bluuebunny/crossref_metadata_2025 huggingface dataset:
Methods of erection of high-rise buildings
Authors: Cherednichenko Nadezhda , Oleinik Pavel
Published: March 2018

The article contains the factors determining the choice of methods for organizing the construction and production of construction and installation work for the construction of high-rise buildings. There are also indicated specific features of their underground parts, characterized by powerful slab-pile foundations, large volumes of earthworks, reinforced bases and foundations for assembly cranes. The work cycle is considered when using reinforced concrete, steel and combined skeletons of high-rise buildings; the areas of application of flow, separate and complex methods are being disclosed. The main conditions for the erection of high-rise buildings and their components are singled out: the choice of formwork systems, delivery and lifting of concrete mixes, installation of reinforcement, the formation of lifting and transporting and auxiliary equipment. The article prescribes the reserves of reduction in the duration of construction due to the creation of: complex mechanized technologies for the efficient construction of foundations in various soil conditions, including in the heaving, swelling, hindered, subsidence, bulk, water-saturated forms; complex mechanized technologies for the erection of monolithic reinforced concrete structures, taking into account the winter conditions of production and the use of mobile concrete-laying complexes and new generation machines; modular formwork systems, distinguished by their versatility, ease, simplicity in operation suitable for complex high-rise construction; more perfect methodology and the development of a set of progressive organizational and technological solutions that ensure a rational relationship between the processes of production and their maximum overlap in time and space.
Current-day matters of administration and law in the field of high-rise construction
Authors: Voskresenskaya Elena , Snetkov Vitaly , Tebryaev Alexander
Published: March 2018

The article touches upon main reasons for high-rise construction: increase in energy consumption and limited availability of site in the big cities of Russia. Increase in energy consumption is related with construction, transportation and applying of ventilation and air conditioning systems. Nowadays, there are developed a lot of design and engineer solutions, that include autonomous systems as well as passive methods with low energy consumption rate, which are interrelated with local climate conditions. Certain architectural solutions contribute to energy consumption decrease: building orientation with respect to the cardinal directions, taking into account the prevailing cold wind directions, maximum glazing of the southern facades and minimum glazing of the northern ones, what plays a big role in hard climate conditions. Limited availability of site for construction in the big cities resulted in rapid development of the high-rise construction, which today prevails in terms of quantitative indicators of civil engineering.
Measures to reduce construction time of high-rise buildings
Authors: Kolchedantsev Leonid , Adamtsevich Aleksey , Stupakova Olga , Drozdov Alexander
Published: March 2018

The organizational and technological solutions for high-rise buildings construction efficiency increase are considered, primarily – decrease of typical floor construction time and improvement of bearing structures concrete quality. The essence of offered technology is: a concrete mixing station and a polygon mainly for load-bearing wall panels with starter bars casting are located on the building site; for reinforced concrete components manufacturing and butt joints grouting the warmed-up concrete mixtures are used. The results of researches and elaborations carried out by the SPSUACE in area of a preliminary warming-up of concrete mixtures are presented. The possibility and feasibility of their usage in high-rise buildings and of excess height buildings construction including cast-in-place and precast execution are shown. The essence of heat-vibro treating of concrete mixture is revealed as a kind of prior electroresistive curing, and the achieved results are: accelerated concrete strength gain, power inputs decrease, concrete quality improvement. It is shown that the location of a concrete mixing station on the building site enables to broaden possibilities of the “thermos” method use and to avoid concrete mixtures warming up in medium-mass structures erection (columns, girders) during the high-rise buildings construction. It is experimentally proved that the splice between precast elements encased with warmed-up concrete mixture is equal with conjugated elements in strength.
Socioecological Aspects of High-rise Construction
Authors: Eichner Michael , Ivanova Zinaida
Published: March 2018

In this article, the authors consider the socioecological problems that arise in the construction and operation of high-rise buildings. They study different points of view on high-rise construction and note that the approaches to this problem are very different. They also analyse projects of modern architects and which attempts are made to overcome negative impacts on nature and mankind. The article contains materials of sociological research, confirming the ambivalent attitude of urban population to high-rise buildings. In addition, one of the author’s sociological survey reveals the level of environmental preparedness of the university students, studying in the field of "Construction of unique buildings and structures", raising the question of how future specialists are ready to take into account socioecological problems. Conclusion of the authors: the construction of high-rise buildings is associated with huge social and environmental risks, negative impact on the biosphere and human health. This requires deepened skills about sustainable design methods and environmental friendly construction technologies of future specialists. Professor M. Eichner presents in the article his case study project results on implementation of holistic eco-sustainable construction principles for mixed-use high-rise building in the metropolis of Cairo.
Prompt fission neutron emission in the reaction 235U(n,f)
Authors: Göök Alf , Hambsch Franz-Josef , Oberstedt Stephan
Published: March 2018

