bluuebunny/crossref_metadata_2025 huggingface dataset:
Utilization of Augmented Reality for Introduction of a Ship Ballast System
Authors: Pitana Trika , Zaman Muhammad Badruz , Prastowo Hari , Priyanta Dwi , Siswantoro Nurhadi , Zakarias Muhammad Dzulfiqar
Published: February 2022

In the field of education, virtual reality has major advantages for the transfer of knowledge faster than conventional approaches and allows businesses to provide their workers with an efficient training program. By offering step-by-step guidance to create particular tasks, the Augmented Reality technology will assist during the training process. The knowledge in the AR application is made omnipresent, allowing the worker to be able to obtain the instructions with less effort, understandable and effective, avoiding the faults in the operation of the real ballast system. The process begins by evaluating the current components of the ballast system to understand how to incorporate augmented reality technology to boost the performance of the process. The ballast system is then made into a 3D model, including the proportional dimension and exact position of each part of the ballast system as mounted, and the potential real-world scenario. The outcome of this work is called the application of Ballast Component AR. A testing process is carried out to determine whether the application of augmented reality is prepared for implementation and preliminarily checked during the development stage. The AR framework is fully run and checked by the use of Android smartphones or tablets in the process. To evaluate input from users of the AR application, a questionnaire is used with defined parameters regarding the performance and the usefulness of the application.
The Evaluation of Maturity Level on Heavy Equipment Maintenance Management According to ISO 55001:2014
Authors: Siswantoro Nurhadi , Priyanta Dwi , Gautama Steven , Zaman Muhammad Badrus , Pitana Trika , Prastowo Hari , Ratu Balqis F , Yulianto Ardi Nugroho
Published: February 2022

One of the challenges experienced by companies nowadays is keeping their value of assets which will affect the value of the companies. The companies need to provide certainty to the stakeholders from both internal and external perspectives. These things are important for companies that have a high and large value asset. PT. X is one of the shipping lines in Indonesia and with the large task of shipping companies, it has a large number and high value of assets. Heavy equipment is of the assets that have supported the company’s main business process in the loading-unloading process. By now, there has never been an asset management maturity level on PT. X. Therefore, an evaluation of measurement of the heavy equipment maintenance management system is conducted based on the guidelines of ISO 55001: 2014. The results of the assessment showed that the maturity level of heavy equipment management is 2.7 and there are 13 sub-optimal sub-clauses that need improvement by the company.
Analysis of Exhaust Gas Emissions on Dual Fuel Diesel Engine Single Cylinder Four-stroke with LPG-Diesel Oil
Authors: Iswantoro Adhi , Made Ariana I , Syuhri Muhammad
Published: February 2022

Diesel engine is one of type of internal combustion engine that is applied in industry, including the maritime industry. The increasing use of diesel engines, has a effect on increasing emissions. Diesel engines emissions consist of SOx, NOx, HC, and others. To reduce the emissions, there are many method, one of them is using dual-fuel system. The alternative fuel can be used is Gas, which is easily available, namely LPG or liquefied petroleum gas. To supply LPG to combustion chamber, a converter-kit are needed to be install on diesel engine. There are several previous research that prove that LPG can be used as an alternative in a dual-fuel system and can reduce the emissions. One of them by Ma’amuri (2016) who designed a mechanical LPG-diesel oil as dual-fuel, using a membrane converter. Result of this research provide that good diesel engine performance. In this research, LPG-diesel oil as dual-fuel using converter kit based on ECU or electronic control unit, and then, analyze the diesel engine emissions with experimental method. The purpose of this research is to determine the emissions produced by LPG-diesel oil as dual-fuel with converter kit based ECU. After taking and analytical data, known that the NOx emission from dual fuel diesel engine using ECU-based converter kit is lower than NOx emission from conventional diesel engine with B30 diesel fuel with percentage is 25,61 % for 3ms opening duration of gas injector, 39,99 % for 4 ms opening duration of gas injector and 26,5 % for 5 ms opening duration of gas injector. The NOx emission of conventional diesel engine is 2,46 g/kWh.
Psychological wellbeing and sustainable development of coastal community: a literature review
Authors: Palupi L. S.
Published: February 2022

