bluuebunny/crossref_metadata_2025 huggingface dataset:
Finite element modeling of a moving load using contact conditions
Authors: Gridnev Sergey , Ravodin Ilya
Published: September 2018

The article deals with the issues of simulation of the dynamic moving load on a span structure in the modern finite element systems. The possibility of using the contact conditions in the Midas NFX program to describe the coupled vibrations of a beam and a movable load is investigated. To verify the results obtained, the method of separate modeling of the moving load by use of several forces on the trafficway line is used. The series of numerical studies of an elastically supported dynamical system was performed using two techniques. Graphic charts are obtained mapping vertical displacements of the vibration system characteristic points, depending on the inertial properties of the moving load, on the nodal forces application step, the parameters of surface conditions.
Analysis of the Constructive Features of the Earth Dam
Authors: Balzannikov Mikhail
Published: September 2018

The article considers the earth dam of the run-of-river unit – Kuibyshev hydroelectric power station on the Volga river (Russia). The main parameters of the earth dam, peculiarities of its erection and operation are described. The article notes the importance of ensuring a high degree of reliability of water structures constructed near major cities. It is especially important to monitor the condition of retaining structures with long service life. The factors influencing the change of the initial design conditions of operation of the Kuibyshev run-of-river unit dam are discussed. The results of examination of the geometric parameters of the body of the dam, performed at different periods of its maintenance, are analyzed. Examination results revealed significant deviations of the elevation marks of the earth dam surface on the upstream side from the design values. Possible causes of the discrepancy between these parameters and the design solutions are considered. The conclusion is drawn that the most likely reason for these features of the dam design lies in the initial incompleteness of construction. The measures for carrying out repair work to improve the reliability of the earth dam are being recommended.
Static analysis of a reinforced bimodulus beam on elastic foundation
Authors: Beskopylny Alexey , Kadomtseva Elena , Strelnikov Grigory
Published: September 2018

The work considers a reinforced concrete beam made of bimodule material on an elastic Winkler base. The influence of the number of reinforcing bars located in the stretched zone on the maximum normal stress and the maximum deflection is numerically investigated. The choice of the cross-section dimensions, such as the width and thickness of the flanges, the height of the beam, causes particular difficulties and is limited by the need to determine specific ratios of I-beam sizes. Numerical investigation allows analyzing the influence of the width of the I-beam flange that is in contact with the elastic base on the maximum tensile stresses and maximum deflection. The effect on the stressed-deformed state of the various cross-section forms is carried out in work for an I-beam, a rectangle, and a T-beam. Related to the fact that for many building materials the elastic moduli for tension and compression differ, it became necessary to determine the influence of material heterogeneity on the stress-strain state of the elements of building structures. In particular, the widespread use of reinforced concrete beams as elements of band foundations requires a refinement of the stress-strain state study taking into account the heterogeneity of concrete.
Self-contained ventilation system of civil buildings built into window structures
Authors: Kostuganov Arman , Vytchikov Yuri , Prilepskiy Andrey
Published: September 2018

The article describes development and application of self-contained ventilation systems in civil buildings. It suggests several models of air exchange within the building, compares these models and points out the variant of ventilating with self-contained mechanical systems with utilization of heat. The researchers conclude that structurally self-contained systems of mechanical ventilation with utilization of heat are most efficiently built into window constructions. This installation variant makes it possible to keep the interior, avoid building construction strengthening, shorten time and labor input of construction-assembling works, allow rational use of the vertical building envelopes area without extra space using. The paper key issue is the development of constructive solutions of self-contained ventilation systems main elements to ensure the possibility of their use in window structures. This research stage was developed with account of previous results of field tests and of such ventilation systems theoretical descriptions. The authors assess limit dimensions of the systems suitable for installment into window constructions of civil buildings in the view of modern Russian requirements to thermal protection. The research suggests a general constructive solution of such a ventilation system and a heat exchanger model which can be used as an air heat utilizer in these systems.
Determining internal forces in modular building elements under action wind load
Authors: Shirokov Viacheslav , Soloviev Alexey , Gordeeva Tatiana
Published: September 2018

The research paper focuses on internal forces determination in the elements of modular buildings under wind load. It provides a methodology for determining dynamic characteristics of a building and for calculating wind loads. This method is based on the following assumptions: coupling of the modules elements is rigid; coupling of block-modules with foundations is hinged-fixed; connection of blocks to each other is hinged in angular points; the floor disk in its plane is not deformed. On the basis of these assumptions the authors derived approximate and refined equations for determining forces in modules elements under static and pulsation components of wind load. The equation of bending moments determination in the pillar bearing cross-section is obtained by approximation of the graph of moments variation, calculated for the spectrum of the ratio of the pillar stiffness and the floor beam in the range from 1/64 to 64. The paper further introduces the calculation results of forces based on the proposed methodology and on the finite element method. The calculations were done while taking different values of wind load and different number of storeys in a building (from 1 to 4 floors). The obtained results are similar, the error does not exceed 5%.
Fire safety issues in the design and construction of high-rise buildings
Authors: Poliakova Tatiana , Grigoryan Marina
Published: September 2018