Experimental activities at JRC-Geel on prompt fission neutron (PFN) emission in response to OECD/NEA nuclear data requests are presented in this contribution. Specifically, on-going investigations of PFN emission from the reaction 235U(n,f) in the region of the resolved resonances, taking place at the GELINA facility, are presented. The focus of this contribution lies on studies of PFN correlations with fission fragment properties. The experiment employs a scintillation detector array for neutron detection, while fission fragment properties are determined via the double kinetic energy technique using a position sensitive twin ionization chamber. This setup allows us to study several correlations between properties of neutron and fission fragments simultaneously. Results on PFN correlations with fission fragment properties from the present study differ significantly from earlier studies on this reaction, induced by thermal neutrons.
The 4-dimensional Langevin approach to low energy nuclear fission
Authors: Ivanyuk F.A. , Ishizuka C. , Usang M.D. , Chiba S.
Published: March 2018

We applied the four-dimensional Langevin approach to the description of fission of 235U by neutrons and calculated the dependence of the excitation energy of fission fragments on their mass number. For this we have fitted the compact just-before-scission configuration obtained by the Langevin calculations by the two separated fragments and calculated the intrinsic excitation and the deformation energy of each fragment accurately taking into account the shell and pairing effects and their dependence on the temperature and mass of the fragments. For the sharing of energy between the fission fragments we have used the simplest and most reliable assumption - the temperature of each fragment immediately after the neck rupture is the same as the temperature of mother nucleus just before scission. The calculated excitation energy of fission fragments clearly demonstrates the saw-tooth structure in the dependence on fragment mass number.
Implementing and testing theoretical fission fragment yields in a Hauser-Feshbach statistical decay framework
Authors: Jaffke Patrick , Möller Peter , Stetcu Ionel , Talou Patrick , Schmitt Christelle
Published: March 2018

We implement fission fragment yields, calculated using Brownian shape-motion on a macroscopic-microscopic potential energy surface in six dimensions, into the Hauser-Feshbach statistical decay code CGMF. This combination allows us to test the impact of utilizing theoretically-calculated fission fragment yields on the subsequent prompt neutron and γ-ray emission. We draw connections between the fragment yields and the total kinetic energy TKE of the fission fragments and demonstrate that the use of calculated yields can introduce a difference in the 〈TKE〉 and, thus, the prompt neutron multiplicity v, as compared with experimental fragment yields. We deduce the uncertainty on the 〈TKE〉 and v from this procedure and identify possible applications.
A new electron density model of the plasmasphere for operational applications and services
Authors: Jakowski Norbert , Hoque Mohammed Mainul
Published: March 2018

The Earth's plasmasphere contributes essentially to total electron content (TEC) measurements from ground or satellite platforms. Furthermore, as an integral part of space weather, associated plasmaspheric phenomena must be addressed in conjunction with ionosphere weather monitoring by operational space weather services. For supporting space weather services and mitigation of propagation errors in Global Navigation Satellite Systems (GNSS) applications we have developed the empirical Neustrelitz plasmasphere model (NPSM). The model consists of an upper L shell dependent part and a lower altitude dependent part, both described by specific exponential decays. Here the McIllwain parameter L defines the geomagnetic field lines in a centered dipole model for the geomagnetic field. The coefficients of the developed approaches are successfully fitted to numerous electron density data derived from dual frequency GPS measurements on-board the CHAMP satellite mission from 2000 to 2005. The data are utilized for fitting up to the L shell L = 3 because a previous validation has shown a good agreement with IMAGE/RPI measurements up to this value. Using the solar radio flux index F10.7 as the only external parameter, the operation of the model is robust, with 40 coefficients fast and sufficiently accurate to be used as a background model for estimating TEC or electron density profiles in near real time GNSS applications and services. In addition to this, the model approach is sensitive to ionospheric coupling resulting in anomalies such as the Nighttime Winter Anomaly and the related Mid-Summer Nighttime Anomaly and even shows a slight plasmasphere compression of the dayside plasmasphere due to solar wind pressure. Modelled electron density and TEC values agree with estimates reported in the literature in similar cases.
Immunohistochemical Detection of Motor Endplates in the Long-Term Denervated Muscle
Authors: Chen Jingming , Li Jing , Nyirenda Themba , Fowkes Mary , Sobotka Stanislaw , Mu Liancai
Published: March 2018

Background We have demonstrated that the native motor zone (NMZ) within a muscle is an ideal target for performing nerve-muscle-endplate band grafting (NMEG) to restore motor function of a denervated muscle. This study was designed to determine spatiotemporal alterations of the myofibers, motor endplates (MEPs), and axons in the NMZ of long-term denervated muscles for exploring if NMEG-NMZ technique would have the potential for delayed reinnervation.

Methods Sternomastoid (SM) muscles of adult female Sprague-Dawley rats (n = 21) were experimentally denervated and denervation-induced changes in muscle weight, myofiber size, MEPs, and intramuscular nerve axons were evaluated histomorphometrically and immunohistochemically at the end of 3, 6, and 9 months after denervation. The values obtained from the ipsilateral normal side served as control.

Results The denervated SM muscles exhibited a progressive reduction in muscle weight (38%, 31%, and 19% of the control) and fiber diameter (52%, 40%, and 28% of the control) for 3-, 6-, and 9-month denervation, respectively. The denervated MEPs were still detectable even 9 months after denervation. The mean number of the denervated MEPs was 79%, 65%, and 43% of the control in the 3-, 6-, and 9-month denervated SM, respectively. Degenerated axons in the denervated muscles became fragmented.

