bluuebunny/crossref_metadata_2025 huggingface dataset:
Suture Anchors Fixation in MPFL Reconstruction using a Bioactive Synthetic Ligament
Authors: Berruto Massimo , Ferrua Paolo , Tradati Daniele , Uboldi Francesco , Usellini Eva , Marelli Bruno
Published: September 2017

Medial patellofemoral ligament (MPFL) reconstruction has a key role in patellofemoral instability surgery. Many surgical techniques have been described so far using different types of grafts (autologous, heterologous, or synthetic) and fixation techniques. The hereby described technique for MPFL reconstruction relies on the use of a biosynthetic graft (LARS Arc Sur Tille, France). Fixation is obtained by means of suture anchors on the patellar side and a resorbable interference screw on the femoral side locating the insertion point according to Schottle et al. An early passive range of motion (ROM) recovery is fundamental to reduce the risk of postoperative stiffness; a partial weight bearing with crutches is allowed until 6 weeks after the surgery. In our experience, the use of a biosynthetic graft and suture anchors provides stable fixation, minimizing donor site morbidity and reducing the risk of patellar fracture associated with transosseous tunnels. This technique represents a reliable and reproducible alternative for MPFL reconstruction, thereby minimizing the risk of possible complications.
Effectiveness and Safety of Needle Medial Collateral Ligament Pie-Crusting in Total Knee Arthroplasty: A Cadaveric Study
Authors: Ohmori Takaaki , Kabata Tamon , Kajino Yoshitomo , Takagi Tomoharu , Tsuchiya Hiroyuki
Published: September 2017

Medial collateral ligament (MCL) pie-crusting technique in total knee arthroplasty (TKA) is one of the methods of medial release. The effects and risks of blade pie-crusting have been reported in previous studies. However, only a few have reported the safety and efficacy of needle pie-crusting. In this cadaveric study, we quantitatively evaluated the amount of gap change by MCL needle pie-crusting. We investigated five knees of four fresh human cadavers and performed posterior-stabilized TKA. Only deep MCL release as the medial release was conducted. We punctured the MCL from the deep layer to the superficial layer using a 18 G needle in a 90-degree flexion position for 0, 10, 20, 50, 75, and 100 times. Medial and lateral gaps were measured accurately with a balancer at determined times in 0 and 90-degree flexion positions. Changes in medial and lateral gaps were not significant differences in flexion and extension position. However, in 90-degree flexion, medial gap changes were tended to be larger than lateral gap changes. A 0.6 mm additional medial release and a 0.2 mm additional lateral release were found per 10 times pie crust in flexion position (100 times, p: 0.08). However, large differences existed among the cases. Needle pie-crusting is safer than blade pie-crusting because of the small efficacy of one-time pie crust. MCL needle pie-crusting showed varied effects for each case. This result indicates the risk of relaxation of an unexpected gap. Caution should be taken when choosing between needle pie-crusting and blade pie-crusting.
Die Entdeckung der Schüßler-Salze
Authors: Emmrich Peter
Published: September 2017

Schüßler-Salze werden seit mehr als 140 Jahren täglich weltweit erfolgreich als Therapieoption eingesetzt, unabhängig davon, ob es sich um
ein akutes oder chronisches Leiden handelt. Schüßler gelangte zu der Überzeugung, dass Krankheit letztlich auf einen gestörten
Mineralsalzhaushalt innerhalb und außerhalb der Zelle beruhe, den es gilt auszugleichen. Namhafte Wissenschaftler der damaligen Zeit wie
Moleschott, Virchow und von Liebig beeinflussten seine Überlegungen nachhaltig und gaben ihm das Fundament, auf das er, trotz der kritischen
Stimmen von Zeitgenossen, seine „Abgekürzte homöopathische Therapie“ stellte. Die Kunst besteht darin, aus den zwölf Schüßler-Salzen das für
den Patienten angezeigte Mittel richtig auszuwählen. Kommt das passende Mittel zur Anwendung, normalisiert sich der gestörte
Mineralsalzhaushalt und die Heilung wird vom Organismus vollzogen – bei Menschen und Tieren.
Growth and characterization of β-Ga2O3 thin films by molecular beam epitaxy for deep-UV photodetectors
Authors: Ghose Susmita , Rahman Shafiqur , Hong Liang , Rojas-Ramirez Juan Salvador , Jin Hanbyul , Park Kibog , Klie Robert , Droopad Ravi
Published: September 2017