The construction of high-rise buildings has revealed new problems related to fire safety. The peculiarity of the architecture, which is covered in high-rise, in fires creates a danger for a large number of people there, reduces the possibility of their evacuation and rescue. The multifunctionality of such buildings, taking into account the originality of the external and internal views, leads to the difficulty of choosing a constructive system, a large number of utilities and technical systems. To address the issues related to safe operation, stay and evacuation of people is the development of a fire protection system for high-rise buildings, based on the development of:

• measures to ensure the durability of buildings or parts thereof againstprogressive collapse due to * ensuring the fire resistance of structures and buildings;

• measures to limit the spread of fire in high-rise buildings through theinstallation of fire barriers inside the building and the device of fire breaks between buildings;

• measures for ensuring timely and unimpeded evacuation of people andtheir rescue at emergency in high-rise buildings;

• systems of active protection of buildings from fire, namely: fire alarm andfire fighting, strong points of fire extinguishing.
Dynamic stability analysis and basic action for struggle with dynamic soil liquefaction
Authors: Sobolev Evgeny , Buslov Anatoly
Published: September 2018

The construction of buildings and structures in seismically hazardous areas is closely connected with the solution of the question of the dynamic stability of the soil base. World experience shows that the most destructive effect of seismic action is dynamic liquefaction. The probability of occurrence and intensity of this process are determined by the geological and hydrogeological structure of the soil massif. Based on the results of special laboratory and field dynamic tests of soils, it is not always possible to completely exclude the possibility of developing this extremely negative process. In this paper, the main stages of the analysis of the dynamic stability of the soil of the foundations of buildings and structures in complex engineering-geological conditions are presented. A brief review of existing domestic and foreign measures for the protection of buildings and structures from the dynamic dilution of soils is given. Information is provided on the applicability and comparative effectiveness of the methods in question.
Modification of Wood with Monoethanolamino-borate by The Data of X-Ray Photoelectron Spectroscopy
Authors: Stepina Irina , Kotlyarova Irina
Published: September 2018

The difficulty of wood protection from biocorrosion and fire is due to the fact that modifiers in use are washed out from the surface of the substrate under the influence of environmental factors. This results in a rapid loss of the protective effect and other practically important wood characteristics caused by the modification. To solve this problem is the aim of our work. Here, monoethanolaminoborate is used as a modifier, where electron-donating nitrogen atom provides a coordination number equal to four to a boron atom, which determines the hydrolytic stability of the compounds formed. Alpha-cellulose ground mechanically to a particle size of 1 mm at most was used as a model compound for the modification. X-ray photoelectron spectra were recorded on the XSAM-800 spectrometer (Kratos, UK). Prolonged extraction of the modified samples preceded the registration of the photoelectron spectra to exclude the fixation of the modifier molecules unreacted with cellulose. As a result of the experiment, boron and nitrogen atoms were found in the modified substrate, which indicated the hydrolytic stability of the bonds formed between the modifier molecules and the substrate. Therefore monoethanolaminoborate can be considered as a non-extractable modifier for wood-cellulose materials.
Composition and early-age temperature regime in massive concrete foundation
Authors: Van Tang Lam , Trong Nguyen Chuc , Bulgakov Boris , Ngoc Pham Anh
Published: September 2018

The usage of monolithic concrete technology in massive structure construction has created a need for a more detailed design focused on crack control. In this study, the American standard ACI 211.1-09 and absolute volume method were used to determine the composition of heavy weight concrete for the high-rise building foundation. The concrete block temperature behavior has been analyzed by a three-dimensional thermal model in program Midas Civil. The conducted studies' result provided the possibility of obtaining heavy weight concrete from Vietnam local raw materials regarding to the concrete mixture workability of 16 cm standard cone, compressive strength of 42.3 MPa and average tensile strength of 3.5 MPa at the age of 28 days. According to the model analysis results, the maximum temperatures of the massive concrete foundation at the first (after 72 hours) and second pour (after 144 hours) from the beginning of construction are respectively 55.70C and 65.50C. In addition, the temperature differences at the core of each concrete pours with respect to the concrete outer portion, which induces a risk of through cracking in structure body or surface were determined.
Transient method measured thermal properties of concrete with microspheres and latex based addition
Authors: Jaskulski Roman , Kubissa Wojciech
Published: September 2018

