bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual-Component Ontograph Visualization
Authors: Guraliuk A G , Rostoka M L , Cherevychnyi G S , Zakatnov D O , Pavlysh T H
Published: February 2021

Today there are several generally accepted methods of storing data in an information network. One of the most modern is the presentation of data in the form of a semi-structured (with the possibility of fuzzy formalization) set – a knowledge base. Compared to databases, this view has several advantages: the ability to store complex heterogeneous information; the ability to expand and supplement the description of the subject area without reprogramming; visibility and accessibility of knowledge presentation to the user. But this advantage of them turns into a problem, which currently has been only partially solved. The data in the knowledge base can be in such a form that their presentation according to formalized rules and algorithms is impossible or ineffective. Currently, the most promising in terms of representing data structures is considered to be an ontological representation that copes well with displaying an arbitrary structure. Most of the visual representations of ontologies (Protégé in integration with OWLViz, OntoGraf, 3D Hyperbolyc, Tree, etc.) are images of nodes as a set of conditional points (small geometric shapes) connected by lines –ontographs. This approach to visualization is less informative and inconvenient to apply to the educational process. The need to create new approaches to the presentation of information, implement its accessibility and efficiency of usage is becoming increasingly important. Along with traditional information support in the form of databases, knowledge bases have begun to develop at a tremendous pace, which, when used effectively, provide significant competitive advantages. An important feature of knowledge bases is the ability to work with approximate sets. The authors developed ontograph visualization technology, partially implemented on the Ontos.xyz web resource. This resource allows you to visualize the vertices of the ontograph, the connections between them and assign each set of contexts that are related to it. Each of the nodes of the ontograph contains a specific descriptive context. The main feature of the Ontos editor is the ability to assign each node a context of all types supported by the browser. Including html pages, web 2.0 resources, etc. Also, the proposed system implements the visualization of knowledge bases, consisting of two components: a navigator that determines the path to some node of the ontograph that has children and a visualization slider for this node that displays these elements. The knowledge base viewer is a slider that resembles a photo gallery slider with advanced navigation. The ontological approach to servicing knowledge bases can be not only a means of organizing knowledge. The knowledge bases developed on the basis of the ontological approach make it possible to work actively with knowledge, to solve problems associated with education, the development of artificial intelligence, decision-making systems, and many other areas where approximate sets can be used.
Organization of the interface of games and applications, developed for children with intellectual disability
Authors: Markova Gergana V , Byalmarkova Petya Y
Published: February 2021

In this article will be discussed the issues related to the requirements for the development of digital games for children with intellectual disability. We proposed structured requirements for the design of different types of games in terms of interface, design technologies, color models, object shape and brightness, scope in applications of sound, game duration, and so on.
Naval Architectural Aspects in The Design of a Hybrid Hydrofoil-Submarine Craft
Authors: Wardhana W , Wardhana E M , Soetardjo M , Nichita O F
Published: February 2021

Indonesia is the largest archipelago country in the world. Territorial disputes and illegal fishing are some main threat of maritime defense. One of the solutions is to provide a multi-mission vehicle. Submarine craft has the advantage of undetectable to ambush the threats. Hydrofoil craft has the advantage of higher speed than the conventional high-speed craft. The purpose of this research is to combine two distinctive and one conventional concept into one craft. This craft has to has a light structure to support hydrofoil mode and able to submerge. The material of the hull uses aluminum and for wing and propulsion system structure use carbon steel. This craft uses hydraulic propulsion that the main engine moves the hydraulic pump. The hydraulic pump flows oil to the hydraulic motor where located in the nacelle. The hydraulic motor rotates the shaft and propeller. This propulsion system requires the propeller to submerge in the water, therefore the strut which supports the wing and propulsion system has to design retractable. All important parameters are included in this paper.
Impact of seabed slope on steel catenary riser touchdown zone response
Authors: Ogbeifun A. M. , Oterkus S. , Race J. , Naik H. , Moorthy D. , Bhowmik S. , Ingram J.
Published: February 2021

Several factors can affect the response of steel catenary risers (SCR) around its touch down zone (TDZ). These include the stiffness of the soil, the soil suction force on the riser TDZ, the soil degradation with cyclic TDZ loading, etc. Riser strength and fatigue response computation are usually performed considering flat seabed and with the use of rigid or linear (spring) riser soil interaction model. However, bathymetric information obtained for the SCR lay path on the seabed reveal complex seabed profile variation, indicating that the seabed is far from being flat around the SCR TDZ. This paper presents findings from an investigation conducted on the influence of seabed slopes on the strength and fatigue response of SCRs, using a non-linear (NL) riser soil interaction model. The responses of SCRs on positively and negatively sloped seabed (rotated about the static touch down point on flat seabed) are compared with responses of SCRs on flat seabed. From the results, it can be deduced that the SCR dynamic and fatigue responses may be overpredicted or underpredicted in magnitudes dependent on the slope deviation of actual seabed from a flat seabed.
Societal risk assessment of terminal and oil refinery unit
Authors: Dinariyana AAB , Artana KB , Handani DW , Sarasvati FI , Aprilia PW
Published: February 2021

