data literacy
to refer to the fact that non-technical learners may need pathways towards data which do not come from technical fields. Here I offer five
tactics to cultivate creative data literacy for empowerment. They are grounded in my experience as a data literacy researcher, educator and
software developer. Each tactic is explained and introduced with examples. I assert that working towards creative data literacy is not only
the work of educators but also of data creators, data publishers, tool developers, tool and visualization designers, tutorial authors,
government, community organizers and artists.
Anticipative interfaces for emergency situations
Authors: Kremer Klaus
Published: July 2017

This case study explores concepts and methodologies in user interface (UI) and user experience (UX) design with a view to increasing information retention and memorisation through the inclusion of human-centred design principles. It focuses on the participants’ individual context, mental state and abilities. In emergencies, visual perception and situation awareness may be restricted due to the impact of sensory symptoms (panic, tunnel vision or limited motor skills), thus calling for a linear course of action. This applied research project, ‘Floodscape’, is a mobile application designed to educate its user about possible inundation zones resulting from a tsunami. Ongoing user engagement through interactive simulation is the prime focus of the initial (dormant) state of the app. In case of an actual tsunami the app registers the event and adapts its UI accordingly. Crucial life-saving wayfinding information will then be displayed in a contextual manner considering contrast, typography, limited user attention and ease of use.
“When Noah built the ark…”
Authors: Pihlaja Stephen
Published: July 2017

This article investigates the use of biblical stories and text in the preaching of Joshua Feuerstein, a popular Facebook evangelist, and focuses on how biblical stories are used to position the viewer in comparison to biblical characters and texts. Taking a discourse dynamics approach (Cameron & Maslen, 2010), a corpus of 8 short videos (17 minutes 34 seconds) and their comments (2,295) taken from the Facebook are analysed first, for the presence of metaphorical language and stories taken from the Bible. Second, they are analysed for the role of metaphor in the narrative positioning (Bamberg, 1997) of the viewer, particularly as it relates to Gibbs’s notion of ‘allegorises’, or the ‘allegoric impulse’ (Gibbs, 2011). The corresponding text comments from the videos are then also analysed for the presence of the same biblical metaphor, focusing on how commenters interact with the metaphor and Feuerstein’s positioning of them. Findings show that biblical metaphorical language is used to position viewers and their struggles in the context of larger storylines that compare everyday experiences to biblical texts. This comparison can happen both in explicit narrative positioning of viewers with explicit reference to the Bible, and implicit positioning, through the use of unmarked biblical language. Analysis of viewer comments shows that use of metaphorical language is successful in building a sense of camaraderie and shared belief among the viewer and Feuerstein, as well as viewers with one another.
Proto-Quechua and Proto-Aymara agropastoral terms
Authors: Emlen Nicholas Q. , Adelaar Willem F. H.
Published: July 2017

This chapter presents reconstructed Proto-Quechua and Proto-Aymara lexical items related to cultivation and herding, and draws conclusions about language and subsistence in the ancient Andes. The patterns of lexical borrowing between the two lineages offer a novel empirical perspective on how early Quechuan and Aymaran speakers lived. When the many layers of borrowing are stripped away, it is clear that both were engaged in agropastoral economies before the languages first came into contact. Furthermore, the presence of terms from a wide range of ecological zones, from the high grasslands to (in the case of Quechua) the tropical lowlands, suggests that both languages cross-cut elevations in a manner consistent with the typically Andean system of ecological complementarity.
Subsistence terms in Unangam Tunuu (Aleut)
Authors: Berge Anna
Published: July 2017

The Eskimo-Aleut are arctic and subarctic hunter-gatherers known for their geographic spread and successful adaptation to a harsh climate; they are one of the canonical examples of a people that spread without agriculture. One of the most prehistoric recent spreads in this language family occurred about 1000 years ago, with effects felt throughout coastal Alaska. One area of language contact and possible spread was in Southeast Alaska, between the Pacific Coast Yupik language Alutiiq and the Aleutian language Unangam Tunuu. In this paper, I look at the distribution of cognates and borrowings of subsistence terminology in Unangam Tunuu, and I show that Alutiiq must have spread into a previously Unangax̂ area as a result of warfare rather than subsistence activities.
Lexical recycling as a lens onto shared Japano-Koreanic agriculture
Authors: Francis-Ratte Alexander
Published: July 2017