The goal of the performed research was to determine the influence of microspheres from fly ash and the latex based addition on the thermal properties of concrete. The tested additions were used in two different proportions each and they were combined with each other. As a reference two series of concrete were used: one without any addition and another with 0.2% of air entraining agent. The thermal properties were measured using transient method with ISOMET 2114 apparatus. No clear trends were observed in case of the results of the measurements of the thermal diffusivity and the volumetric heat capacity. While the results of the thermal conductivity coefficient show that both additions has a potential of lowering the thermal conductivity but they are not so efficient as air entraining agent.
Scheduling Construction Projects Under Fuzzy Modelling of Resource Constraints
Authors: Kulejewski Janusz , Ibadov Nabi , Krzemiński Michał
Published: September 2018

Paper presents the original method of construction scheduling using fuzzy sets theory. The essence of the method is to obtain an optimal construction schedule based on the solution of the fuzzy RCPS problem with flexible restrictions. The article introduces two important modifications of the considered issue. These modifications are: maximization of the degree of fulfillment of customer preferences regarding the time span of the project implementation and the contractor's preference regarding the level of use of renewable resources, for example - the level of employment of workers. The article also contains a numerical example showing the procedure for applying the described method.
The influence of construction and material solutions on the level of air tightness in single energy buildings
Authors: Miszczuk Artur
Published: September 2018

This publication focuses on the assessment of the impact of structural solutions of single-family buildings with an increased energy standard on their air-tightness level. The first part presents the threats resulting from the low tightness of the building. To formulate the conclusions, quantitative and qualitative casing tightness tests of existing single-family energy-efficient buildings were carried out. Construction and material solutions used in buildings were also analysed. The obtained results indicate that there is no impact of the building structure on its level of air tightness.
Comparative characteristics of binders resistance for building composites to mold fungi
Authors: Nelyubova Viktoria , Strokova Valeria , Vasilenko Marina , Rykunova Marina , Danakin Dmitry
Published: September 2018

The article presents comparative characteristics of fungal resistance of geopolymer and cement stone. According to the data obtained, the artificial aging of samples of cement stone and a geopolymer based on fly ash promotes their capturing by some microscopic fungi. In the case of a geopolymer stone based on perlite, expressed fungicidal properties were noted.
Methodological and organizational problems of professional risk management in construction
Authors: Sugak Evgeny
Published: September 2018

The construction industry is one of the most traumatic industries, therefore, the improvement of the occupational safety and health management system (OSH) in construction is an urgent problem. The Russian government has set the task of reforming the national OSH on the basis of professional risk management, which will allow switching from the practice of responding to the incidents that have already occurred to preventive detection and elimination of potential threats. This article discusses the issues of the objective nature of occupational risks, methods for assessing the probability and severity of damage from risk events, and also provides recommendations on the content of the functional responsibilities of officials of the construction organization.
The influence of the mineral additives on the carbonation of cement composites
Authors: Woliński Paweł , Woyciechowski Piotr , Jaworska Beata , Adamczewski Grzegorz , Tokarski Daniel , Grudniewski Tomasz , Chodyka Marta , Antoni Nitychoruk Jerzy
Published: September 2018

In practice, it is usually assumed that the durability of basic structural elements should not be less than the expected durability of the building. Reinforced concrete constructions, designed and made with quality requirements, are durable. However, each reinforced concrete structure, from the moment it is made, is gradually degraded, and one of the reasons for its destruction is often the corrosion of the concrete and hence the reinforcement. For the long-term use of reinforced concrete constructions, the most important thing is that a thin protective layer on the steel surface protects the reinforcing steel from rusting. One of the most common causes of corrosion in the reinforcement is the damage of this layer as a result of the carbonation of the concrete cover. The rate of carbonation depends on many factors, such as concrete compactness, concentration of CO2, concrete moisture, content of free calcium dioxide, content of mineral additives, etc. When the carbonated layer reaches the steel reinforcement layer, protection of steel from corrosion ceases to exist. The aim of the presented research was to determine the influence of mineral additives used as a compound of concrete on the carbonation of concrete and polymer-cement composites.
Sustainable Maintenance of low level road network
Authors: Mikolaj Jan , Remek L’uboš
Published: September 2018

Main goal of Road Network Management System is to ensure safety and continuity of road traffic on road network with low intensity and lower technical requirements. This is achieved with pavement management system (main component of road network management system). Most countries developed custom Pavement management systems (PMS) based on deterministic or probabilistic approach. Local road administrators of low level road networks often lack the software equipment such as HDM-4, RoSy, Exor, etc. These and similar PMS Most PMS, however effective, are often cumbersome, demanding in regard to energy, know-how and software equipment. The majority of local road administrators of rural road networks thus resort to non-effective reactive maintenance strategies. This article describes an easy to use method, based on predetermined maintenance repair & rehabilitation standards. Secondly, a simple method, based on road user cost, is introduced that administrator can use to prepare a list of road section eligible for repair according to their repair priority.
Development and Assessment of VR/AR Solution for Verification During the Construction Process
Authors: Protchenko Kostiantyn , Dąbrowski Piotr , Garbacz Andrzej
Published: September 2018