This paper presents the societal risk assessment of oil refinery in one of the oil companies in East Java. The oil company operates-a terminal for loading and unloading of variety petrochemical products. The products are categorized as flammable which could be hazardous. To prevent unlikely event of hazards such as fire, risk assessment is needed to know the level of risk and propose any mitigation if the risk is unacceptable. The risk assessment is done for all the processes that occurs such as loading and unloading of products and the chemical process in the oil refinery. The system is categorized into 8 nodes based on their function. Firstly, Hazard and Operability (HAZOP) is carried out using BS IEC 61882 standard to identify the deviation of the system, the causes and how to prevent it. The frequency analysis of failure of component is done by using Fault Tree Analysis (FTA) and Event Tree Analysis (ETA) which based on the DNV failure guidance and Oil and Gas Producers (OGP) data as input. In order to know the level of consequence, fire modelling is carried out to simulate how the jet fire and pool fire could impact into the social around the oil refinery in form of heat intensity. The fire modelling for the pool fire and jet fire results the pool radius and flame length respectively, based on the heat intensity of 4 kW/m2, 12.5 kW / m2, and 37.5 kW / m2. Risk is represented using F-N curve with UK-HSE standard. There is unacceptable risk that incurred for jet fire in pipeline and its components from the feedstock tank into pre-cut column, scenario 200 mm hole diameter. Mitigation is done using LOPA to bring the risk to the acceptable region by adding a gas detector which has changed the frequency of system failure from 1.44E-03 to 2.88E-06.
Analysis of Human Factors in Ship-to-ship Collision Accident: A Semi-quantitative Approach Based on Network Theory
Authors: Adhita I G M S , Furusho M
Published: February 2021

As long as human beings operate the ship, human factors always have a substantial contribution to ship operation success and failure. Thereby, a study related to human factors, especially about the officer on board, is essential to create better maritime transportation. This research proposed the semi-quantitative analysis to determine how human factors are involved in a ship-to-ship collision using a network theory perspective. The study was conducted by describing the dependency amongst human activities (officer onboard) during ship-ship encounters. The ship-to-ship encounters model has been done in an undirected graph consisting of nodes and arcs. Through the vertex performance rate, system performance could be evaluated. Hence this research aimed to define the weight evolution when the unintended action emerges in a node and distributes its weight to its couplings. In conclusion, the network model for ship-to-ship collision accidents can describe the weight spreading process among functions and how it affects system performance then causes an accident.
The effect of low tempering, medium tempering, and high tempering heating temperature variations in the type of medium carbon steel ST 60 on microstructure, hardness, and toughness
Authors: Yudo H , Jokosisworo S
Published: February 2021

To determine the changes in the microstructure, impact strength, and hardness of the carbon steel medium type ST 60 with variations in temperature: quenching, tempering 200°C, tempering 400°C and tempering 600°C, then a heat treatment was given at 850°C for 30 minutes then quenched with brine solution with a salt content of 10% and continued with tempering for 30 minutes with variations in tempering temperature: 200°C, 400°C and 600°C. The chemical composition of the ST 60 steel specimen obtained that the main constituent elements are iron (Fe) = 98.1%, manganese (Mn) = 0.572%, silisium (Si) = 0.246%, and carbon (C) = 0.362%. Meanwhile, the hardness, impact, and microstructure test results show that the quenching specimen has the hardest and softest material properties. This is indicated by the highest hardness value of 772.67 VHN and the smallest impact value of 1.24 J / mm2. The martensite phase structure formed causes the material properties to be the hardest. In the 200°C tempering specimen the hardness began to decrease and the ductility increased as indicated by the hardness value of 625 VHN and the impact value of 2.02 J / mm2. In this specimen, a tempered martensite phase was formed, which is softer than martensite. In the 400°C tempering specimen, the hardness value was getting smaller, but the ductility increased as indicated by the hardness value of 448.67 VHN and the impact value of 2.56 J / mm2. The bainite phase structure with ductile / malleable properties was formed in this specimen. In the 600°C tempering specimen the properties of the resulting material were the most ductile and softest indicated by the lowest hardness value of 295 VHN and the highest impact value of 3.11 J / mm2. The structure of the ferrite and fine pearlite phases with very soft properties was formed in this specimen.
Implementation Study of Activity Based Costing System to Define Indirect Costs on Ship Repair Industries
Authors: Wahidi S I , Pribadi T W , Pribadi S R W , Megawati S
Published: February 2021