Conclusions Persistence of MEPs in the long-term denervated SM suggests that some surgeries targeting the MEPs such as NMEG-NMZ technique should be effective for delayed reinnervation. However, more work is needed to develop strategies for preservation of muscle mass and MEPs after denervation.
Development of a Device-Assisted Nerve-Regeneration Procedure in Disruptive Lesions of the Brachial Plexus
Authors: Manunta Maria , Mao Yong , Masala Gerolamo , Careddu Giovanni , Cubeddu Francesca , Evangelisti Maria , Guida Maria , Verardi Caroline , Proietti Claudio , Manunta Andrea , D'Urso Labate Giuseppe , Catapano Gerardo , Polunas Marianne , Louro Pedro , Passino Eraldo , Merolli Antonio
Published: March 2018

Background We describe the development of a new surgical procedure to be used in the treatment of disruptive brachial plexus (BP) lesions. It is centered on an artificial device designed to assist nerve regeneration by providing a confined and protected environment. Nerve fibers can repair inside the device, while the adverse massive scar-tissue formation is limited to the outside of the device.

Methods Steps in the development of the procedure were (1) definition of the rationale, (2) design of the device, (3) choice of an in vivo translational model, (4)refinement of the surgical procedure, and (5) performance of an in vivo pilot study as a proof of concept. An interdisciplinary team from several laboratories was involved in this work over a period of 6 years.

Results Results showed the absence of significant scar tissue in the regenerate and the presence of myelinated fibers aligned proximodistally between the stumps. This surgical approach can be seen not only as a definitive treatment but also as an early examination and stabilization before some different surgery will be later performed. It may also be used as additional protection for traditional surgery like end-to-end coaptation.

Conclusions We conclude that the availability of a suitable device-assisted early treatment, even if not to be considered definitive, could help in addressing the BP lesions at an earlier stage and this may improve the final outcome. Our evidence justifies further experimentation on this approach.
Genetic Variation, Magnesium Sulfate Exposure, and Adverse Neurodevelopmental Outcomes Following Preterm Birth
Authors: Weiner Steven , Rouse Dwight , Mercer Brian , Reddy Uma , Iams Jay , Wapner Ronald , Sorokin Yoram , Malone Fergal , O'Sullivan Mary , Peaceman Alan , Hankins Gary , Dudley Donald , Caritis Steve , Clark Erin ,   for the Eunice Kennedy Shriver National Institute of Child Health Human Development Maternal-Fetal Medicine Units (MFMU) Network
Published: March 2018

Objective To evaluate the association of magnesium sulfate (MgSO4) exposure and candidate gene polymorphisms with adverse neurodevelopmental outcomes following preterm birth.

Study Design We performed a nested case–control analysis of a randomized trial of maternal MgSO4 before anticipated preterm birth for the prevention of cerebral palsy (CP). Cases were children who died within 1 year of life or were survivors with abnormal neurodevelopment at age 2 years. Controls were race- and sex-matched survivors with normal neurodevelopment. We analyzed 45 candidate gene polymorphisms in inflammation, coagulation, and vascular regulation pathways and their association with (1) psychomotor delay, (2) mental delay, (3) CP, and (4) combined outcome of death/CP. Logistic regression analyses, conditional on maternal race and child sex, and adjusted for treatment group, gestational age at birth and maternal education, were performed.

Results Four hundred and six subjects, 211 cases and 195 controls, were analyzed. The strongest association was for IL6R (rs 4601580) in which each additional copy of the minor allele was associated with an increased risk of psychomotor delay (adjusted odds ratio 3.3; 95% confidence interval, 1.7–6.5; p < 0.001).

Conclusion Candidate gene polymorphisms are associated with death and adverse neurodevelopmental outcomes following preterm birth. MgSO4 may abrogate this genotype association for some loci.
Perioperative Complications in Neonatal Surgery: Biliary Atresia and Choledochal Malformations
Authors: Wilde Jim , Calinescu Ana , Wildhaber Barbara
Published: March 2018

Biliary atresia (BA) and congenital choledochal malformations (CCM) are rare. Both pathologies must (BA) or may (CCM) be operated during the neonatal period or early infancy. We briefly describe the classical operative techniques for both pathologies, followed by the most common and severe perioperative complications encountered during and up to 30 days after surgery in children operated for BA and CCM early in life. For patients with BA, intestinal complications represent the most common and hazardous perioperative surgical complications. Cholangitis is the most frequently encountered medical complication post hepato-porto-enterostomy. For CCM, it seems that neonates encounter little perioperative complications; however, reports are scarce; bile leak and/or cholangitis are the most reported. Overall, for patients with CCM, the literature is ambivalent whether more perioperative complications occur in the younger or in the older patient, and whether these occur more frequently in those symptomatic or asymptomatic at operation. It is difficult to give clear advice for when children with asymptomatic CCM should be operated, and benefits and risks must be carefully counterbalanced. Perioperative mortality for both BA and CCM is low and is reported to be around 1 to 2%.
In Vitro Studies on Physiological and Chemical Stability of New LE404-Derivatives with Extended Half-Life
Authors: Zergiebel Stephanie , Seeling Andreas
Published: March 2018