Despite the existence of strong cognates in other realms of basic vocabulary, it remains unclear why Korean and Japanese share so few words for grain and agriculture. This paper proposes that pre-rice vocabulary has undergone a process of lexical recycling in Korean to refer to later rice-related practices. The observation that Korean words for ‘rice’ contain initial p suggests common derivations from pre-MK *po ‘rice(?)’ that is relatable to Old Japanese po ‘a grain’. This paper uncovers important Japano-Koreanic cognates, including ‘buckwheat,’ ‘millet,’ and ‘rice plant’. This analysis also shows how linguists may retrieve early agricultural terminology that has been replaced by more advanced practices.
Expanding the methodology of lexical examination in the investigation of the intersection of early agriculture and language dispersal
Authors: Joseph Brian D.
Published: July 2017

Analysis of agricultural vocabulary remains one of the most compelling methodologies bearing on Renfrew’s Farming/Language Dispersal Hypothesis, by which the reconstructed lexicon for a proto-language of a well-dispersed language family is predicted to contain several agricultural items. Mostly, though, this methodology has involved noting the presence or absence of particular lexical items for a given proto-language and drawing inferences from that, or working out root derivations and drawing appropriate inferences. I propose here two new types of lexically based argument, by way of expanding the methodology of lexical examination and analysis, looking first at derivational processes involved in the creation of relevant words and the meaning that such processes add to the derivative, and then at religious rituals and mythology to examine the embedding of agricultural vocabulary into the religious practices and mythological tales associated with early Indo-European culture. Ultimately, then, I argue that it is not enough to just look at the meanings of particular words and to try to develop a sense of what they originally meant, nor is it enough to determine the source of the words (derivation, etymology). Rather, one also has to look at how the words were used, what is reconstructible about the use and form of the word, and what the cultural context was for the words. Only then can insights derived from lexical examination be used in developing a sense of prehistory.
Milk and the Indo-Europeans
Authors: Garnier Romain , Sagart Laurent , Sagot Benoît
Published: July 2017

Recent evidence from archaeology and ancient DNA converge to indicate that the Yamnaya culture, often regarded as the bearer of the Proto-Indo-European language, underwent a strong population expansion in the late 4th and early 3rd millennia BCE. It suggests that the underlying reason for that expansion might be the then unique capacity to digest animal milk in adulthood. We examine the early Indo-European milk-related vocabulary to confirm the special role of animal milk in Indo-European expansions. We show that Proto-Indo-European did not have a specialized root for ‘to milk’ and argue that the IE root *h2melg̑- ‘to milk’ is secondary and post-Anatolian. We take this innovation as an indication of the novelty of animal milking in early Indo-European society. Together with a detailed study of language-specific innovations in this semantic field, we conclude that the ability to digest milk played an important role in boosting Proto-Indo-European demography.
Dissemination of advanced directives as a tool to promote health in death and grief / La difusión del documento de voluntades anticipadas como una herramienta de promoción de la salud en muerte y duelo
Authors: Landa Víctor , García Jesús
Published: July 2017

Basing ourselves on the assumption that healthy deaths are associated with healthy grieving processes, we proposed using Advance Directives (ADs) as a tool to promote health in death and grief. The sample from the general population for the study was recruited through four community associations, from which we convened people who wished to make an AD. The sample from health professionals was collected through two palliative care teams and five health centres, with the stated objective of informing them about ADs and to ‘learn by doing’. These samples were put into groups and two sessions were held with each group: one session was to present ADs and the other was to formalize them. In one year, 111 people from 10 groups from the general population participated, and 102 (92%) of those formalized an AD. In six months, 140 professionals from seven groups from the health system collaborated. We conclude that disseminating ADs in a general population is possible through community associations and that the role played by the health system is yet to be clarified.
“It feels as if she might return one day”: A sense of unrealness as a predictor of bereavement-related emotional distress / “Tengo la sensación de que ella puede volver algún día”: la sensación de irrealidad como un predictor del sufrimiento emocional relacionado con la pérdida
Authors: Boelen Paul A.
Published: July 2017