It is common occurrence that on-site workers misunderstand various detailing aspects of the provided documentation. Some of them can be unclear and should be discussed again due to construction related processes. In order to deal with this issue the application for mobile devices was proposed. The developed application allows to visualize two-dimensional print projects with the help of VR/AR (Virtual Reality/Augmented Reality) technology. The paper is focused on the assessment of the possibility to use the VR/AR technology during the process of construction. The feasibility of the solution is tested on the basis of a three-dimensional model created with the software operating in accordance with Building Information Modeling (BIM) technology. The developed mobile VR/AR solution was enhanced with basic functionality to verify structural members as well as entire structural system. Moreover, it allows to communicate in a simple manner, which can lead to the improving of the effectiveness and preventing the risk of construction errors.
Development of technical and economic systems in construction and their homeostatic balance
Authors: Sborshikov Sergey , Bobin Alexey
Published: September 2018

Development of technical and economic systems, their direction and functionality is a continuous process of transition from one condition to another, includes random components, which got different impact on the trajectory of growth. In this work, we performed analysis of element of technical and economic system (construction sphere) at the level of the economic entity. Overcoming negative phenomena in the sustainable growth of technical and economic systems is closely connected with the successful solution of tasks in investment and construction sphere, based on an effective management.
Predicting model of thickness distribution and rolling force in angular rolling process based on influence function method
Authors: Hao Pujun , He Anrui , Sun Wenquan
Published: September 2018

As a special rolling method, angular rolling can meet various gauge demands of customized production. Due to the asymmetry of angular rolling, the rolling forces on the two sides of the roll system are different and the thickness distribution of the plate will be complex. To accurately obtain the thickness distribution and predict the rolling force during the angular rolling process, a mathematical model based on the influence function method is developed. An experiment is also adopted to validate the results of the rolling force. The results show that the change in the total rolling force comprises three stages: increasing, stable, and decreasing. During most of the rolling time, the rolling forces on the two sides of the mill are different. Then the predicted results of the rolling force are validated by experiment. After the first pass of angular rolling, a serious wedge appears at the head and tail ends of the plate. But when the angular rolling is finished, the wedge has almost disappeared. Considering the short calculation time, this model can be applied in the actual production process for making effective shape control strategies and flexible rolling schedules to meet various gauge demands of customized production.
metaGraphite–a new layer of pathway annotation to get metabolite networks
Authors: Sales Gabriele , Calura Enrica , Romualdi Chiara
Published: September 2018

Motivation

Metabolomics is an emerging ‘omics’ science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements.

Results

We have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks.

Availability and implementation

The new graphite version (1.24) is available on Bioconductor.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis
Authors: Sedgewick Andrew J , Buschur Kristina , Shi Ivy , Ramsey Joseph D , Raghu Vineet K , Manatakis Dimitris V , Zhang Yingze , Bon Jessica , Chandra Divay , Karoleski Chad , Sciurba Frank C , Spirtes Peter , Glymour Clark , Benos Panayiotis V
Published: September 2018

Motivation

Integration of data from different modalities is a necessary step for multi-scale data analysis in many fields, including biomedical research and systems biology. Directed graphical models offer an attractive tool for this problem because they can represent both the complex, multivariate probability distributions and the causal pathways influencing the system. Graphical models learned from biomedical data can be used for classification, biomarker selection and functional analysis, while revealing the underlying network structure and thus allowing for arbitrary likelihood queries over the data.

Results

In this paper, we present and test new methods for finding directed graphs over mixed data types (continuous and discrete variables). We used this new algorithm, CausalMGM, to identify variables directly linked to disease diagnosis and progression in various multi-modal datasets, including clinical datasets from chronic obstructive pulmonary disease (COPD). COPD is the third leading cause of death and a major cause of disability and thus determining the factors that cause longitudinal lung function decline is very important. Applied on a COPD dataset, mixed graphical models were able to confirm and extend previously described causal effects and provide new insights on the factors that potentially affect the longitudinal lung function decline of COPD patients.

Availability and implementation

The CausalMGM package is available on http://www.causalmgm.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
Machine learning based automated dynamic quantification of left heart chamber volumes
Authors: Narang Akhil , Mor-Avi Victor , Prado Aldo , Volpato Valentina , Prater David , Tamborini Gloria , Fusini Laura , Pepi Mauro , Goyal Neha , Addetia Karima , Gonçalves Alexandra , Patel Amit R , Lang Roberto M
Published: September 2018

Aims

Studies have demonstrated the ability of a new automated algorithm for volumetric analysis of 3D echocardiographic (3DE) datasets to provide accurate and reproducible measurements of left ventricular and left atrial (LV, LA) volumes at end-systole and end-diastole. Recently, this methodology was expanded using a machine learning (ML) approach to automatically measure chamber volumes throughout the cardiac cycle, resulting in LV and LA volume–time curves. We aimed to validate ejection and filling parameters obtained from these curves by comparing them to independent well-validated reference techniques.