Dibenzoazecines are a class of potential neuroleptics with high affinity to dopamine and serotonin receptors. The efficacy and high therapeutic range has already been demonstrated in vivo with the lead structure 7-methyl-5,6,7,8,9,14-hexahydrodibenzo[d,g]azecin-3-ol (LE404) and selected derivatives. There is a variety of new synthesized structurally different dibenzoazecine derivatives with the aim to improve pharmacokinetic parameters, all of which contain the lead structure LE404. For a multitude of these substances is still a lack of information, inclusive of stability, physicochemical parameters, pharmacokinetics and metabolism. Therefore, the present study investigated the stability properties of 17 new azecine derivatives, including esterase cleavage, stability in simulated gastrointestinal fluid, stability at different pH-values and determination of octanol/water-partition coefficients. These findings, in correlation to the properties and efficacy of the already in vivo tested substances, will be useful for safety and efficacy in further in vivo tests.
Kα emission by the electrons with bi-Maxwellian distribution in a Cu foil
Authors: Zhao J. C. , Cao L. H. , Zhao Z. Q. , Liu Z. J. , Zheng C. Y. , Zhang H. , Gu Y. Q. , Liu J.
Published: March 2018

In our previous research [J. C. Zhao et al., Laser Part. Beams 35, 483 (2017)], we studied the influence of the electron refluxing on the electron transport and Kα emission in a solid target. In this work, the electrons with the bi-Maxwellian distribution of low temperature T1 and high temperature T2 interacting with Cu foil to produce Kα emission are investigated when the electron refluxing effect is included or excluded. Simulation results show that including the refluxing effect, high temperature T2 plays a more significant role in the Kα photon yield, while in the absence of the refluxing effect, the low temperature T1 has a dominant effect. In addition, at the target thickness d ≈ 20 μm, the maximum Kα yield is achieved when the electrons with bi-Maxwellian distribution interact with the Cu target including the refluxing effect. As emitted electrons have the bi-Maxwellian distribution of T1 = 0.1 MeV and T2 = 1.4 MeV, the Kα photon yield is always higher than that in other bi-Maxwellian distributions. Therefore, when the low temperature T1 tends towards a larger value and the high temperature T2 tends towards a smaller one, the maximum Kα photon yield will be obtained whether the electron refluxing effect is considered or not.
Solvent effect on FRET spectroscopic ruler
Authors: Qu Songyuan , Liu Chuanbo , Liu Qiong , Wu Wei , Du Baoji , Wang Jin
Published: March 2018

A discrepancy has emerged in recent years between single-molecule Förster resonance energy transfer (smFRET) measurements and small angle X-ray scattering (SAXS) or small angle neutron scattering experiments in the study of unfolded or intrinsically disordered proteins in denaturing solutions. Despite significant advances that have been made in identifying various factors which may have contributed to the manifestation of the so-called smFRET-SAXS discrepancy, no consensus has been reached so far on its original source or eventual resolution. In this study, we investigate this problem from the perspective of the solvent effect on FRET spectroscopic ruler (SEFSR), a generic term we use to describe various solvent-dependent factors affecting the accuracy of the FRET experimental method that is known as a “spectroscopic ruler.” Some factors belonging to SEFSR, such as direct dye-solvent interaction and labeling configuration, seem to have not received due attention regarding their significance in contributing to the discrepancy. We identify SEFSR by measuring a rigid segment of a double-stranded DNA in various solutions using the smFRET method and evaluate its relative importance in smFRET experiments by measuring segments of a single-stranded DNA and polyethylene glycol (PEG) in solutions. We find that SEFSR can produce non-negligible FRET-inferred interdye distance changes in various solutions, with an intensity following the Hofmeister series in ionic solutions and dependent on labeling configurations. SEFSR is found to be significant in GuHCl and urea solutions, which can fully cover the apparent expansion signal of dye-labeled PEG. Our findings suggest that SEFSR may have played an important role in contributing to the smFRET-SAXS discrepancy.
Versatile silicon-waveguide supercontinuum for coherent mid-infrared spectroscopy
Authors: Nader Nima , Maser Daniel L. , Cruz Flavio C. , Kowligy Abijith , Timmers Henry , Chiles Jeff , Fredrick Connor , Westly Daron A. , Nam Sae Woo , Mirin Richard P. , Shainline Jeffrey M. , Diddams Scott
Published: March 2018