Impaired integration of the loss within autobiographical memory has been proposed as a critical factor in emotional distress following loss. Impaired integration is mainly an implicit process, but has an explicit counterpart, in the form of ‘a sense of unrealness’. Unrealness can be defined as a subjective sense of uncertainty or ambivalence about the irreversibility of the separation. The current study used data from 199 individuals, bereaved in the previous year, to examine the cross-sectional and longitudinal linkage of unrealness with symptom levels of prolonged grief disorder (PGD), posttraumatic stress disorder (PTSD), and depression. Confirmatory factor analysis showed that manifestations of unrealness were distinguishable from (rather than overlapping with) symptoms of PGD. Regression analyses with the cross-sectional data showed that unrealness was concurrently associated with all three symptom outcomes. Regression analyses using the longitudinal data indicated that unrealness tapped at baseline predicted PGD-severity and depression-severity one year later, above and beyond baseline symptom levels and sociodemographic and loss-related variables.
gVolante for standardizing completeness assessment of genome and transcriptome assemblies
Authors: Nishimura Osamu , Hara Yuichiro , Kuraku Shigehiro
Published: July 2017

Motivation

Along with the increasing accessibility to comprehensive sequence information, such as whole genomes and transcriptomes, the demand for assessing their quality has been multiplied. To this end, metrics based on sequence lengths, such as N50, have become a standard, but they only evaluate one aspect of assembly quality. Conversely, analyzing the coverage of pre-selected reference protein-coding genes provides essential content-based quality assessment, but the currently available pipelines for this purpose, CEGMA and BUSCO, do not have a user-friendly interface to serve as a uniform environment for assembly completeness assessment.

Results

Here, we introduce a brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section. Completeness assessments performed on gVolante report scores based on not just the coverage of reference genes but also on sequence lengths (e.g. N50 scaffold length), allowing quality control in multiple aspects. Using gVolante, one can compare the quality of original assemblies between their multiple versions (obtained through program choice and parameter tweaking, for example) and evaluate them in comparison to the scores of public resources found in the database section.

Availability and implementation

gVoalte is freely available at https://gvolante.riken.jp/.
Boundary Convex Cocompactness and Stability of Subgroups of Finitely Generated Groups
Authors: Cordes Matthew , Durham Matthew Gentry
Published: July 2017

A Kleinian group $\Gamma < \mathrm{Isom}(\mathbb H^3)$ is called convex cocompact if any orbit of $\Gamma$ in $\mathbb H^3$ is quasiconvex or, equivalently, $\Gamma$ acts cocompactly on the convex hull of its limit set in $\partial \mathbb H^3$. Subgroup stability is a strong quasiconvexity condition in finitely generated groups which is intrinsic to the geometry of the ambient group and generalizes the classical quasiconvexity condition above. Importantly, it coincides with quasiconvexity in hyperbolic groups and convex cocompactness in mapping class groups. Using the Morse boundary, we develop an equivalent characterization of subgroup stability which generalizes the above boundary characterization from Kleinian groups.
Tissue specificity of in vitro drug sensitivity
Authors: Yao Fupan , Madani Tonekaboni Seyed Ali , Safikhani Zhaleh , Smirnov Petr , El-Hachem Nehme , Freeman Mark , Manem Venkata Satya Kumar , Haibe-Kains Benjamin
Published: July 2017

Objectives

We sought to investigate the tissue specificity of drug sensitivities in large-scale pharmacological studies and compare these associations to those found in drug clinical indications.

Materials and Methods

We leveraged the curated cell line response data from PharmacoGx and applied an enrichment algorithm on drug sensitivity values’ area under the drug dose-response curves (AUCs) with and without adjustment for general level of drug sensitivity.