The growth of high quality epitaxial beta-gallium oxide (β-Ga2O3) using a compound source by molecular beam epitaxy has been demonstrated on c-plane sapphire (Al2O3) substrates. The compound source provides oxidized gallium molecules in addition to oxygen when heated from an iridium crucible in a high temperature effusion cell enabling a lower heat of formation for the growth of Ga2O3, resulting in a more efficient growth process. This source also enabled the growth of crystalline β-Ga2O3 without the need for additional oxygen. The influence of the substrate temperatures on the crystal structure and quality, chemical bonding, surface morphology, and optical properties has been systematically evaluated by x-ray diffraction, scanning transmission electron microscopy, x-ray photoelectron spectroscopy, atomic force microscopy, spectroscopic ellipsometry, and UV-vis spectroscopy. Under optimized growth conditions, all films exhibited pure 2¯01  oriented β-Ga2O3 thin films with six-fold rotational symmetry when grown on a sapphire substrate. The thin films demonstrated significant absorption in the deep-ultraviolet (UV) region with an optical bandgap around 5.0 eV and a refractive index of 1.9. A deep-UV photodetector fabricated on the high quality β-Ga2O3 thin film exhibits high resistance and small dark current (4.25 nA) with expected photoresponse for 254 nm UV light irradiation suggesting that the material grown using the compound source is a potential candidate for deep-ultraviolet photodetectors.
Multispectral mid-infrared light emitting diodes on a GaAs substrate
Authors: Aziz Mohsin , Xie Chengzhi , Pusino Vincenzo , Khalid Ata , Steer Matthew , Thayne Iain G. , Cumming David R. S.
Published: September 2017

We have designed, simulated, and experimentally demonstrated four-colour mid-infrared (mid-IR) Light Emitting Diodes (LEDs) integrated monolithically into a vertical structure on a semi-insulating GaAs substrate. In order to finely control the peak wavelength of the emitted mid-IR light, quantum well (QW) structures based on AlInSb/InSb/AlInSb are employed. The completed device structure consists of three p-QW-n diodes with different well widths stacked on top of one bulk AlInSb p-i-n diode. The epitaxial layers comprising the device are designed in such a way that one contact layer is shared between two LEDs. The design of the heterostructure realising the multispectral LEDs was aided by numerical modelling, and good agreement is observed between the simulated and experimental results. Electro-Luminescence measurements, carried out at room temperature, confirm that the emission of each LED peaks at a different wavelength. Peak wavelengths of 3.40 μm, 3.50 μm, 3.95 μm, and 4.18 μm are observed in the bulk, 2 nm, 4 nm, and 6 nm quantum well LEDs, respectively. Under zero bias, Fourier Transform Infrared photo-response measurements indicate that these fabricated diodes can also be operated as mid-IR photodetectors with an extended cut-off wavelength up to 4.6 μm.
Vapor-solid-solid grown Ge nanowires at integrated circuit compatible temperature by molecular beam epitaxy
Authors: Zhu Zhongyunshen , Song Yuxin , Zhang Zhenpu , Sun Hao , Han Yi , Li Yaoyao , Zhang Liyao , Xue Zhongying , Di Zengfeng , Wang Shumin
Published: September 2017

We demonstrate Au-assisted vapor-solid-solid (VSS) growth of Ge nanowires (NWs) by molecular beam epitaxy at the substrate temperature of ∼180 °C, which is compatible with the temperature window for Si-based integrated circuit. Low temperature grown Ge NWs hold a smaller size, similar uniformity, and better fit with Au tips in diameter, in contrast to Ge NWs grown at around or above the eutectic temperature of Au-Ge alloy in the vapor-liquid-solid (VLS) growth. Six ⟨110⟩ growth orientations were observed on Ge (110) by the VSS growth at ∼180 °C, differing from only one vertical growth direction of Ge NWs by the VLS growth at a high temperature. The evolution of NWs dimension and morphology from the VLS growth to the VSS growth is qualitatively explained by analyzing the mechanism of the two growth modes.
Effects of the deposition rate on growth modes of Ag islands on the hydrogen-terminated Si(111)-(1 × 1) surface: The role of surface energy and quantum size effect
Authors: Kang Jungmin , Eguchi Toyoaki , Kawamoto Erina , Matsushita Stephane Yu , Haga Kenya , Kanagawa Shino , Wawro Andrzej , Czajka Ryszard , Kato Hiroki , Suto Shozo
Published: September 2017

We have investigated the early stage of Ag island growth at 2 monolayer (ML) coverage on the hydrogen-terminated Si(111)–(1 × 1) surface using low-energy electron-diffraction (LEED) and scanning tunneling microscopy (STM) at room temperature. First, it is found that the Ag(10) LEED pattern varies from arc-like spots to three spots by changing the Ag deposition rate from 1.0×10−1 (a fast deposition rate) to 1.1×10−4 (a slow deposition rate) ML/s. Second, STM observation reveals that adsorbed Ag atoms grow into dome-like three dimensional (3D) clusters at the fast deposition rate and flat-top two dimensional (2D) islands at the slow deposition rate. Third, most abundant 2D islands show the 8 atomic layer height, which coincides with that obtained from the quantum size effect. The side structures of 2D islands agree well with those calculated from Wulff theory. We will discuss the exact nature of 3D clusters and 2D islands of Ag grown on the hydrogen-terminated Si(111)–(1 × 1) surface and these results indicate the possibility of using kinetic controlled growth to investigate the physics of crystal growth.
Effect of germanium doping on the formation kinetics of vacancy-dioxygen complexes in high dose neutron irradiated crystalline silicon
Authors: Dong Peng , Yu Xuegong , Chen Lin , Ma Xiangyang , Yang Deren
Published: September 2017