Laser frequency combs, with their unique combination of precisely defined spectral lines and broad bandwidth, are a powerful tool for basic and applied spectroscopy. Here, we report offset-free, mid-infrared frequency combs and dual-comb spectroscopy through supercontinuum generation in silicon-on-sapphire waveguides. We leverage robust fabrication and geometrical dispersion engineering of nanophotonic waveguides for multi-band, coherent frequency combs spanning 70 THz in the mid-infrared (2.5 μm–6.2 μm). Precise waveguide fabrication provides significant spectral broadening with engineered spectra targeted at specific mid-infrared bands. We characterize the relative-intensity-noise of different bands and show that the measured levels do not pose any limitation for spectroscopy applications. Additionally, we use the fabricated photonic devices to demonstrate dual-comb spectroscopy of a carbonyl sulfide gas sample at 5 μm. This work forms the technological basis for applications such as point sensors for fundamental spectroscopy, atmospheric chemistry, trace and hazardous gas detection, and biological microscopy.
Dynamic load mitigation using dissipative elastic metamaterials with multiple Maxwell-type oscillators
Authors: Alamri Sagr , Li Bing , Tan K. T.
Published: March 2018

Dissipative elastic metamaterials have attracted increased attention in recent times. This paper presents the development of a dissipative elastic metamaterial with multiple Maxwell-type resonators for stress wave attenuation. The mechanism of the dissipation effect on the vibration characteristics is systematically investigated by mass-spring-damper models with single and dual resonators. Based on the parameter optimization, it is revealed that a broadband wave attenuation region (stopping band) can be obtained by properly utilizing interactions from resonant motions and viscoelastic effects of the Maxwell-type oscillators. The relevant numerical verifications are conducted for various cases, and excellent agreement between the numerical and theoretical frequency response functions is shown. The design of this dissipative metamaterial system is further applied for dynamic load mitigation and blast wave attenuation. Moreover, the transient response in the continuum model is designed and analyzed for more robust design. By virtue of the bandgap merging effect induced by the Maxwell-type damper, the transient blast wave can be almost completely suppressed in the low frequency range. A significantly improved performance of the proposed dissipative metamaterials for stress wave mitigation is verified in both time and frequency domains.
Normal-mode-based analysis of electron plasma waves with second-order Hermitian formalism
Authors: Ramos J. J. , White R. L.
Published: March 2018

The classic problem of the dynamic evolution and Landau damping of linear Langmuir electron waves in a collisionless plasma with Maxwellian background is cast as a second-order, self-adjoint problem with a continuum spectrum of real and positive squared frequencies. The corresponding complete basis of singular normal modes is obtained, along with their orthogonality relation. This yields easily the general expression of the time-reversal-invariant solution for any initial-value problem. Examples are given for specific initial conditions that illustrate different behaviors of the Landau-damped macroscopic moments of the perturbations.
High thermal conductivity for ultrapure semiconductors proven experimentally
Authors: Johnson Sally Cole
Published: March 2018

With an ultrapure crystal made of Si-28, researchers demonstrate the impact of impurities on thermal conductivity and establish a new theoretical reference.
Comparing Australian gay and bisexual men with undiagnosed and recently diagnosed HIV infection to those in the National HIV Registry
Authors: Down Ian , Prestage Garrett , Brown Graham , Ellard Jeanne , Guy Rebecca , Hellard Margaret , Wilson David , de Wit John , Stoové Mark , Holt Martin
Published: March 2018

Background Gay and bisexual men (GBM) with recent HIV infection are a key population to inform HIV-prevention. The National HIV Registry (NHR) provides details about all individuals diagnosed with HIV, but it is unclear how. Methods: Basic sociodemographic characteristics of GBM in the NHR who were diagnosed between 2010 and 2014 were compared with three samples of GBM: men with undiagnosed HIV infection from the Community-Based Study of Undiagnosed HIV and Testing (COUNT) study of HIV prevalence and undiagnosed infection that was conducted during 2013–14; men in the Australian Gay Community Periodic Surveys (GCPS) who were diagnosed with HIV between 2010 and 2014; and men in the HIV Seroconversion Study (SCS) who were also diagnosed in those years. Results: The NHR identified 3629 men who reported male-to-male sex as the exposure risk for their diagnosis between 2010 and 2014. COUNT identified 19 (8.9% of all men who tested HIV positive) men as having undiagnosed HIV. In the GCPS sample, 185 (2.5%) reported being diagnosed with HIV in 2010–14. In total, 367 men in the SCS received their diagnosis during 2010–14. The mean age of men in the NHR (36.8 years) was similar to that in GCPS (36.3 years) and SCS (35.1 years), while undiagnosed men in COUNT were younger (32.6 years), with no other significant differences between the samples. Conclusions: The undiagnosed men were somewhat younger than diagnosed men. To achieve earlier diagnosis of new HIV infections, improved HIV testing frequency is needed among younger men.
Susceptibility of brain atrophy to
TRIB3
in Alzheimer’s disease, evidence from functional prioritization in imaging genetics
Authors: Lorenzi Marco , Altmann Andre , Gutman Boris , Wray Selina , Arber Charles , Hibar Derrek P. , Jahanshad Neda , Schott Jonathan M. , Alexander Daniel C. , Thompson Paul M. , Ourselin Sebastien ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: March 2018