Good quality, the right turnaround time, and affordable service costs are three important points that must be paid attention to in repair shops offering their services. In determining the selling price of repair services, companies need accurate information about the cost of goods manufactured, which consists of direct costs and indirect costs. In general, the imposition of indirect costs to products uses a traditional cost accounting system so that costs distortions often occur. With the development of existing knowledge, companies must be able to increase their competitiveness and find alternative methods than traditional cost accounting systems. The activity based costing method developed and became a cost accounting method by assigning costs to activities based on the consumption / use of resources. First, activity identification is carried out based on existing business processes, both direct and supporting repair activities. Second, from the results of the identification of existing activities, identification of needs that trigger an activity that can be called an activity driver is carried out. After identifying the activity driver, the type of activity in the ship repair process is obtained which affects the high indirect cost expenditures. By using the activity based costing method, the indirect cost value on ship 1 is IDR 78,994,805, - and on ship 2 of IDR 57,890,169, -. These values are true values and can be traced to each activity through the use of resources. From these results it can be seen that the value of indirect costs when calculated by the activity based costing method produces a smaller value when compared to the existing method. On ship 1, using the activity based costing method, indirect costs decreased by 44% from the calculation of the existing conditions and on ship 2 decreased by 38% from the calculation of the existing conditions.
The Application of 2nd Generation Intact Stability Criteria to Ship Operating in Indonesia Waterway: Pureloss Stability
Authors: Anggara S , Maskar R D , Hariadi M R F , Ichsan L M , Zaky M , Kurniawan A
Published: February 2021

The development of 2nd Generation intact stability criteria has entered final chapter since nearly one-decade intensive work. The instrument is intended to measure ship stability in dynamic aspect on wave which has not been considered by its predecessor, IS Code 2008. Prior to enforcement, BKI has taken early preparation to establish inhouse calculation tool independently for assessing ship stability in accordance with the first 2 level of vulnerability criteria, i.e. Pureloss Stability. Semi performance based and direct assessment are introduced as the concept behind the calculation, thus the procedure is quite complex and need more time to proceed which leads to utilize automation. Furthermore, a set number of types of ship with various dimension have been tested to the system in respect to Indonesia environmental condition. The results show that typical ships are vulnerable to certain criteria which may beneficial for operator to gain initial precaution.
Theoretical Study for Predicting Response Water Column in a Moonpool
Authors: Turbaningsih O , Nur H I
Published: February 2021

Moonpool commonly installed in production barge, drilling vessel, pipe laying vessel, survey vessel and offshore diving vessel. Moonpool is an opening vertical wall through the deck from top to bottom of the vessel. The main purpose of using moonpool is to perform lifting/lowering of subsea equipment. It considers as the most effective subsea handling method, but it has disadvantages with oscillation of water column inside moon pool. The purpose of this study is to understand the correlation between response water column inside the moonpool with environmental load and the motion of the floating structure during operational time or transit condition. During transit condition, the forward speed of the barge is zero, the excitation force only caused by incoming waves and barge heave motion. The study started by defining the barge vertical movement and all the forces acting in the body of moonpool to obtain simplified harmonic equation for water column motion and plotting the result using MATLAB software. The amplitude of heave barge and water column piston mode is strongly influenced by environmental conditions, in this case the significant wave height and also the dimension of the moonpool area since it is giving additional added mass into the motion. The large amplitude of the water column likely to occur if critical frequency is in the range of wave excitation. Thus, to prevent any over flowing condition during lowering/lifting operation via moonpool, the limiting sea-state condition should be identified for the designated location.
Bedroom Module Design on Offshore Hotel as a Support for Maritime Based Tourism Accommodation (Study Case in Sendang Biru, Malang, Jawa Timur, Indonesia)
Authors: Rucitra A A , Sambodho K , Wardani K K , Mulyadi Y
Published: February 2021