Results

We observed tissue specificity in 63% of tested drugs, with 8% of total interactions deemed significant (false discovery rate <0.05). By restricting the drug-tissue interactions to those with AUC > 0.2, we found that in 52% of interactions, the tissue was predictive of drug sensitivity (concordance index > 0.65). When compared with clinical indications, the observed overlap was weak (Matthew correlation coefficient, MCC = 0.0003, P > .10).

Discussion

While drugs exhibit significant tissue specificity in vitro, there is little overlap with clinical indications. This can be attributed to factors such as underlying biological differences between in vitro models and patient tumors, or the inability of tissue-specific drugs to bring additional benefits beyond gold standard treatments during clinical trials.

Conclusion

Our meta-analysis of pan-cancer drug screening datasets indicates that most tested drugs exhibit tissue-specific sensitivities in a large panel of cancer cell lines. However, the observed preclinical results do not translate to the clinical setting. Our results suggest that additional research into showing parallels between preclinical and clinical data is required to increase the translational potential of in vitro drug screening.
Decidability of interpretability logics ILM0 and ILW*
Authors: Mikec Luka , Perkov Tin , Vuković Mladen
Published: July 2017

The finite model property is a key step in proving decidability of modal logics. By adapting the filtration method to the generalized Veltman semantics for interpretability logics, we have been able to prove the finite model property of interpretability logic ILM0 w.r.t. generalized Veltman models. We use the same technique to prove the finite model property of interpretability logic ILW* w.r.t. generalized Veltman models. The missing link needed to prove the decidability of ILM0 was completeness w.r.t. generalized Veltman models, which we obtain in this article. Thus, we prove the decidability of ILM0, which was an open problem. Using the same technique, we prove that ILW* is also decidable.
Associations Between Armillaria Species and Host Plants in U.K. Gardens
Authors: Drakulic Jassy , Gorton Caroline , Perez-Sierra Ana , Clover Gerard , Beal Liz
Published: July 2017

Honey fungus (Armillaria spp.) root rot is the disease most frequently inquired about by U.K. gardeners to the Royal Horticultural Society. Armillaria epidemiology has been studied within forestry and agriculture, but data are lacking within gardens, which have greater host plant diversity than orchards and vineyards and greater disturbance than woodlands. Which Armillaria species are responsible for garden disease, and how the broad range of susceptible ornamentals are differentially affected is not known. To address this, isolates of Armillaria were obtained from dead and dying plants from across the U.K. over a 4-year period (2004 to 2007). Species were identified by PCR-RFLP for IGS, and further verified by species-specific PCR for EF-1 α. Of the seven species known in the U.K., three were identified: A. mellea (83.1%), A. gallica (15.8%), and A. ostoyae (1.1%). Armillaria was isolated from trees, shrubs, and nonwoody plants including bulbs and vegetables, with newly recorded hosts listed herein. A. mellea was associated with infections of multiple hosts, and with all infections of the most common host, Ligustrum. In sites where more than one Armillaria species was found, the combination was of A. mellea and A. gallica, raising questions regarding the interactions of these species in U.K. gardens.
Tomato chlorotic spot virus Identified in Marsdenia floribunda in Florida
Authors: Dey K. K. , Melzer M. J. , Xiaoan S. , Adkins S.
Published: July 2017

Marsdenia floribunda (Brongn.), also known as Madagascar jasmine, waxflower, and Hawaiian wedding flower, is a flowering plant in the milkweed family, Apocynaceae, and is native to Madagascar. Marsdenia floribunda plants with typical tospovirus symptoms were found in a Miami-Dade County nursery. Representative leaf tissue tested positive in serological testing with commercially available reagents, indicating the presence of one or more tospoviruses. RT-PCR analysis was used to confirm Tomato chlorotic spot virus (TCSV). This is the first report of TCSV infection of M. floribunda in Florida or any other location. The recent identification of TCSV in annual vinca, Hoya wayetii, and Schlumbergera truncata, together with the current report, demonstrates that the TCSV host range has expanded into ornamental crops.
Technologic Distractions (Part 1): Summary of Approaches to Manage Alert Quantity With Intent to Reduce Alert Fatigue and Suggestions for Alert Fatigue Metrics
Authors: Kane-Gill Sandra L. , O’Connor Michael F. , Rothschild Jeffrey M. , Selby Nicholas M. , McLean Barbara , Bonafide Christopher P. , Cvach Maria M. , Hu Xiao , Konkani Avinash , Pelter Michele M. , Winters Bradford D.
Published: July 2017

Objective:

To provide ICU clinicians with evidence-based guidance on tested interventions that reduce or prevent alert fatigue within clinical decision support systems.