Significance

In this study, we use an experimental imaging–genetics approach for investigating the genetic underpinnings of brain atrophy in Alzheimer’s disease. We successfully combined state-of-the-art imaging–genetics methods and experimental gene expression data to uncover biology in brain atrophy. The experimental paradigm highlighted a significant role of tribbles pseudokinase 3 (
TRIB3
) in modulating the typical pattern of Alzheimer’s brain pathology. This result corroborates through rigorous data-driven statistical methods evidence emerging from previous studies about the role of
TRIB3
in modulating known mechanisms of neurodegeneration, such as neuronal death, cellular homeostasis, and interaction with established genes causing autosomal dominant Alzheimer’s disease:
APP
and
PSEN1
. The developed integrated statistical–experimental methodology could serve as a roadmap for investigations in other disorders.
Solution of the multistep pathway for assembly of corynanthean, strychnos, iboga, and aspidosperma monoterpenoid indole alkaloids from 19
E
-geissoschizine
Authors: Qu Yang , Easson Michael E. A. M. , Simionescu Razvan , Hajicek Josef , Thamm Antje M. K. , Salim Vonny , De Luca Vincenzo
Published: March 2018

Significance

The multistep assembly of catharanthine and tabersonine from strictosidine remains poorly characterized for understanding the biochemistry of anticancer monoterpenoid indole alkaloid (MIA) biosynthesis in the medicinal plant,
Catharanthus roseus
. The seven-step pathway from 19
E
-geissoschizine to four major MIA skeletons enables the assembly of catharanthine and tabersonine that complete the pathway for biosynthesis of the anticancer drugs, anhydrovinblastine and vincristine as well as for production of other biologically active MIAs.
Murine knockin model for progranulin-deficient frontotemporal dementia with nonsense-mediated mRNA decay
Authors: Nguyen Andrew D. , Nguyen Thi A. , Zhang Jiasheng , Devireddy Swathi , Zhou Ping , Karydas Anna M. , Xu Xialian , Miller Bruce L. , Rigo Frank , Ferguson Shawn M. , Huang Eric J. , Walther Tobias C. , Farese Robert V.
Published: March 2018

Significance

Mutations in the
GRN
gene cause frontotemporal dementia, a devastating neurological disease. The majority of these
GRN
mutations are nonsense and frameshift mutations. Here, we generated a knockin mouse model with a
Grn
mutation corresponding to the most prevalent human disease mutation,
GRN

R493X

. We show that mice harboring this mutation phenocopy progranulin-deficient mice, and that the mutation triggers mRNA decay and, as a consequence, low production of
Grn
. However, the truncated mutant protein that would be produced from this allele is functional, suggesting inhibiting mRNA decay as a therapeutic approach for individuals with progranulin-deficient frontotemporal dementia caused by nonsense mutations.
To be Black. to be a Woman. Can Dramatherapy help Black Women to Discover Their True Self despite Racial and Gender Oppression?
Authors: Maynard Kairo
Published: March 2018

This article is part of an arts-based, auto-ethnographic report that focuses on the complexities of Black women's identity, in relation to my own journey of self-discovery when navigating societal racism and sexism. The body of work documents my process as I devised a 30-minute solo performance, while the rehearsal process highlights assimilation similarities between Hans Christian Anderson's The Little Mermaid and the experiences faced by Black women. This revelation opened new dramatic possibilities for me to create four characters based on the negative roles ascribed to Black women in Western society. Moreover, role theory has been applied to promote psychological healing, while the dramatic metaphor acts as a container. Embodiment and role are central to dramatherapeutic practice; by exploring ourselves through role, we can understand the roles and masks we adopt, through either choice or obligation. Throughout history, Black women are said to experience harsher societal and cultural pressures, including disproportionately high levels of racism. Prolonged racial chastisement through Western external and culture-based messages can negatively inform identity and sense of self. This can lead to mental health issues caused by internalised racism, defined as integrating as true the negative stereotypes perpetuated by white-dominant society.
Optimizing a Sensor Network with Data from Hazard Mapping Demonstrated in a Heavy-Vehicle Manufacturing Facility
Authors: Berman Jesse D , Peters Thomas M , Koehler Kirsten A
Published: March 2018

Objectives

To design a method that uses preliminary hazard mapping data to optimize the number and location of sensors within a network for a long-term assessment of occupational concentrations, while preserving temporal variability, accuracy, and precision of predicted hazards.

Methods

Particle number concentrations (PNCs) and respirable mass concentrations (RMCs) were measured with direct-reading instruments in a large heavy-vehicle manufacturing facility at 80–82 locations during 7 mapping events, stratified by day and season. Using kriged hazard mapping, a statistical approach identified optimal orders for removing locations to capture temporal variability and high prediction precision of PNC and RMC concentrations. We compared optimal-removal, random-removal, and least-optimal-removal orders to bound prediction performance.

Results

The temporal variability of PNC was found to be higher than RMC with low correlation between the two particulate metrics (ρ = 0.30). Optimal-removal orders resulted in more accurate PNC kriged estimates (root mean square error [RMSE] = 49.2) at sample locations compared with random-removal order (RMSE = 55.7). For estimates at locations having concentrations in the upper 10th percentile, the optimal-removal order preserved average estimated concentrations better than random- or least-optimal-removal orders (P < 0.01). However, estimated average concentrations using an optimal-removal were not statistically different than random-removal when averaged over the entire facility. No statistical difference was observed for optimal- and random-removal methods for RMCs that were less variable in time and space than PNCs.