Aaquaculture in Indonesia has only been used as a place for aquatic biota cultivation. At the same time, the structure of the building above the grove has not been used to the fullest. Therefore, with the development of the existing floating net design, support facilities for the offshore tourism sector are being developed, one of which is the Hotel. Hotel on aquaculture is an interesting development concept because it utilizes space on offshore sea buildings with facilities that educate about aquaculture and maritime potential in Indonesia for tourists staying at hotels. In designing the hotel on top of the aquaculture building, it is necessary to analyze the space requirements for hotel users to be comfortable on top of the building in the middle of the sea. Apart from that, the hotel design aesthetic is also needed, in order to attract the attention of tourists. Based on the design by considering the macro and micro concepts, as well as the arrangement of the hotel space, a design with a natural minimalist concept is obtained but still can meet the needs of the user space.
Rnd2 differentially regulates oligodendrocyte myelination at different developmental periods
Authors: Miyamoto Yuki , Torii Tomohiro , Terao Miho , Takada Shuji , Tanoue Akito , Katoh Hironori , Yamauchi Junji
Published: February 2021

The unique biphasic role of Rnd2, an atypical branch of the Rho family GTPases, in oligodendrocyte myelination is described. Rnd2 positively regulates myelination in the early myelinating period and negatively regulates it in the subsequent period, by changes of the Rho-kinase activities, a common downstream molecule of Rho GTPases.
Insomnia Symptoms and Acute Coronary Syndrome-Induced Posttraumatic Stress Symptoms: A Comprehensive Analysis of Cross-sectional and Prospective Associations
Authors: von Känel Roland , Meister-Langraf Rebecca E , Pazhenkottil Aju P , Barth Jürgen , Schnyder Ulrich , Schmid Jean-Paul , Znoj Hansjörg , Princip Mary
Published: February 2021

Background

Acute coronary syndrome (ACS) induces clinically significant posttraumatic stress symptoms (PTSS) in 12% of patients. Subjective sleep problems are a risk factor for the development of PTSS, but this is underexplored in patients with ACS.

Purpose

To examine the association of insomnia symptoms with ACS-induced PTSS.

Methods

In this longitudinal study with 154 patients (all white, 84.4% male, mean age 58.7 years) with a verified ACS, insomnia symptoms were interviewer assessed at hospital admission and at 3 months, using the Jenkins Sleep Scale (JSS)-4. ACS-induced PTSS were assessed with the Clinician-Administered Posttraumatic Stress Disorder Scale 3 months after hospital admission. In multivariable linear models, insomnia symptoms were regressed on PTSS, adjusting for demographics, clinical variables, health behaviors, and psychological data, including cognitive depressive symptoms.

Results

Greater insomnia symptoms at admission (β = .165, p = .034), greater increase in insomnia symptoms from admission to 3 months (β = .233, p = .008), and greater insomnia symptoms at 3 months (β = .239, p = .002) were independently associated with more severe total PTSS at 3 months. Concerning the individual PTSS clusters, both insomnia symptoms at admission (β = .214, p = .007) and at 3 months (β = .213, p = .012) were independently associated with reeexperiencing symptoms. Removing sleep items from PTSS scores and excluding patients on antidepressants in two sensitivity analyses did not substantially change the results.

Conclusions

Insomnia symptoms could play an important role in the development and severity of ACS-induced PTSS. This relationship seems not simply explained by the fact that sleeping difficulties are inherent to the phenotype of posttraumatic stress disorder.

Clinical Trial information

NCT01781247.
The usefulness of an ambulatory care pharmacy performance dashboard during the COVID-19 pandemic in a complex tertiary care system
Authors: Al-Jazairi Abdulrazaq S , Horanieh Bashar K , Alswailem Osama A
Published: February 2021

Purpose

To describe the usefulness of an innovative “semi–real-time” pharmacy dashboard in managing workload during the unpredictable coronavirus disease 2019 (COVID-19) pandemic.

We created a pharmacy dashboard to monitor workload and key performance indicators during the dynamic COVID-19 crisis. The dashboard accessed the prescribing workload from our clinical information system and filled prescriptions from robotic prescription dispensing systems. The aggregated data was visualized using modern tools. The dashboard presents performance data in near real time and is updated every 15 minutes. After validation during the early weeks of the COVID-19 crisis, the dashboard provided reliable data and served as a great decision support aid in calculating the backlog of prescribed but unfilled prescriptions. It also aided in adjusting manpower, identifying prescribing and dispensing patterns, identifying trends, and diverting staff resources to appropriate locations. The dashboard has been useful in clearing the backlog in a timely manner, staff planning, and predicting the next coming surge so that we can proactively minimize accumulation of backlogged prescriptions.