Methods and results

We studied 20 patients referred for cardiac magnetic resonance (CMR) examinations, who underwent 3DE imaging the same day. Volume–time curves were obtained for both LV and LA chambers using the ML algorithm (Philips HeartModel), and independently conventional 3DE volumetric analysis (TomTec), and CMR images (slice-by-slice, frame-by-frame manual tracing). Automatically derived LV and LA volumes and ejection/filling parameters were compared against both reference techniques. Minor manual correction of the automatically detected LV and LA borders was needed in 4/20 and 5/20 cases, respectively. Time required to generate volume–time curves was 35 ± 17 s using ML algorithm, 3.6 ± 0.9 min using conventional 3DE analysis, and 96 ± 14 min using CMR. Volume–time curves obtained by all three techniques were similar in shape and magnitude. In both comparisons, ejection/filling parameters showed no significant inter-technique differences. Bland–Altman analysis confirmed small biases, despite wide limits of agreement.

Conclusion

The automated ML algorithm can quickly measure dynamic LV and LA volumes and accurately analyse ejection/filling parameters. Incorporation of this algorithm into the clinical workflow may increase the utilization of 3DE imaging.
The Evolution of EUS-Guided Transluminal Drainage for the Treatment of Pancreatic Fluid Collections: A Comparison of Clinical and Cost Outcomes with Double-Pigtail Plastic Stents, Conventional Metal Stents and Lumen-Apposing Metal Stents
Authors: Falk Vanessa , Kenshil Sana , Sandha Simrat , Teshima Christopher , D’Souza Pernilla , Sandha Gurpal
Published: September 2018

Background

While most pancreatic fluid collections (PFCs) resolve spontaneously, endoscopic ultrasound-guided transluminal drainage (EUS-TD) may be necessary. EUS-TD has evolved from multiple double-pigtail plastic stents (DPPS) to fully covered self-expanding metal stents (FCSEMS) and lumen-apposing metal stents (LAMS). This study compares clinical attributes of DPPS, FCSEMS and LAMS.

Methods

This is a single-centre retrospective review of EUS-TD for PFCs. The primary outcome was clinical success. Secondary outcomes were technical success, procedure time, hospital length of stay (HLOS), number of endoscopies, need for necrosectomy, adverse events (AEs) and overall cost.

Results

Fifty-eight patients (37 male, average age 49 years) underwent a total of 60 EUS-TD procedures for PFCs (average size 11.2 cm with 29 pseudocysts and 29 walled-off necrosis). Ten patients (17%) underwent EUS-TD with DPPS and 48 patients (83%) with metal stents (32 FCSEMS, 16 LAMS). Overall technical and clinical success was 100% and 84%, respectively. Lumen-apposing metal stents had shorter procedure times (14.9 versus 63.6 DPPS, 39.1 min FCSEMS, P < 0.001), and no difference in AEs (3 of 16 versus 4 of 10 DPPS, 12 of 34 FCSEMS, ns). Double-pigtail plastic stents required more endoscopies (3.7 versus 2.3 LAMS, 2.3 FCSEMS, P = 0.013) and necrosectomies (4 of 10 [40%]) compared with 5 of 34 [15%] in the FCSEMS group and 3 of 16 [19%] in the LAMS group, respectively, P = 0.001) to achieve clinical resolution. The overall cost and HLOS was not significantly different between groups.

Conclusion

The use of LAMS for PFCs is not associated with any significant increase in cost despite technical (shorter procedure time) and clinical advantages (shorter indwell time, reduced need for necrosectomy and no increase in AEs).
The impact of cored density profiles on the observable quantities of dwarf spheroidal galaxies
Authors: Harvey David , Revaz Yves , Robertson Andrew , Hausammann Loic
Published: September 2018

We modify the chemo-dynamical code gear to simulate the impact of self-interacting dark matter (SIDM) on the observable quantities of 19 low-mass dwarf galaxies with a variety star-forming properties. We employ a relatively high, velocity independent cross-section of $\sigma /m=10\, \rm {cm^2\,g^{ -1}}$ and extract, in addition to integrated quantities, the total mass density profile, the luminosity profile, the line-of-sight velocities, the chemical abundance, and the star formation history. We find that despite the creation of large cores at the centre of the dark matter haloes, the impact of SIDM on the observable quantities of quenched galaxies is indiscernible, dominated mostly by the stochastic build up of the stellar matter. As such we conclude that it is impossible to make global statements on the density profile of dwarf galaxies from single or small samples. Although based mostly on quenched galaxies, this finding supports other recent work putting into question the reliability of inferred cored density profiles that are derived from observed line-of-sight velocities.
Transient cooling episodes during Cretaceous Oceanic Anoxic Events with special reference to OAE 1a (Early Aptian)
Authors: Jenkyns Hugh C.
Published: September 2018