Conclusions

Optimized removal performed better than random-removal in preserving high temporal variability and accuracy of hazard map for PNC, but not for the more spatially homogeneous RMC. These results can be used to reduce the number of locations used in a network of static sensors for long-term monitoring of hazards in the workplace, without sacrificing prediction performance.
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank
Authors: You Ronghui , Zhang Zihan , Xiong Yi , Sun Fengzhu , Mamitsuka Hiroshi , Zhu Shanfeng
Published: March 2018

Motivation

Gene Ontology (GO) has been widely used to annotate functions of proteins and understand their biological roles. Currently only <1% of >70 million proteins in UniProtKB have experimental GO annotations, implying the strong necessity of automated function prediction (AFP) of proteins, where AFP is a hard multilabel classification problem due to one protein with a diverse number of GO terms. Most of these proteins have only sequences as input information, indicating the importance of sequence-based AFP (SAFP: sequences are the only input). Furthermore, homology-based SAFP tools are competitive in AFP competitions, while they do not necessarily work well for so-called difficult proteins, which have <60% sequence identity to proteins with annotations already. Thus, the vital and challenging problem now is how to develop a method for SAFP, particularly for difficult proteins.

Methods

The key of this method is to extract not only homology information but also diverse, deep-rooted information/evidence from sequence inputs and integrate them into a predictor in a both effective and efficient manner. We propose GOLabeler, which integrates five component classifiers, trained from different features, including GO term frequency, sequence alignment, amino acid trigram, domains and motifs, and biophysical properties, etc., in the framework of learning to rank (LTR), a paradigm of machine learning, especially powerful for multilabel classification.

Results

The empirical results obtained by examining GOLabeler extensively and thoroughly by using large-scale datasets revealed numerous favorable aspects of GOLabeler, including significant performance advantage over state-of-the-art AFP methods.

Availability and implementation

http://datamining-iip.fudan.edu.cn/golabeler.

Supplementary information

Supplementary data are available at Bioinformatics online.
AnaCoDa: analyzing codon data with Bayesian mixture models
Authors: Landerer Cedric , Cope Alexander , Zaretzki Russell , Gilchrist Michael A
Published: March 2018

AnaCoDa is an R package for estimating biologically relevant parameters of mixture models, such as selection against translation inefficiency, non-sense errors and ribosome pausing time, from genomic and high throughput datasets. AnaCoDa provides an adaptive Bayesian MCMC algorithm, fully implemented in C++ for high performance with an ergonomic R interface to improve usability. AnaCoDa employs a generic object-oriented design to allow users to extend the framework and implement their own models. Current models implemented in AnaCoDa can accurately estimate biologically relevant parameters given either protein coding sequences or ribosome foot-printing data. Optionally, AnaCoDa can utilize additional data sources, such as gene expression measurements, to aid model fitting and parameter estimation. By utilizing a hierarchical object structure, some parameters can vary between sets of genes while others can be shared. Genes may be assigned to clusters or membership may be estimated by AnaCoDa. This flexibility allows users to estimate the same model parameter under different biological conditions and categorize genes into different sets based on shared model properties embedded within the data. AnaCoDa also allows users to generate simulated data which can be used to aid model development and model analysis as well as evaluate model adequacy. Finally, AnaCoDa contains a set of visualization routines and the ability to revisit or re-initiate previous model fitting, providing researchers with a well rounded easy to use framework to analyze genome scale data.

Availability and implementation

AnaCoDa is freely available under the Mozilla Public License 2.0 on CRAN (https://cran.r-project.org/web/packages/AnaCoDa/).
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework
Authors: Tsiantis Nikolaos , Balsa-Canto Eva , Banga Julio R
Published: March 2018

Motivation

Optimality principles have been used to explain many biological processes and systems. However, the functions being optimized are in general unknown a priori. Here we present an inverse optimal control framework for modeling dynamics in systems biology. The objective is to identify the underlying optimality principle from observed time-series data and simultaneously estimate unmeasured time-dependent inputs and time-invariant model parameters. As a special case, we also consider the problem of optimal simultaneous estimation of inputs and parameters from noisy data. After presenting a general statement of the inverse optimal control problem, and discussing special cases of interest, we outline numerical strategies which are scalable and robust.

Results

We discuss the existence, relevance and implications of identifiability issues in the above problems. We present a robust computational approach based on regularized cost functions and the use of suitable direct numerical methods based on the control-vector parameterization approach. To avoid convergence to local solutions, we make use of hybrid global-local methods. We illustrate the performance and capabilities of this approach with several challenging case studies, including simulated and real data. We pay particular attention to the computational scalability of our approach (with the objective of considering large numbers of inputs and states). We provide a software implementation of both the methods and the case studies.

Availability and implementation

The code used to obtain the results reported here is available at https://zenodo.org/record/1009541.