Conclusion

Developing a dynamic, semi–real-time pharmacy dashboard during unstable circumstances such as those that have arisen during the COVID-19 pandemic can be very useful in ambulatory care pharmacy workload management.
Improved ammonia production from soybean residues by cell surface-displayed l-amino acid oxidase on yeast
Authors: Watanabe Yukio , Aoki Wataru , Ueda Mitsuyoshi
Published: February 2021

Ammonia is critical for agricultural and chemical industries. The extracellular production of ammonia by yeast (Saccharomyces cerevisiae) using cell surface engineering can be efficient approach because yeast can avoid growth deficiencies caused by knockout of genes for ammonia assimilation. In this study, we produced ammonia outside the yeast cells by displaying an l-amino acid oxidase with a wide substrate specificity derived from Hebeloma cylindrosporum (HcLAAO) on yeast cell surfaces. The HcLAAO-displaying yeast successfully produced 12.6 m m ammonia from a mixture of 20 proteinogenic amino acids (the theoretical conversion efficiency was 63%). We also succeeded in producing ammonia from a food processing waste, soybean residues (okara) derived from tofu production. The conversion efficiency was 88.1%, a higher yield than reported in previous studies. Our study demonstrates that ammonia production outside of yeast cells is a promising strategy to utilize food processing wastes.
Oxygen concentration affects frequency and range of transconjugants for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1
Authors: Ochi Kentaro , Tokuda Maho , Yanagiya Kosuke , Suzuki-Minakuchi Chiho , Nojiri Hideaki , Yuki Masahiro , Ohkuma Moriya , Kimbara Kazuhide , Shintani Masaki
Published: February 2021

The frequency of transconjugants were compared for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1 under aerobic and anaerobic conditions. Filter mating assays were performed with one donor strain and one recipient strain using different donors of Pseudomonas and recipient strains, including Pseudomonas, Pantoea, and Buttiauxella. Under anaerobic condition, frequencies of transconjugants for both plasmids were 101-103-fold lower than those under aerobic condition regardless of whether aerobically or anaerobically grown donors and recipients were used. To compare the transconjugant ranges under aerobic and anaerobic conditions, conjugation was performed between the donor of pBP136 and recipient bacteria extracted from environmental samples. Several transconjugants were uniquely obtained from each aerobic or anaerobic condition. Our findings indicate that a plasmid can differently spread among bacteria depending on the oxygen concentrations of the environment.
Post-transplant outcomes of standard and extended criteria donation after circulatory death donor lungs categorized by donation after brain death lung criteria
Authors: Tanaka Shin , Campo-Cañaveral de la Cruz Jose Luis , Barturen Mariana Gil , Carrasco Silvana Crowley , Román Alejandra Romero , León María Trujillo Sánchez de , Mejía Lucas Hoyos , Gómez Jose Manuel Naranjo , Peláez Mar Córdoba , Calle Álvaro Sánchez , Redondo Marina Pérez , Fadul Christian García , Ugarte Andrés Varela de , de-Antonio David Gómez-
Published: February 2021

OBJECTIVES

Most transplant centres use donation after brain death (DBD) criteria to assess the quality of controlled donation after circulatory death (cDCD) lungs. However, research on the relationship between DBD extended criteria and cDCD lung transplantation outcomes is limited. We investigated the outcomes of using DBD extended criteria donor organs in cDCD lung transplantation, compared to the standard criteria cDCD lung transplantation.

METHODS

A retrospective chart review of consecutive cDCD lung referrals to Hospital Universitario Puerta de Hierro-Majadahonda from June 2013 to December 2019 was undertaken. Donors were divided into standard and extended criteria groups. Early outcomes after lung transplant were compared between these groups using the Kaplan–Meier method and log-rank test.

RESULTS

Thirty out of 91 cDCD donor lung offers were accepted for transplantation, of which 11 were from standard criteria donors and 19 were extended criteria donors. The baseline characteristics of the 2 recipient groups were similar. There were no differences in the rates of grade 3 primary graft dysfunction at 72 h after lung transplantation (21% vs 18%), duration of mechanical ventilation (48 h vs 36 h), total intensive care unit stay (10 days vs 7 days) and 1-year survival (89% vs 90%).

CONCLUSIONS

Carefully selecting cDCD lungs from outside the standard acceptability criteria may expand the existing donor pool with no detrimental effects on lung transplantation outcomes.
Fluorescent toys ‘n’ tools lighting the way in fungal research
Authors: Van Genechten Wouter , Van Dijck Patrick , Demuyser Liesbeth
Published: February 2021

Although largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.
First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes
Authors: Tran Van Patrick , Anselmetti Yoann , Bast Jens , Dumas Zoé , Galtier Nicolas , Jaron Kamil S , Martens Koen , Parker Darren J , Robinson-Rechavi Marc , Schwander Tanja , Simion Paul , Schön Isa
Published: February 2021

Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335–382 Mb) and with scaffold numbers and their N50 (19–56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92–96. The number of predicted genes (13,771–17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
Uniparental Genome Elimination in Australian Carp Gudgeons
Authors: Majtánová Zuzana , Dedukh Dmitrij , Choleva Lukáš , Adams Mark , Ráb Petr , Unmack Peter J , Ezaz Tariq
Published: February 2021

Metazoans usually reproduce sexually, blending the unique identity of parental genomes for the next generation through functional crossing-over and recombination in meiosis. However, some metazoan lineages have evolved reproductive systems where offspring are either full (clonal) or partial (hemiclonal) genetic replicas. In the latter group, the process of uniparental genome elimination selectively eliminates either the maternal or paternal genome from germ cells, and only one parental genome is selected for transmission. Although fairly common in plants, hybridogenesis (i.e., clonal haploidization via chromosome elimination) remains a poorly understood process in animals. Here, we explore the proximal cytogenomic mechanisms of somatic and germ cell chromosomes in sexual and hybrid genotypes of Australian carp gudgeons (Hypseleotris) by tracing the fate of each set during mitosis (in somatic tissues) and meiosis (in gonads). Our comparative study of diploid hybrid and sexual individuals revealed visually functional gonads in male and female hybrid genotypes and generally high karyotype variability, although the number of chromosome arms remains constant. Our results delivered direct evidence for classic hybridogenesis as a reproductive mode in carp gudgeons. Two parental sets with integral structure in the hybrid soma (the F1 constitution) contrasted with uniparental chromosomal inheritance detected in gonads. The inheritance mode happens through premeiotic genome duplication of the parental genome to be transmitted, whereas the second parental genome is likely gradually eliminated already in juvenile individuals. The role of metacentric chromosomes in hybrid evolution is also discussed.
Rapid evolution at the Drosophila telomere: transposable element dynamics at an intrinsically unstable locus
Authors: McGurk Michael P , Dion-Côté Anne-Marie , Barbash Daniel A
Published: February 2021

Drosophila telomeres have been maintained by three families of active transposable elements (TEs), HeT-A, TAHRE, and TART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85  Drosophila melanogaster genomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we instead suggest that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than one-third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes, with niche specialization and telomere instability being previously underappreciated and likely predominant.
Evading resistance to gene drives
Authors: Gomulkiewicz Richard , Thies Micki L , Bull James J
Published: February 2021

Gene drives offer the possibility of altering and even suppressing wild populations of countless plant and animal species, and CRISPR technology now provides the technical feasibility of engineering them. However, population-suppression gene drives are prone to select resistance, should it arise. Here, we develop mathematical and computational models to identify conditions under which suppression drives will evade resistance, even if resistance is present initially. Previous models assumed resistance is allelic to the drive. We relax this assumption and show that linkage between the resistance and drive loci is critical to the evolution of resistance and that evolution of resistance requires (negative) linkage disequilibrium between the two loci. When the two loci are unlinked or only partially so, a suppression drive that causes limited inviability can evolve to fixation while causing only a minor increase in resistance frequency. Once fixed, the drive allele no longer selects resistance. Our analyses suggest that among gene drives that cause moderate suppression, toxin-antidote systems are less apt to select for resistance than homing drives. Single drives of moderate effect might cause only moderate population suppression, but multiple drives (perhaps delivered sequentially) would allow arbitrary levels of suppression. The most favorable case for evolution of resistance appears to be with suppression homing drives in which resistance is dominant and fully suppresses transmission distortion; partial suppression by resistance heterozygotes or recessive resistance are less prone to resistance evolution. Given that it is now possible to engineer CRISPR-based gene drives capable of circumventing allelic resistance, this design may allow for the engineering of suppression gene drives that are effectively resistance-proof.
The heat is on: Gulf of Alaska Pacific cod and climate-ready fisheries
Authors: Peterson Williams Megan J , Robbins Gisclair Becca , Cerny-Chipman Elizabeth , LeVine Michael , Peterson Theresa
Published: February 2021

Rapidly changing ocean conditions pose substantial challenges for coastal communities, fishermen, and managers. From 2014 to 2016, the Gulf of Alaska (GOA) experienced a marine heatwave and corollary decline in Pacific cod (Gadus macrocephalus). Here, we explore the 2020 closure of the directed Pacific cod federal fishery in the GOA as a case study of the needs and opportunities for managing fisheries in the context of environmental change. We build on climate-ready fishery research and conversations with experienced commercial fishermen, including Alutiiq fishers, and fishery managers to: (i) discuss ecosystem-based management in Alaska, (ii) explore early warning signs and management challenges preceding the decline of Pacific cod, (iii) recommend tools to enhance adaptive capacity in fishery management. We conclude that a strong foundation of science-based management that incorporates ecosystem information and multiple ways of knowing, increased monitoring and evaluation of indicators, and new tools for managers to respond and adapt will be essential to sustainable fishery management. New mechanisms highlighted in this essay include: a GOA Fishery Ecosystem Plan, climate risk and vulnerability analyses, habitat protections, and the development of original metrics, such as food web production or function targets to inform stock assessments and fishery management.
Exotic Nonleaves with Infinitely Many Ends
Authors: Meniño Cotón Carlos , Schweitzer Paul A
Published: February 2021