The two major oceanic anoxic events of the Cretaceous, those of the Early Aptian (OAE 1a) and the Cenomanian–Turonian boundary (OAE 2), registered some of the highest temperatures reconstructed for the Cretaceous Period, and are thought to be related to the input of volcanically derived carbon dioxide from one or more Large Igneous Provinces. Widely distributed deposition of marine organic matter, the hallmark of OAEs, and intensified silicate weathering in response to a globally accelerated hydrological cycle and/or reaction of seawater with freshly extruded basalt, are both potential mechanisms whereby the content of atmospheric carbon dioxide could have been drawn down to promote cooling, on the assumption that this potential effect was not offset by increased addition of this volcanically derived greenhouse gas. Reduction in the supply of such carbon dioxide, with deposition of organic matter and silicate weathering continuing at the same rate, could also have produced cooling. A transient fall in temperature and increase in marine dissolved oxygen levels is well documented for OAE 2, in the form of the so-called Plenus Cold Event or Benthic Oxic Event, associated with southward invasion of certain boreal faunas and an increase in many redox-sensitive and/or chalcophilic elements in seawater caused by temporary loss of anoxic–euxinic sinks as basalt–seawater interaction continued apace. High-resolution studies of OAE 1a show at least three cooling episodes of probable global distribution, one of which (recorded in the stratigraphy of the so-called C4 Segment) is documented at high enough resolution to show correlation with an increase in carbon-isotope values that was probably due to a rise in the quantities of organic matter being buried globally, with consequent potential drawdown of atmospheric CO2and/or reduction in volcanic input of this greenhouse gas. Both calcium- and lithium-isotope records suggest an increase in silicate weathering over the OAE 1a interval but current relatively low-resolution records cannot at present be tied to any one cooling episode, although the lowest Li-isotope values do derive from the C4 Segment. Evidence for reoxygenation of the ocean during the transient cooling episodes of OAE 1a is meagre, due to the lack of suitable sedimentary archives, although a negative sulfur-isotope excursion in a Pacific shallow-water carbonate section, which can be interpreted as due to oxidation of pyrite and/or sulfur-rich organic matter in the global ocean, suggests that this phenomenon may also have been a feature of the C4 Segment. Further work is required to elucidate the similarities and differences between OAE 2 and OAE 1a, but both phenomena are demonstrably global in reach and represent major disturbances to the carbon cycle with attendant effects on marine temperatures.

This article is part of a discussion meeting issue ‘Hyperthermals: rapid and extreme global warming in our geological past’.
Warm plankton soup and red herrings: calcareous nannoplankton cellular communities and the Palaeocene–Eocene Thermal Maximum
Authors: Gibbs Samantha J. , Sheward Rosie M. , Bown Paul R. , Poulton Alex J. , Alvarez Sarah A.
Published: September 2018

Past global warming events such as the Palaeocene–Eocene Thermal Maximum (PETM—56 Ma) are attributed to the release of vast amounts of carbon into the ocean, atmosphere and biosphere with recovery ascribed to a combination of silicate weathering and organic carbon burial. The phytoplanktonic nannoplankton are major contributors of organic and inorganic carbon but their role in this recovery process remains poorly understood and complicated by their contribution to marine calcification. Biocalcification is implicated not only in long-term carbon burial but also both short-term positive and negative climatic feedbacks associated with seawater buffering and responses to ocean acidification. Here, we use exceptional records of preserved fossil coccospheres to reconstruct cell size distribution, biomass production (particulate organic carbon, POC) and (particulate) inorganic carbon (PIC) yields of three contrasting nannoplankton communities (Bass River—outer shelf, Maud Rise—uppermost bathyal, Shatsky Rise—open ocean) through the PETM onset and recovery. Each of the sites shows contrasting community responses across the PETM as a function of their taxic composition and total community biomass. Our results indicate that nannoplankton PIC:POC had no role in short-term climate feedback and, as such, their importance as a source of CO2to the environment is a red herring. It is nevertheless likely that shifts to greater numbers of smaller cells at the shelf site in particular led to greater carbon transfer efficiency, and that nannoplankton productivity and export across the shelves had a significant modulating effect on carbon sequestration during the PETM recovery.