The effect of germanium (Ge) doping on the formation kinetics of vacancy-dioxygen (VO2) complexes in high dose neutron irradiated crystalline silicon (c-Si) has been quantitatively investigated using infrared spectroscopy at 10 K. It is observed that Ge doping of 1019 cm−3 enhances the formation of vacancy-oxygen (VO) complexes by ∼15% during neutron irradiation and slightly suppresses the conversion of VO into VO2 complexes. By studying the generation kinetics of VO2 complexes in the temperature range of 300–345 °C, it is found that the activation energies of VO2 generation are determined to be 1.52 and 1.71 eV in the reference and Ge-doped c-Si, respectively. According to the theory for diffusion limited reactions, it is suggested that Ge doping can retard the VO diffusion in c-Si and therefore reduce the capture probability of Oi for VO complexes. This may be attributed to the temporary trapping of vacancies by Ge atoms. Hence, the formation of VO2 complexes in c-Si is slightly suppressed by Ge doping.
Bullet-shaped ionization front of plasma jet plumes driven by microwave pulses at atmospheric gas pressure
Authors: Chen Zhaoquan , Xia Guangqing , Zou Changlin , Liu Xiaodong , Feng Deren , Li Ping , Hu Yelin , Stepanova Olga , Kudryavtsev A. A.
Published: September 2017

Ionization waves (propagating bullet-shaped plasma) are always present in atmospheric-pressure plasma jets generated by a pulsed DC power supply or low-frequency voltages. Nevertheless, whether these ionization waves exist for pulsed microwave plasma jets remains unclear. In this paper, a coaxial transmission line resonator driven by microwave pulses is capable of generating atmospheric pressure plasma jet plumes. Depending on the discharges, these plasma jet plumes exhibit distinctive characteristics, such as bullet-shaped ionization fronts for argon plasma and ball-shaped for helium plasma. Fast images show argon plasma plumes generating several small branches but only one dominant ionization front travels more distance along the jet axis. Both ionization-wave images and electromagnetic simulation results indicate that the bullet-shaped ionization front forms a plasma jet plume immediately. The dominant ionization wave is resonantly excited by the local enhanced electric field, which originates from the local net charge of the streamer plus surface plasmon polariton located at the open end of the resonator.
Dorsolateral prefrontal cortex GABA deficit in older adults with sleep-disordered breathing
Authors: Pereira Ana C. , Mao Xiangling , Jiang Caroline S. , Kang Guoxin , Milrad Sara , McEwen Bruce S. , Krieger Ana C. , Shungu Dikoma C.
Published: September 2017

Significance

Sleep-disordered breathing (SDB), characterized by intermittent hypoxia and sleep fragmentation during sleep, is common in the elderly and can contribute to cognitive decline, with significant impairment of executive function, including mental flexibility, problem solving, and working memory, which are under dorsolateral prefrontal cortex (DLPFC) control. The results of the present study suggest a potential mechanism of SDB in which a hypoxia-driven deficit of DLPFC γ-aminobutyric acid (GABA), the major inhibitory neurotransmitter, disrupts the neural excitation/inhibition balance which could lead to hyperexcitability, and potentially neuronal damage and cognitive decline. If validated, these findings, along with the proposed model, would represent a significant advance toward achieving a better understanding of the neurobiology of SDB and novel targets for interventions for the disorder.
Tolerance of effective ingroup deviants as a function of moral disengagement / Tolerancia de la disidencia efectiva de los miembros del endogrupo como función de la desconexión moral
Authors: Aguiar Tiago , Campos Miguel , Pinto Isabel R. , Marques José M.
Published: September 2017

The subjective group dynamics theory posits that individuals derogate ingroup members who deviate from prescriptive moral norms. Research on moral disengagement suggests that deviants may, sometimes, be tolerated. This study’s goal was to test whether leniency towards effective ingroup deviants is accounted for by mechanisms of moral disengagement. Portuguese participants ( N = 75) judged a Portuguese (ingroup) or Spanish (outgroup) manager whose deviant conduct was either effective (i.e., had positive consequences) or ineffective (i.e., had negative consequences) for a Portuguese company. As predicted, participants favoured deviant but effective ingroup members. This was mediated by an increase in moral disengagement and a decrease in negative emotional reactions. Results suggest that individuals downplay the importance of moral norms when facing ambiguous ingroup deviants, as a means to protect their social identity. We discuss these results in light of subjective group dynamics theory.
Recursion-transform method and potential formulae of the m × n cobweb and fan networks*
Authors: Tan Zhi-Zhong
Published: September 2017

In this paper, we made a new breakthrough, which proposes a new Recursion–Transform (RT) method with potential parameters to evaluate the nodal potential in arbitrary resistor networks. For the first time, we found the exact potential formulae of arbitrary

m
×
n

cobweb and fan networks by the RT method, and the potential formulae of infinite and semi-infinite networks are derived. As applications, a series of interesting corollaries of potential formulae are given by using the general formula, the equivalent resistance formula is deduced by using the potential formula, and we find a new trigonometric identity by comparing two equivalence results with different forms.
Is the Natural Label Misleading? Examining Consumer Preferences for Natural Beef
Authors: Syrengelas Konstantinos G , DeLong Karen Lewis , Grebitus Carola , Nayga Rodolfo M
Published: September 2017