We show that any simply connected topological closed $4$-manifold punctured along any compact, totally disconnected tame subset $\Lambda $ admits a continuum of smoothings, which are not diffeomorphic to any leaf of a $C^{1,0}$ codimension one foliation on a compact manifold. This includes the remarkable case of $S^4$ punctured along a tame Cantor set. This is the lowest reasonable regularity for this realization problem. These results come from a new criterion for nonleaves in $C^{1,0}$ regularity. We also include a new criterion for nonleaves in the $C^2$-category. Some of our smooth nonleaves are “exotic”, that is, homeomorphic but not diffeomorphic to leaves of codimension one foliations on a compact manifold, being the 1st examples in this class.
Theorizing Liberal Orders in Crisis Then and Now: Returning to Carr and Horkheimer
Authors: Molloy Seán
Published: February 2021

This article pursues an original line of inquiry by placing E.H. Carr in direct relation with his contemporary, Max Horkheimer. Although Carr is often cited as a progenitor by realists and critical theorists, these invocations of ancestry rarely go beyond passing references to Carr in presentist terms—i.e., how he relates to their present-day projects. By means of an extensive engagement with Horkheimer and Carr, the article reveals a shared commitment to ideology critique directed at bourgeois civilization. The article demonstrates that Carr's epistemology, critique of the harmony of interests, complex treatment of utopianism, and theorization of social transformation all have their counterparts in Horkheimer. The recovery of Carr's depth and sophistication as a theorist by means of a comparison of his positions with those of Horkheimer shows that at the time of its composition The Twenty Years’ Crisis was a cutting-edge exercise in critique by a theorist working on an ambitious canvas of civilizational scale. The article concludes with a section that demonstrates the continued relevance of Carr and Horkheimer by reference to contemporary debates about the crises currently affecting the liberal international order.
Forum: Nonuse of Nuclear Weapons in World Politics: Toward the Third Generation of “Nuclear Taboo” Research
Authors: Smetana Michal , Wunderlich Carmen
Published: February 2021

That nuclear weapons have not been used in war since 1945 is one of the most intriguing research puzzles in the field of international relations. It has sparked a fruitful scholarly debate: Can the persistence of the nonuse of nuclear weapons be understood with reference to a normative “taboo” subject to a constructivist logic of appropriateness, or does it rather constitute a prudent tradition based on a logic of consequences as rationalist scholars would have it? Recently, a study by Daryl Press, Scott Sagan, and Benjamin Valentino provided further impetus for this debate and opened up a “second generation” of “taboo” research. Unlike the first generation, the second wave examined attitudes toward nuclear use among the general public rather than elite decision-makers and used large-N experimental surveys rather than in-depth interviews and archival research. In particular, these studies raised several methodological questions on how to capture the “atomic aversion”: Is it meaningful to examine public attitudes in order to grasp the validity of the nuclear “taboo” (as opposed to elite perspectives) and can we infer a weakening of the normative aversion toward nuclear use from public surveys? Bringing together the pioneers of the original debate as well as more recent contributors, this special forum seeks to take stock of the progress that has been made by discussing the theoretical, conceptual, and methodological underpinnings of the research on the nonuse of nuclear weapons. Specifically, the contributions critically reflect upon the second wave of nuclear taboo scholarship with the overall aim to build bridges between different theoretical approaches and to identify avenues for further research in this area. Ultimately, this forum seeks to present the relevance of re-envisioning nuclear taboo research to a broader audience.
Deep sequencing analysis of M184V/I mutation at the switch and at the time of virological failure of boosted protease inhibitor plus lamivudine or boosted protease inhibitor maintenance strategy (substudy of the ANRS-MOBIDIP trial)
Authors: Delaugerre Constance , Nere Marie-Laure , Eymard-Duvernay Sabrina , Armero Alix , Ciaffi Laura , Koulla-Shiro Sinata , Sawadogo Adrien , Ngom Gueye Ndaye Fatou , Ndour Cheik Tidiane , Mpoudi Ngolle Mireille , Amara Ali , Chaix Marie-Laure , Reynes Jacques ,   the ANRS 12286/MOBIDIP study group
Published: February 2021

Background

The ANRS12286/MOBIDIP trial showed that boosted protease inhibitor (bPI) plus lamivudine dual therapy was superior to bPI monotherapy as maintenance treatment in subjects with a history of M184V mutation.