Design:

Systematic review of PubMed, Embase, SCOPUS, and CINAHL for relevant literature from 1966 to February 2017.

Patients:

Focus on critically ill patients and included evaluations in other patient care settings, as well.

Interventions:

Identified interventions designed to reduce or prevent alert fatigue within clinical decision support systems.

Measurements and Main Results:

Study selection was based on one primary key question to identify effective interventions that attempted to reduce alert fatigue and three secondary key questions that covered the negative effects of alert fatigue, potential unintended consequences of efforts to reduce alert fatigue, and ideal alert quantity. Data were abstracted by two reviewers independently using a standardized abstraction tool. Surveys, meeting abstracts, “gray” literature, studies not available in English, and studies with non-original data were excluded. For the primary key question, articles were excluded if they did not provide a comparator as key question 1 was designed as a problem, intervention, comparison, and outcome question. We anticipated that reduction in alert fatigue, including the concept of desensitization may not be directly measured and thus considered interventions that reduced alert quantity as a surrogate marker for alert fatigue. Twenty-six articles met the inclusion criteria.

Conclusion:

Approaches for managing alert fatigue in the ICU are provided as a result of reviewing tested interventions that reduced alert quantity with the anticipated effect of reducing fatigue. Suggested alert management strategies include prioritizing alerts, developing sophisticated alerts, customizing commercially available alerts, and including end user opinion in alert selection. Alert fatigue itself is studied less frequently, as an outcome, and there is a need for more precise evaluation. Standardized metrics for alert fatigue is needed to advance the field. Suggestions for standardized metrics are provided in this document.
Empirically Identified Subgroups of Children Served in Part C Early Intervention Programs
Authors: Elbaum Batya , Celimli-Aksoy Seniz
Published: July 2017

Objective:

Early intervention (EI) programs under Part C of the Individuals with Disabilities Education Act serve a developmentally heterogeneous population of infants and toddlers with or at risk of developmental delays or disabilities. The aim of this study was to identify empirically distinct subgroups of children in EI so as to inform early prognosis and service planning.

Methods:

We applied mixture modeling to developmental assessment data from 1513 children who enrolled in a large, urban EI program between 2009 and 2013. The observed variables were children's EI-entry developmental quotients (DQs) in 5 domains (communication, cognitive, motor, adaptive, and personal–social) as assessed by the Battelle Developmental Inventory, Second Edition.

Results:

A 4-class model showed the best fit to the data, revealing subgroups with distinct developmental profiles. Children in the first subgroup showed a severe delay in communication with less severe delays in the other domains. Children in the second subgroup likewise showed a severe delay in communication, but with comparably severe delays in the cognitive and motor domains. Profiles for the third and fourth subgroups showed the same overall patterns as those for the first and second subgroups, respectively, but to a less severe degree. Developmental trajectories differed by subgroup.

Conclusion:

Consideration of subgroups based on children's developmental assessment scores provides insight into underlying commonalities among children with different presenting diagnoses on entry into EI. The subgroups also have clinical relevance in terms of both practitioners' and parents' understanding of children's likely service needs and developmental trajectories.
Validation of Risk Factors for Fecal Incontinence in Patients With Crohn’s Disease
Authors: Vollebregt Paul F. , Visscher Arjan P. , van Bodegraven Adriaan A. , Felt-Bersma Richelle J. F.
Published: July 2017

BACKGROUND:

Fecal incontinence has a great impact on daily life, and many patients are reluctant to report it.

OBJECTIVE:

The purpose of this study was to estimate the prevalence of fecal incontinence in patients with Crohn’s disease, validate risk factors, and relate outcome with quality of life.

DESIGN:

The design was cross-sectional.

SETTINGS:

The study was conducted at an academic tertiary center.