A petition to the USDA claims that natural labeling misleads consumers. We investigate this claim using an online choice experiment to determine consumer willingness to pay for steak labeled as natural. Half of the sample was provided with the definition of natural, while half was not. The absence of the definition resulted in consumers placing a premium on “natural” steak, while those provided with the definition were not willing to pay a premium. Similarly, participants who consider themselves familiar with the natural definition did not place a premium on “natural” steak. Results indicate that consumers may misinterpret the natural label.
Microbial genome analysis: the COG approach
Authors: Galperin Michael Y , Kristensen David M , Makarova Kira S , Wolf Yuri I , Koonin Eugene V
Published: September 2017

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.
Asking Questions with Reflexive Focus: A Tutorial on Designing and Conducting Interviews
Authors: Arsel Zeynep
Published: September 2017

Interviews have been a key primary data source for research published in the Journal of Consumer Research. This tutorial aims to walk readers through the design and execution of interview-based empirical research on consumers and consumption.
An evolutionary scheduling approach for trading-off accuracy vs. verifiable energy in multicore processors
Authors: Liqat U , Banković Z , Lopez-Garcia P , Hermenegildo M V
Published: September 2017

This work addresses the problem of energy-efficient scheduling and allocation of tasks in multicore environments, where the tasks can allow a certain loss in accuracy in the output, while still providing proper functionality and meeting an energy budget. This margin for accuracy loss is exploited by using computing techniques that reduce the work load, and thus can also result in significant energy savings. To this end, we use the technique of loop perforation, that transforms loops to execute only a subset of their original iterations, and integrate this technique into our existing optimization tool for energy-efficient scheduling. To verify that a schedule meets an energy budget, both safe upper and lower bounds on the energy consumption of the tasks involved are needed. For this reason, we use a parametric approach to estimate safe (and tight) energy bounds that are practical for energy verification (and optimization applications). This approach consists in dividing a program into basic (‘branchless’) blocks, establishing the maximal (resp. minimal) energy consumption for each block using an evolutionary algorithm, and combining the obtained values according to the program control flow, by using static analysis to produce energy bound functions on input data sizes. The scheduling tool uses evolutionary algorithms coupled with the energy bound functions for estimating the energy consumption of different schedules. The experiments with our prototype implementation were performed on multicore XMOS chips, but our approach can be adapted to any multicore environment with minor changes. The experimental results show that our new scheduler enhanced with loop perforation improves on the previous one, achieving significant energy savings (31% on average for the test programs) for acceptable levels of accuracy loss.
Great Optically Luminous Dropout Research Using Subaru HSC (GOLDRUSH). I. UV luminosity functions at z ∼ 4–7 derived with the half-million dropouts on the 100 deg2 sky
Authors: Ono Yoshiaki , Ouchi Masami , Harikane Yuichi , Toshikawa Jun , Rauch Michael , Yuma Suraphong , Sawicki Marcin , Shibuya Takatoshi , Shimasaku Kazuhiro , Oguri Masamune , Willott Chris , Akhlaghi Mohammad , Akiyama Masayuki , Coupon Jean , Kashikawa Nobunari , Komiyama Yutaka , Konno Akira , Lin Lihwai , Matsuoka Yoshiki , Miyazaki Satoshi , Nagao Tohru , Nakajima Kimihiko , Silverman John , Tanaka Masayuki , Taniguchi Yoshiaki , Wang Shiang-Yu
Published: September 2017

We study the UV luminosity functions (LFs) at z ∼ 4, 5, 6, and 7 based on the deep large-area optical images taken by the Hyper Suprime-Cam (HSC) Subaru Strategic Program (SSP). On the 100 deg2 sky of the HSC SSP data available to date, we take enormous samples consisting of a total of 579565 dropout candidates at z ∼ 4–7 by the standard color selection technique, 358 out of which are spectroscopically confirmed by our follow-up spectroscopy and other studies. We obtain UV LFs at z ∼ 4–7 that span a very wide UV luminosity range of ∼0.002–100$\, L_{\rm UV}^\ast$ (−26 < MUV < −14 mag) by combining LFs from our program and the ultra-deep Hubble Space Telescope legacy surveys. We derive three parameters of the best-fit Schechter function, ϕ*, $M_{\rm UV}^{\,\ast}$, and α, of the UV LFs in the magnitude range where the active galactic nucleus (AGN) contribution is negligible, and find that α and ϕ* decrease from z ∼ 4 to 7 with no significant evolution of $M_{\rm UV}^{\,\ast}$. Because our HSC SSP data bridge the LFs of galaxies and AGNs with great statistical accuracy, we carefully investigate the bright end of the galaxy UV LFs that are estimated by the subtraction of the AGN contribution either aided by spectroscopy or the best-fit AGN UV LFs. We find that the bright end of the galaxy UV LFs cannot be explained by the Schechter function fits at >2 σ significance, and require either double power-law functions or modified Schechter functions that consider a magnification bias due to gravitational lensing.
Identification of Indirect Effects in a Cognitive Patient Education (COPE) Intervention for Low Back Pain
Authors: Mansell Gemma , Storheim Kjersti , Løchting Ida , Werner Erik L. , Grotle Margreth
Published: September 2017

Background

Many interventions for the treatment of low back pain exist, but the mechanisms through which such treatments work are not always clear. This situation is especially true for biopsychosocial interventions that incorporate several different components and methods of delivery.