Objectives

We aimed to deep analyse the detection of M184V/I variants at time of switch and at the time of virological failure (VF).

Methods

Ultra-deep sequencing (UDS) was performed on proviral HIV-DNA at inclusion among 265 patients enrolled in the ANRS 12026/MOBIDIP trial, and on plasma from 31 patients experiencing VF. The proportion of M184V/I variants was described and the association between the M184V/I mutation at 1% of threshold and VF was explored with logistic regression models.

Results

M184V and I mutations were detected in HIV-DNA for 173/252 (69%) and 31/252 (12%) of participants, respectively. Longer duration of first-line treatment, higher plasma viral load at first-line treatment failure and higher baseline HIV-DNA load were associated with the archived M184V. M184I mutation was always associated with a STOP codon, suggesting defective virus. The 48 week estimated probability of remaining free from VF was comparable with or without the M184V/I mutation for dual therapy. At failure, M184V and major PI mutations were detected in 1/17 and 5/15 patients in the bPI arm and in 2/2 and 0/3 in the bPI+lamivudine arm, respectively.

Conclusions

Using UDS evidenced that archiving of M184V in HIV-DNA is heterogeneous despite past historical M184V in 96% of cases. The antiviral efficacy of lamivudine-based dual therapy regimens is mainly due to the residual lamivudine activity.
Uniformed Services and the Field Hospital Experience During Coronovirus Disease 2019 (SARS-CoV-2) Pandemic: Open to Closure in 30 Days With 1,100 Patients: The Javits New York Medical Station
Authors: Brady Kevin , Milzman Dave , Walton Edward , Sommer Darren , Neustadtl Alan , Napoli Anthony
Published: February 2021

Introduction

The surge of SARS-CoV-2-virus infected (COVID-19) patients presenting to New York City (NYC) hospitals quickly overwhelmed and outnumbered the available acute care and intensive care resources in NYC in early March 2020. Upon the arrival of military medical assets to the Javits Convention Center in NYC, the planned mission to care for non-SARS-CoV-2 patients was immediately changed to manage patients with (SARS-CoV-2)COVID-19 and their comorbid conditions.

Healthcare professionals from every branch of the uniformed services, augmented by state and local resources, staffed the Javits New York Medical Station (JNYMS) from April 2020.

Methods

The data review reported aggregated summary statistics and participant observations collected by N.Y. State and U.S. military officials.

Results

During the 28 days of patient intake at the JNYMS, 1,095 SARS-CoV-2-positive patients were transferred from NYC hospitals to the JNYMS. At its peak, the JNYMS accepted 119 patients in a single day, had a maximum census of 453, and had a peak intensive care unit census of 35. The median length of stay was 4.6 days (interquartile range: 3.1-6.9 days). A total of 103 patients were transferred back to local hospitals, and there were 6 deaths, with an overall mortality rate of 0.6% (95% CI, 0.3-1.2).

Discussion and Conclusions

This is the first report of the care provided at the JNYMS. Within 2 weeks, this multi-agency effort was able to mobilize to care for over 1,000 SARS-CoV-2 patients with varying degrees of illness in a 1-month period. This was the largest field hospital mobilization in the U.S. medical history in response to a non-wartime pandemic. Its success with huge patient throughput including disposition and low mortality relieved critical overcrowding and supply deficiencies throughout NYC hospitals. The downstream impact likely saved additional hundreds of lives and reduced stress on the system during this healthcare crisis.
Intraoperative Transesophageal Echocardiography in Management of Acute Type I Aortic Dissection With Malperfusion: A Case Report
Authors: Beyrau Kaitlin E , Finne Huckelberry A , Wilson Sara M , Gibson Steven L , Koelling Erin E , Hudson Arlene J
Published: February 2021

Acute type I aortic dissection is a life-threatening emergency with potentially devastating complications, including end-organ malperfusion. Early detection of malperfusion with intraoperative imaging allows for efficient transition to appropriate interventions. We present a case of a 65-year-old male with acute type I aortic dissection who underwent emergent surgical repair of the aortic root and hemiarch followed by acutely worsening distal malperfusion. The use of intraoperative transesophageal echocardiography played a critical role in visualizing diversion of flow to the false lumen, prompting urgent vascular surgery consultation and life-saving thoracic endovascular aortic repair.