This article is part of a discussion meeting issue ‘Hyperthermals: rapid and extreme global warming in our geological past’.
Hyperthermal-driven mass extinctions: killing models during the Permian–Triassic mass extinction
Authors: Benton Michael J.
Published: September 2018

Many mass extinctions of life in the sea and on land have been attributed to geologically rapid heating, and in the case of the Permian–Triassic and others, driven by large igneous province volcanism. The Siberian Traps eruptions raised ambient temperatures to 35–40°C. A key question is how massive eruptions during these events, and others, could have killed life in the sea and on land; proposed killers are reviewed here. In the oceans, benthos and plankton were killed by anoxia–euxinia and lethal heating, respectively, and the habitable depth zone was massively reduced. On land, the combination of extreme heating and drought reduced the habitable land area, and acid rain stripped forests and soils. Physiological experiments show that some animals can adapt to temperature rises of a few degrees, and that some can survive short episodes of increases of 10°C. However, most plants and animals suffer major physiological damage at temperatures of 35–40°C. Studies of the effects of extreme physical conditions on modern organisms, as well as assumptions about rates of environmental change, give direct evidence of likely killing effects deriving from hyperthermals of the past.

This article is part of a discussion meeting issue ‘Hyperthermals: rapid and extreme global warming in our geological past’.
Microbe Profile: Saccharomyces eubayanus, the missing link to lager beer yeasts
Authors: Sampaio José Paulo
Published: September 2018

Saccharomyces eubayanus was described less than 10 years ago and its discovery settled the long-lasting debate on the origins of the cold-tolerant yeast responsible for lager beer fermentation. The largest share of the genetic diversity of S. eubayanus is located in South America, and strains of this species have not yet been found in Europe. One or more hybridization events between S. eubayanus and S. cerevisiae ale beer strains gave rise to S. pastorianus, the allopolyploid yeasts responsible for lager beer production worldwide. The identification of the missing progenitor of lager yeast opened new avenues for brewing yeast research. It allowed not only the selective breeding of new lager strains, but revealed also a wild yeast with interesting brewing abilities so that a beer solely fermented by S. eubayanus is currently on the market.
Neural Flip-Flops I: Short-Term Memory
Authors: Yoder Lane
Published: September 2018

The networks proposed here show how neurons can be connected to form flip-flops, the basic building blocks in sequential logic systems. The novel neural flip-flops (NFFs) are explicit, dynamic, and can generate known phenomena of short-term memory.

For each network design, all neurons, connections, and types of synapses are shown explicitly. The neurons’ operation depends only on explicitly stated, minimal properties of excitement and inhibition. This operation is dynamic in the sense that the level of neuron activity is the only cellular change, making the NFFs’ operation consistent with the speed of most brain functions. Memory tests have shown that certain neurons fire continuously at a high frequency while information is held in short-term memory. These neurons exhibit seven characteristics associated with memory formation, retention, retrieval, termination, and errors. One of the neurons in each of the NFFs produces all of the characteristics. This neuron and a second neighboring neuron together predict eight unknown phenomena. These predictions can be tested by the same methods that led to the discovery of the first seven phenomena. NFFs, together with a decoder from a previous paper, suggest a resolution to the longstanding controversy of whether short-term memory depends on neurons firing persistently or in brief, coordinated bursts.

Two novel NFFs are composed of two and four neurons. Their designs follow directly from a standard electronic flip-flop design by moving each negation symbol from one end of the connection to the other. This does not affect the logic of the network, but it changes the logic of each component to a logic function that can be implemented by a single neuron. This transformation is reversible and is apparently new to engineering as well as neuroscience.
RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis
Authors: Anton Bernat , Besalú Mireia , Fornes Oriol , Bonet Jaume , De las Cuevas Gemma , Fernández-Fuentes Narcís , Oliva Baldo
Published: September 2018

Motivation

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. Current algorithms for DCA, although efficient, have a high computational cost of determining Direct Information (DI) values for large proteins or domains. In this paper, we present RADI (Reduced Alphabet Direct Information), a variation of the original DCA algorithm that simplifies the computation of DI values by grouping physicochemically equivalent residues.

Results

We have compared the first top ranking 40 pairs of DI values and their closest paired contact in 3D. The ranking is also compared with results obtained using a similar but faster approach based on Mutual Information (MI). When we simplify the number of symbols used to describe a protein sequence to 9, RADI achieves similar results as the original DCA (i.e. with the classical alphabet of 21 symbols), while reducing the computation time around 30-fold on large proteins (with length around 1000 residues) and with higher accuracy than predictions based on MI. Interestingly, the simplification produced by grouping amino acids into only two groups (polar and non-polar) is still representative of the physicochemical nature that characterizes the protein structure, having a relevant and useful predictive value, while the computation time is reduced between 100 and 2500-fold.