Objective

The study objective was to examine the indirect effects of the Cognitive Patient Education (COPE) intervention via illness perceptions, back pain myths, and pain catastrophizing on disability outcome.

Design

This study was a secondary analysis of the COPE randomized controlled trial.

Methods

Mediation analysis techniques were employed to examine the indirect effects of the COPE intervention via residualized change (baseline – posttreatment) in the 3 variables hypothesized to be targeted by the COPE intervention on posttreatment disability outcome. Pain intensity at baseline, pain duration, clinician type, and a treatment-mediator interaction term were controlled for in the analysis.

Results

Preliminary analyses confirmed that changes in pain catastrophizing and illness perceptions (not back pain myths) were related to both allocation to the intervention arm and posttreatment disability score. The treatment exerted statistically significant indirect effects via changes in illness perceptions and pain catastrophizing on posttreatment disability score (illness perceptions standardized indirect effect = 0.09 [95% CI = 0.03 to 0.16]; pain catastrophizing standardized indirect effect = 0.05 [95% CI = 0.01 to 0.12]). However, the inclusion of an interaction term led to the indirect effects being significantly reduced, with the effects no longer being statistically significant.

Limitations

This study presents a secondary analysis of variables not identified a priori as being potentially important treatment targets; other, unmeasured factors could also be important in explaining treatment effects.

Conclusions

The finding that small indirect effects of the COPE intervention via changes in illness perceptions and pain catastrophizing on posttreatment disability could be estimated indicates that these variables may be viable treatment targets for biopsychosocial interventions; however, this finding must be viewed in light of the adjusted analyses, which showed that the indirect effects were significantly reduced through the inclusion of a treatment-mediator interaction term.
Program synthesis: challenges and opportunities
Authors: David Cristina , Kroening Daniel
Published: September 2017

Program synthesis is the mechanized construction of software, dubbed ‘self-writing code’. Synthesis tools relieve the programmer from thinking about how the problem is to be solved; instead, the programmer only provides a description of what is to be achieved. Given a specification of what the program should do, the synthesizer generates an implementation that provably satisfies this specification. From a logical point of view, a program synthesizer is a solver for second-order existential logic. Owing to the expressiveness of second-order logic, program synthesis has an extremely broad range of applications. We survey some of these applications as well as recent trends in the algorithms that solve the program synthesis problem. In particular, we focus on an approach that has raised the profile of program synthesis and ushered in a generation of new synthesis tools, namely counter-example-guided inductive synthesis (CEGIS). We provide a description of the CEGIS architecture, followed by recent algorithmic improvements. We conjecture that the capacity of program synthesis engines will see further step change, in a manner that is transparent to the applications, which will open up an even broader range of use-cases.

This article is part of the themed issue ‘Verified trustworthy software systems’.
Draft genome of the Eutardigrade Milnesium tardigradum sheds light on ecdysozoan evolution
Authors: Bemm Felix , Burleigh Laura , Förster Frank , Schmucki Roland , Ebeling Martin , Janzen Christian J. , Dandekar Thomas , Schill Ralph O. , Certa Ulrich , Schultz Jörg
Published: September 2017

Tardigrades are among the most stress tolerant animals and survived even unassisted exposure to space in low earth orbit. Still, the adaptations leading to these unusual physiological features remain unclear. Even the phylogenetic position of this phylum within the Ecdysozoa is unclear. Complete genome sequences might help to address these questions as genomic adaptations can be revealed and phylogenetic reconstructions can be based on new markers. Here, we present a first draft genome of a species from the family Milnesiidae, namelyMilnesium tardigradum. We consistently placeM. tardigradumand the two previously sequenced Hypsibiidae species,Hypsibius dujardiniandRamazzottius varieornatus, as sister group of the nematodes with the arthropods as outgroup. Based on this placement, we identify a massive gene loss thus far attributed to the nematodes which predates their split from the tardigrades. We provide a comprehensive catalog of protein domain expansions linked to stress response and show that previously identified tardigrade-unique proteins are erratically distributed across the genome ofM. tardigradum. We further suggest alternative pathways to cope with high stress levels that are yet unexplored in tardigrades and further promote the phylum Tardigrada as a rich source of stress protection genes and mechanisms.
A common representation of time across visual and auditory modalities
Authors: Barne Louise C. , Sato João R. , de Camargo Raphael Y. , Claessens Peter M. E. , Caetano Marcelo S. , Cravo André M.
Published: September 2017

Humans’ and non-human animals’ ability to process time on the scale of milliseconds and seconds is essential for adaptive behaviour. A central question of how brains keep track of time is how specific temporal information across different sensory modalities is. In the present study, we show that encoding of temporal intervals in auditory and visual modalities are qualitatively similar. Human participants were instructed to reproduce intervals in the range from 750 ms to 1500 ms marked by auditory or visual stimuli. Our behavioural results suggest that, although participants were more accurate in reproducing intervals marked by auditory stimuli, there was a strong correlation in performance between modalities. Using multivariate pattern analysis in scalp EEG, we show that activity during late periods of the intervals was similar within and between modalities. Critically, we show that a multivariate pattern classifier was able to accurately predict the elapsed interval, even when trained on an interval marked by a stimulus of a different sensory modality. Taken together, our results suggest that, while there are differences in the processing of intervals marked by auditory and visual stimuli, they also share a common neural representation.
Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Authors: Russell Joseph A. , Campos Brittany , Stone Jennifer , Blosser Erik M. , Burkett-Cadena Nathan , Jacobs Jonathan
Published: September 2017