Supplementary information

Supplementary data are available at Bioinformatics online.
esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis
Authors: Wei Zheng , Zhang Wei , Fang Huan , Li Yanda , Wang Xiaowo
Published: March 2018

ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present ‘esATAC’, a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines and provides flexible interfaces for building customized pipelines.

Availability and implementation

esATAC package is open source under the GPL-3.0 license. It is implemented in R and C++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/esATAC.html).

Supplementary information

Supplementary data are available at Bioinformatics online.
Modelled salmon lice dispersion and infestation patterns in a sub-arctic fjord
Authors: Skarðhamar Jofrid , Albretsen Jon , Sandvik Anne D , Lien Vidar S , Myksvoll Mari S , Johnsen Ingrid A , Asplin Lars , Ådlandsvik Bjørn , Halttunen Elina , Bjørn Pål Arne
Published: March 2018

Salmon lice infestation is a major challenge for the aquaculture industry in Norway, threatening wild salmonid populations and causing welfare problems for farmed salmon. Lice dispersion and infestation patterns are simulated by combining a high-resolution hydrodynamic model for the Norwegian coast and fjords with an individual-based model for salmon lice. We here present results from Altafjorden, a sub-arctic fjord with large stocks of wild salmonids, where the inner part is protected as a National Salmon Fjord. The outer part of the fjord hosts several fish farms, and our simulations demonstrate how ocean currents can disperse lice between farms as well as into the protected part of the fjord. The relative contributions from the farms in the different parts of the fjord depends on their locations relative to the currents and circulation patterns in the fjord. Knowledge of how the highly variable water currents disperse salmon lice within fjord systems is necessary for managing farm locations and production quotas, if the goal is to minimize infestation pressure on wild salmonids and between fish farms.
Mid-infrared multi-wavelength imaging of Ophiuchus IRS 48 transitional disk
Authors: Honda Mitsuhiko , Okada Kazushi , Miyata Takashi , Mulders Gijs D , Swearingen Jeremy R , Kamizuka Takashi , Ohsawa Ryou , Fujiyoshi Takuya , Fujiwara Hideaki , Uchiyama Mizuho , Yamashita Takuya , Onaka Takashi
Published: March 2018

Transitional disks around the Herbig Ae/Be stars are fascinating targets in the contexts of disk evolution and planet formation. Oph IRS 48 is one of such Herbig Ae stars, which shows an inner dust cavity and azimuthally lopsided large dust distribution. We present new images of Oph IRS 48 at eight mid-infrared (MIR) wavelengths from 8.59 to 24.6 μm taken with COMICS mounted on the 8.2 m Subaru Telescope. The N-band (7 to 13 μm) images show that the flux distribution is centrally peaked with a slight spatial extent, while the Q-band (17 to 25 μm) images show asymmetric double peaks (east and west). Using 18.8- and 24.6 μm images, we derived the dust temperature at both east and west peaks to be 135 ±  22 K. Thus, the asymmetry may not be attributed to a difference in the temperature. Comparing our results with previous modeling works, we conclude that the inner disk is aligned to the outer disk. A shadow cast by the optically thick inner disk has a great influence on the morphology of MIR thermal emission from the outer disk.
Revision ACL Reconstruction in Children and Adolescents
Authors: Christino Melissa A. , Tepolt Frances A. , Sugimoto Dai , Micheli Lyle J. , Kocher Mininder S.
Published: March 2018

Background:

Revision anterior cruciate ligament (ACL) reconstruction in pediatric patients has not been well studied. The purpose of this study was to assess the demographics, technique, and results of ACL revision surgery in children and adolescents.

Methods:

This was a retrospective case series with outcomes assessment of patients 18 years old and younger who underwent revision ACL surgery over a 16-year period at a single institution. Medical records were reviewed for demographics, clinical and operative data, and patients were contacted for outcomes at a minimum of 1 year after revision surgery.

Results:

Ninety revision ACL reconstructions were performed by 7 surgeons in 88 patients (44 male, 44 female). Average patient age at the time of revision was 16.6 years (SD, 1.7), and 28.8% of patients were skeletally immature. Time to failure after primary ACL reconstruction was 1.28 years (SD, 1.1) and revision surgery was performed 1.56 years (SD, 1) after the index procedure. Revision graft type included allograft (61.1%), patellar tendon (21.1%), hamstring (16.7%), and iliotibial band (1.1%). There was a 20% graft reinjury rate. Subsequent surgical procedures after revision were required in 25.5% of knees. Twenty percent of revision reconstructions had contralateral ACL injuries, and this percentage was higher (33%) among those who went on to injure their revision graft. Median outcome scores collected from 44 patients (50%) at a mean of 5.1 years following surgery (SD, 3.4) were: Pedi-IKDC 79.9, Lysholm 84.5, and Tegner 9.0. Sixty-nine percent of patients reported returning to sports, however, only 55.2% of these reported being able to return to the same level of play.

Conclusions:

Revision ACL reconstruction in pediatric patients was associated with suboptimal patient-reported outcomes, high complication rates, relatively high graft retear rates, high risk of contralateral ACL injury, and compromised return to sports rates.

Level of Evidence:

Level IV.