Availability

RADI is available at https://github.com/structuralbioinformatics/RADI

Contact

baldo.oliva@upf.edu

Supplementary information

Supplementary data is available in the git repository.
Structural Adaptation of Darunavir Analogs Against Primary Resistance Mutations in HIV-1 Protease
Authors: Lockbaum Gordon J. , Leidner Florian , Rusere Linah N. , Henes Mina , Kosovrasti Klajdi , Nalivaika Ellen A. , Ali Akbar , Yilmaz Nese Kurt , Schiffer Celia A.
Published: September 2018

HIV-1 protease is one of the prime targets of agents used in antiretroviral therapy against HIV. However, under selective pressure of protease inhibitors, primary mutations at the active site weaken inhibitor binding to confer resistance. Darunavir (DRV) is the most potent HIV-1 protease inhibitor in clinic; resistance is limited, as DRV fits well within the substrate envelope. Nevertheless, resistance is observed due to hydrophobic changes at residues including I50, V82 and I84 that line the S1/S1’ pocket within the active site. Through enzyme inhibition assays and a series of 12 crystal structures, we interrogated susceptibility of DRV and two potent analogs to primary S1’ mutations. The analogs had modifications at the hydrophobic P1’ moiety to better occupy the unexploited space in the S1’ pocket where the primary mutations were located. Considerable losses of potency were observed against protease variants with I84V and I50V mutations for all three inhibitors. The crystal structures revealed an unexpected conformational change in the flap region of I50V protease bound to the analog with the largest P1’ moiety, indicating interdependency between the S1’ subsite and the flap region. Collective analysis of protease-inhibitor van der Waals (vdW) interactions in the crystal structures using principle component analysis indicated I84V mutation underlying the largest variation in the vdW contacts. Interestingly, the principle components were able to distinguish inhibitor identity and relative potency solely based on vdW interactions of active site residues in the crystal structures. Our results reveal the interplay between inhibitor P1’ moiety and primary S1’ mutations, as well as suggesting a novel method for distinguishing the interdependence of resistance through principle component analyses.
Relative Reduction of the Biological and phylogenetic diversity of oral microbiome in diabetic and pre-diabetic subjects
Authors: Saeb Amr T. M. , Al-Rubeaan Khalid A. , Aldosary Khalid , Udaya Raja G. K. , Mani Balavenkatesh , Abouelhoda Mohamed , Tayeb Hamsa T.
Published: September 2018

Background

There is a suggested reciprocal relationship between oral health and systemic disease such as type 2 diabetes. In this relationship, a systemic disease predisposing to oral infection, and when that infection is present, the oral infection aggravates the progression of the systemic disease. Several studies suggested that some oral microbiome constituents are linked to both diabetes, metabolic syndrome and obesity. This study aims to compare the microbial diversity and population structure of oral microbiome among normoglycemic, impaired glucose tolerance (IGT) and diabetic subjects.

Methodology

This study followed a case-control design (15 T2D patients, 10 IGTs and, 19 controls). Patient records were screened as per the inclusion and exclusion criteria. Assessment of periodontitis and oral health was performed to all subjects. DNA Isolation purification and quantification from collected Saliva samples were performed. 16SrRNA hypervariable regions were amplified and sequenced. Generated sequences were subjected to bioinformatics analysis. Statistical analysis and diversity indices were computed with the statistical software R, the vegan R-package, and Past318 software.

Results

A total observed number of 551 OTUs. A clear reduction of the number of species (OTUs) was observed in both IGT (412) and diabetic group (372) compared with the normoglycemic group (502). This was associated with a similar pattern of biological diversity among the three groups. Phylogenetic diversity (PD-SBL) value in the normoglycemic group was higher than the diabetic group. The diabetic group had the highest evenness value and the highest microbiome bacterial pathogenic content.

Conclusion

We observed a clear reduction in the biological and phylogenetic diversity in the diabetic and pre-diabetic oral microbiome in comparison with the normoglycemic oral microbiome. However, this reduction was associated with an increase in the pathogenic content of the hyperglycemic microbiomes.
Multilayered mechanisms ensure that short chromosomes recombine in meiosis
Authors: Murakami Hajime , Lam Isabel , Song Jacquelyn , van Overbeek Megan , Keeney Scott
Published: September 2018

To segregate accurately during meiosis, homologous chromosomes in most species must recombine. Very small chromosomes would risk missegregation if recombination were randomly distributed, so the double-strand breaks (DSBs) that initiate recombination are not haphazard. How this nonrandomness is controlled is not under-stood. Here we demonstrate that Saccharomyces cerevisiae integrates multiple, temporally distinct pathways to regulate chromosomal binding of pro-DSB factors Rec114 and Mer2, thereby controlling duration of a DSB-competent state. Homologous chromosome engagement regulates Rec114/Mer2 dissociation late in prophase, whereas replication timing and proximity to centromeres or telomeres influence timing and amount of Rec114/Mer2 accumulation early. A distinct early mechanism boosts Rec114/Mer2 binding quickly to high levels specifically on the shortest chromosomes, dependent on chromosome axis proteins and subject to selection pressure to maintain hyperrecombinogenic properties of these chromosomes. Thus, an organism’s karyotype and its attendant risk of meiotic missegregation influence the shape and evolution of its recombination landscape.