The future of infectious disease surveillance and outbreak response is trending towards smaller hand-held solutions for point-of-need pathogen detection.1–4Although recent advances have paved the way for these technologies to include sequencing of pathogens directly from clinical samples, the ability to carry out unbiased sequencing for pathogen discovery and subtyping directly from environmental samples has yet to be demonstrated with hand-held platforms.5Products such as the two3 qPCR system from Biomeme Inc., as well as the MinION from Oxford Nanopore Technologies, have generated renewed prospects for point-of-need diagnostics and near real-time environmental testing and characterization of viral and microbial pathogens. Here, samples ofCulex cedeceimosquitoes collected in Southern Florida, USA were tested for Venezuelan Equine Encephalitis Virus (VEEV), a previously-weaponized arthropod-borne RNA-virus capable of causing acute and fatal encephalitis in animal and human hosts. A single 20-mosquito pool tested positive for VEEV by real-time reverse transcription quantitative PCR (RT-qPCR) on the Biomeme two3. The virus-positive sample was then subjected to unbiased metatranscriptome sequencing on the MinION and determined to contain Everglades Virus (EVEV), a strain of VEEV transmitted exclusively byCulex cedeceiin South Florida. The result was confirmed on “gold standard” thermocyclers and sequencing machines, and comparison to nanopore results is discussed. Our results demonstrate, for the first time, the use of unbiased sequence-based detection and subtyping of a high-consequence biothreat pathogen directly from an environmental sample using field-forward hardware and protocols. The further development and validation of methods designed for field-based diagnostic metagenomics and pathogen discovery, such as those suitable for use in mobile “pocket laboratories”, will address a growing demand for public health teams to carry out their mission where it is most urgent: at the point-of-need.6
Insights into the relation between noise and biological complexity
Authors: Pucci Fabrizio , Rooman Marianne
Published: September 2017

Understanding under which conditions the increase of systems complexity is evolutionary advantageous, and how this trend is related to the modulation of the intrinsic noise, are fascinating issues of utmost importance for synthetic and systems biology. To get insights into these matters, we analyzed chemical reaction networks with different topologies and degrees of complexity, interacting or not with the environment. We showed that the global level of fluctuations at the steady state, as measured by the sum of the Fano factors of the number of molecules of all species, is directly related to the topology of the network. For systems with zero deficiency, this sum is constant and equal to the rank of the network. For higher deficiencies, we observed an increase or decrease of the fluctuation levels according to the values of the reaction fluxes that link internal species, multiplied by the associated stoichiometry. We showed that the noise is reduced when the fluxes all flow towards the species of higher complexity, whereas it is amplified when the fluxes are directed towards lower complexity species.

PACS numbers: 02.50.Ey, 05.10.Gg, 05.40.Ca, 87.18.-h
A predictive model of rats’ calorie intake as a function of diet energy density
Authors: Beheshti Rahmatollah , Treesukosol Yada , Igusa Takeru , Moran Timothy H.
Published: September 2017

Easy access to high-energy food has been linked to high rates of obesity in the world. Understanding the way that access to palatable (high fat or high calorie) food can lead to overconsumption is essential for both preventing and treating obesity. Although the body of studies focused on the effects of high energy diets is growing, our understanding of how different factors contribute to food choices is not complete. In this study, we present a mathematical model that is able to predict rats’ calorie intake to a high-energy diet based on their ingestive behavior to a standard chow diet. Specifically, we propose an equation that describes the relation between the body weight (W), energy density (E), time elapsed from the start of diet (T), and daily calorie intake (C). We tested our model on two independent data sets. Our results show that the suggested model is able to predict the calorie intake patterns with high accuracy. Additionally, the only free parameter of our proposed equation (ρ), which is unique to each animal, has a strong correlation with their calorie intake and weight gain. Additionally, we discuss the relevance of our derived parameter in the context of measuring reward sensitivity in reinforcement learning based studies.
Cardiac enriched BAF chromatin remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function
Authors: Sun Xin , Hota Swetansu K. , Zhou Yu-Qing , Novak Stefanie , Miguel-Perez Dario , Christodoulou Danos , Seidman Christine E. , Seidman J.G. , Gregorio Carol C. , Henkelman R. Mark , Rossant Janet , Bruneau Benoit G.
Published: September 2017