PATIENTS:

Consecutive patients with Crohn’s disease treated between 2003 and 2013 were included in this study.

MAIN OUTCOME MEASURES:

A questionnaire was sent out in October 2013 to evaluate perianal disease, current symptoms of fecal incontinence, and its impact on quality of life (Fecal Incontinence Quality of Life questionnaire). Risk factors were validated with univariate and multivariate analyses.

RESULTS:

The questionnaire was responded by 325 (62%) of 528 patients. Median age was 42 years (range, 18–91 y), 215 (66%) were women, and a diagnosis of Crohn’s disease was established for a median period of 12 years (interquartile range, 6–21 y). Fecal incontinence was reported by 65 patients (20%). Fecal incontinence was associated with liquid stools (p = 0.0001), previous IBD-related bowel resections (p = 0.001), stricturing behavior of disease (p = 0.02), and perianal disease (p = 0.03). Quality of life (lifestyle, coping, depression, and embarrassment) was poor in patients with fecal incontinence, particularly in patients with more frequent episodes of incontinence.

LIMITATIONS:

There was no correction for disease activity in the multivariate regression analysis.

CONCLUSIONS:

The prevalence of fecal incontinence in a tertiary population with Crohn’s disease is substantially higher than in the community-dwelling population. Considering the reduced quality of life in incontinent patients, active questioning to identify fecal incontinence is recommended in those with liquid stools, perianal disease, or previous (intestinal or perianal) surgery. See Video Abstract at http://journals.lww.com/dcrjournal/Pages/videogallery.aspx.
Evaluation of the Novel Methotrexate Architect Chemiluminescent Immunoassay: Clinical Impact on Pharmacokinetic Monitoring
Authors: Aumente Maria D. , López-Santamaría Julia , Donoso-Rengifo María Concepción , Reyes-Torres Inmaculada , Montejano Hervás Pablo
Published: July 2017

Background:

Fluorescence polarization immunoassay (FPIA) has probably been the most widely used technique for the determination of methotrexate (MTX) concentrations in clinical laboratories. After its replacement by a novel architect chemiluminescent microparticle immunoassay (CMIA), it is essential to verify that there are no differences between the methods that can induce an error in leucovorin rescue with dire consequences for the patient. The objective of our study was to compare plasma/serum MTX measurements between CMIA and FPIA (reference method in this study) in the work conditions of a clinical pharmacokinetics unit to determine whether any difference would affect clinical decisions on the management of this drug.

Methods:

FPIA on TDx/FLx and CMIA on Architect ci8200 were simultaneously used to evaluate 127 clinical samples. Within-run (20 repetitions on same day) and between-run (20 repetitions on different days) imprecision was evaluated using 6 control samples provided by the manufacturer and diluting 2 of them by 50% for 0.03 and 0.22 μmol/L, respectively. The Passing–Bablok regression method, Bland–Altman plot, and concordance correlation coefficient (CCC) were used in the statistical analysis.

Results:

Within-run imprecision was <5% (3.6%–4.39%) and between-run imprecision <11% (2.42%–10.65%). Between-assay correlation for the studied concentration range (0.05–250 μmol/L) was CMIA = −0.026 + 1.033 FPIA (n = 127), r = 0.9963, and CCC = 0.9946. For samples <1.5 μmol/L (nondiluted) included in the assay calibration curve, the correlation was CMIA = −0.009 + 0.955 FPIA (n = 54), r = 0.9819, and CCC = 0.9807. No significant difference was observed between the measurements by the 2 assays, given that the 95% confidence interval of the ordinate at the origin included “0” (−0.020 to 0.0007), and the 95% confidence interval of the slope included 1 (0.923–1.020). The interchangeability of these assays was confirmed by Bland–Altman plot results, which showed a mean difference insignificant at concentrations <10 μmol/L.

Conclusions:

The correlation between methods was excellent, and Passing–Bablok regression analysis detected no virtually difference in their results. Utilization of the CMIA-Architect assay to measure MTX concentrations would therefore not affect clinical decisions on MTX management, supporting its employment in routine MTX monitoring.