How gene networks controlling organ-specific properties are modulated by chromatin remodeling complexes is not well understood.Baf60c(Smarcd3) encodes a cardiac-enriched subunit of the SWI/SNF-like BAF chromatin complex. Its role throughout heart development is not fully understood. We show that constitutive loss ofBaf60cleads to embryonic cardiac hypoplasia and pronounced cardiac dysfunction. Conditional deletion ofBaf60cin cardiomyocytes results in postnatal dilated cardiomyopathy with impaired contractile function.Baf60cregulates a gene expression program that includes genes encoding contractile proteins, modulators of sarcomere function, and cardiac metabolic genes. Many of the genes deregulated inBaf60cnull embryos are targets of the MEF2/SRF co-factor Myocardin (MYOCD). In a yeast two-hybrid screen we identify MYOCD as a BAF60c interacting factor; we show that BAF60c and MYOCD directly and functionally interact. We conclude that Baf60c is essential for coordinating a program of gene expression that regulates the fundamental functional properties of cardiomyocytes.
IMPROVING MIN HASH VIA THE CONTAINMENT INDEX WITH APPLICATIONS TO METAGENOMIC ANALYSIS
Authors: Koslicki David , Zabeti Hooman
Published: September 2017

Min hash is a probabilistic method for estimating the similarity of two sets in terms of their Jaccard index, defined as the ration of the size of their intersection to their union. We demonstrate that this method performs best when the sets under consideration are of similar size and the performance degrades considerably when the sets are of very different size. We introduce a new and efficient approach, called thecontainment min hashapproach, that is more suitable for estimating the Jaccard index of sets of very different size. We accomplish this by leveraging another probabilistic method (in particular, Bloom filters) for fast membership queries. We derive bounds on the probability of estimate errors for the containment min hash approach and show it significantly improves upon the classical min hash approach. We also show significant improvements in terms of time and space complexity. As an application, we use this method to detect the presence/absence of organisms in a metagenomic data set, showing that it can detect the presence of very small, low abundance microorganisms.
An open-source cryo-storage solution
Authors: Ultee Eveline , Schenkel Fred , Yang Wen , Brenzinger Susanne , Depelteau Jamie S. , Briegel Ariane
Published: September 2017

The field of cryo-electron microscopy is a rapidly growing method in structural biology. With this development, access to cryo-EM facilities becomes a bottleneck that results in long wait times between sample preparation and data acquisition. To improve sample storage, we developed a cryo-storage system with a more efficient and larger storage capacity that enables cryo-sample storage in a highly organized manner. This system is simple to use, cost-effective and easily adaptable for any type of grid box and storage dewar and any size cryo-EM laboratory.
ARIGAN: Synthetic Arabidopsis Plants using Generative Adversarial Network
Authors: Giuffrida Mario Valerio , Scharr Hanno , Tsaftaris Sotirios A
Published: September 2017

In recent years, there has been an increasing interest in image-based plant phenotyping, applying state-of-the-art machine learning approaches to tackle challenging problems, such as leaf segmentation (a multi-instance problem) and counting. Most of these algorithms need labelled data to learn a model for the task at hand. Despite the recent release of a few plant phenotyping datasets, large annotated plant image datasets for the purpose of training deep learning algorithms are lacking. One common approach to alleviate the lack of training data is dataset augmentation. Herein, we propose an alternative solution to dataset augmentation for plant phenotyping, creating artificial images of plants using generative neural networks. We propose the Arabidopsis Rosette Image Generator (through) Adversarial Network: a deep convolutional network that is able to generate synthetic rosette-shaped plants, inspired by DC-GAN (a recent adversarial network model using convolutional layers). Specifically, we trained the network using A1, A2, and A4 of the CVPPP 2017 LCC dataset, containing Arabidopsis Thaliana plants. We show that our model is able to generate realistic 128 × 128 colour images of plants. We train our network conditioning on leaf count, such that it is possible to generate plants with a given number of leaves suitable, among others, for training regression based models. We propose a new Ax dataset of artificial plants images, obtained by our ARIGAN. We evaluate this new dataset using a state-of-the-art leaf counting algorithm, showing that the testing error is reduced when Ax is used as part of the training data.
MERIT: a Mutation Error Rate Identification Toolkit for Ultra-deep Sequencing Applications
Authors: Hadigol Mohammad , Khiabanian Hossein
Published: September 2017

Rapid progress in high-throughput sequencing (HTS) has enabled the molecular characterization of mutational landscapes in heterogeneous populations and has improved our understanding of clonal evolution processes. Analyzing the sensitivity of detecting genomic mutations in HTS requires comprehensive profiling of sequencing artifacts. To this end, we introduce MERIT, designed for in-depth quantification of erroneous substitutions and small insertions and deletions, specifically for ultra-deep applications. MERIT incorporates an all-inclusive variant caller and considers genomic context, including the nucleotides immediately at 5′ and 3′, thereby establishing error rates for 96 possible substitutions as well as four singlebase and 16 double-base indels. We apply MERIT to ultra-deep sequencing data (1,300,000×) and show a significant relationship between error rates and genomic contexts. We devise anin silicoapproach to determine the optimal sequencing depth, where errors occur at rates similar to those of true mutations. Finally, we assess nucleotide-incorporation fidelity of four high-fidelity DNA polymerases in clinically relevant loci, and demonstrate how fixed detection thresholds may result in substantial false positive as well as false negative calls.
Local context influences memory for emotional stimuli but not electrophysiological markers of emotion-dependent attention
Authors: Barnacle Gemma E. , Tsivilis Dimitris , Schaefer Alexandre , Talmi Deborah
Published: September 2017

Emotional Enhancement of free recall can be context dependent. It is readily observed when emotional and neutral scenes are encoded and recalled together, in a ‘mixed’ list, but diminishes when these scenes are encoded separately, in ‘pure’ lists. We examined the hypothesis that this effect is due to differences of allocation of attention to neutral stimuli according to whether they are presented in mixed or pure lists, especially when encoding is intentional. Using picture stimuli that were controlled for semantic relatedness, our results contradicted this hypothesis. The amplitude of well-known electrophysiological markers of emotion-related attention - the Early Posterior Negativity (EPN), the Late Positive Potential (LPP), and the Slow Wave (SW) - was higher for emotional stimuli. Crucially, the emotional modulation of these ERPs was insensitive to list context, observed equally in pure and mixed lists. Although list context did not modulate neural markers of emotion-related attention, list context did modulate the effect of emotion on free recall. The apparent decoupling of the emotional effects on attention and memory challenges existing hypotheses accounting for the emotional enhancement of memory. We close by discussing whether findings are more compatible with an alternative hypothesis, where the magnitude of emotional memory enhancement is, at least in part, a consequence of retrieval dynamics.
The INO80 Chromatin Remodeler Sustains Metabolic Stability by Promoting TOR Signaling and Regulating Histone Acetylation
Authors: Beckwith Sean L. , Schwartz Erin K. , Garcia-Nieto Pablo E. , King Devin A. , Gowans Graeme J. , Wong Ka Man , Yao Wei , Eckley Tessa L. , Paraschuk Alexander P. , Peltan Egan , Lee Laura R. , Morrison Ashby J.
Published: September 2017

Chromatin remodeling complexes are essential for gene expression programs that coordinate cell function with metabolic status. However, how these remodelers are integrated in metabolic stability pathways is not well known. Here, we report an expansive genetic screen with chromatin remodelers and metabolic regulators inSaccharomyces cerevisiae. We found that, unlike the SWR1 remodeler, the INO80 chromatin remodeling complex is composed of multiple distinct functional subunit modules. We identified a strikingly divergent genetic signature for the Ies6 subunit module that links the INO80 complex to metabolic homeostasis, including mitochondrial maintenance. INO80 is also needed to communicate TORC1-mediated signaling to chromatin and maintains histone acetylation at TORC1-responsive genes. Furthermore, computational analysis reveals subunits of INO80 and mTORC1 have high co-occurrence of alterations in human cancers. Collectively, these results demonstrate that the INO80 complex is a central component of metabolic homeostasis that influences histone acetylation and may contribute to disease when disrupted.
Berkeley Screen: a set of 96 solutions for general macromolecular crystallization
Authors: Pereira Jose H. , McAndrew Ryan P. , Tomaleri Giovani P. , Adams Paul D.
Published: September 2017

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.
Crystal structure of 7β-hydroxyroyleanone isolated fromTaxodium ascendens(B.)
Authors: Xu Shicheng , Ma Xinhua , Ke Ruifang , Deng Shihao , Yang Xinzhou , Song Ping
Published: September 2017

The title compound, C20H28O4[systematic name: (4bS,8aS,10S)-3,10-dihydroxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthrene-1,4-dione], is an abietane-type diterpene, which was isolated fromTaxodium ascendens(B.). The compound crystallizes in the chiral space groupP21, but it was not possible to determine the absolute structure of the molecule in the crystal by resonant scattering. The molecular structure is stabilized by two intramolecular O—H...O hydrogen bonds, enclosingS(5) andS(6) ring motifs. In the crystal, molecules are linked by O—H...O and C—H...O hydrogen bonds, forming chains along the [010] direction. The crystal structure of the 10Rstereoisomer of the title compound, isolated from the roots ofPremna obtusifolia(Verbenaceae), has been reported. It crystallized in the chiral space groupP212121, and the absolute structure was determined as (4bS,8aS,10R), by resonant scattering using CuKα radiation [Razaket al.(2010).Acta Cryst.E66, o1566–o1567].
(η4-1,5-Cyclooctadiene)[(R)-(+)-5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(diphenylphosphanyl)-1,1′-binaphthyl-κ2P,P′]rhodium(I) tetrafluoroborate 0.72-pentane 0.56-methanol solvate
Authors: Pribbenow Cornelia , Rueger Julia , Drexler Hans-Joachim , Heller Detlef
Published: September 2017

The title compound, [Rh(C8H12)(C44H20P2)]BF4·0.72C5H12·0.56·CH4O, crystallizes in the Sohncke space groupP21. The RhIcentre is coordinated by a H8-BINAP 5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(diphenylphosphanyl)-1,1′-binaphthyl ligand and by a bidentate η2,η2-coordinated cod (cycloocta-1,5-diene) ligand. The asymmetric unit contains one cation, one anion and cocrystallized pentane [occupancy 0.720 (4)] and methanol [2 × 0.280 (4) occupancy] molecules. The rhodium(I) complex [Rh(H8-BINAP)(cod)]BF4has been applied as a precatalyst in the asymmetric intramolecular [2+2+2] cycloaddition of enediynes, affording excellent enantiomeric excesses [Shibataet al.(2007).J. Org. Chem.72, 6521–6525].