Nowadays wellbeing has been closely related to development. The knot was tied in the Sustainable Development Goals. Wellbeing has been acknowledged as the third goals that need to be achieve by all of the member state. Countries need to assure that they provide good health and wellbeing to its people including for the coastal communities. Albeit the important role of wellbeing on sustainable development is recognize, however the relationship between psychological wellbeing and sustainable development between coastal communities is not widely explore. Therefore, aim of this study is to analyse the link between psychological wellbeing and sustainable development of coastal communities using literature review method to assess what has been found in previous study that link psychological wellbeing and sustainable development in the context of coastal communities and what things that need to improve in the future to advance the understanding of the relationship between psychological wellbeing and sustainable development. It is found that the study of the relationship between psychological wellbeing and sustainable development of coastal communities is still limited. Furthermore, psychological wellbeing is still not yet considered in the development of coastal community measurement. Therefore, psychological wellbeing should be integrated in sustainable development of coastal community measurement tool.
The Effect of Trim on Stability and Seakeeping of Tanker, Container, and Bulk Carrier
Authors: Wen Poul , Fadillah Arif
Published: February 2022

Stability and seakeeping are important factor that must be owned by a ship because it related to the safety of the ship, meanwhile the trim also affecting the ship operation. The study has a purpose to find out the impact of the trim to the stability and seaworthiness of the ship. The analysis is carried out on 3 types of ships, namely tankers, containers, and bulk carriers. A.N. Krylov method is using to calculate the stability, whereas the seakeeping is analysed by strip theory. Both of the results for stability and seakeeping are calculated by Maxsurf Software. Stability and seakeeping analysis was carried out when the ship is in even keel condition, trim by bow, and trim by stern in maximum and extreme condition. The results shows that the trim by stern of the ship can increased the ship stability rate by 0.5~5.4%. While the effect of trim on ship motions varies due to the differences characteristics of each ship. The results shows due to the trim impact by values of RAO’s, which some of ship motions have increased meanwhile for some ship motion have decreased of ship motion condition.
Load Flow Simulation of Radial Shipboard Network Structure with Direct Current Distribution Systems
Authors: Kusuma I R , Semin  , Zaman M B , Koenhardono ES
Published: February 2022

The aim of this research is to investigate load flow of direct current distribution system on trimaran ferry ship. Radial Shipboard Network Structure with Direct Current Distribution Systems has been proposed in this research. Load flow simulation has been done by calculating electrical load calculation based on ship operation. Then, the one-line diagram of direct current distribution system is developed on electric power software. Simulation results show that direct current distribution system has been successfully implemented on hybrid powered trimaran Ship. In sailing conditions, the overall real power requirement is 20,201 MW and the reactive power is 7,757 Mvar. While the power distributed is 20,493 MW of real power and 7.816 Mvar of reactive power. In manoeuvring conditions, the actual power requirements are 21,251 MW and the reactive power is 8,16 Mvar and for power distributed is 21,573 MW of real power and 8,224 Mvar of reactive power. In loading and unloading conditions, the actual power requirements in this operating condition are 0.616 MW and the reactive power is 0.292 Mvar and for power distributed is 0,635 MW of real power and 0,296 Mvar of reactive power. In the condition of entering the port, the required power is 12.906 MW for real power and 4.969 MW for reactive power and for power distributed is 13,027 MW of real power and 4,994 Mvar of reactive power. The result showed that the concept direct current distribution system has been successfully developed in this research to combine diesel generators with marine renewable energy to make sure that the distributed power stay adequate all through operation.
Integrated ship recycling industrial estate design concept for Indonesia
Authors: Sunaryo  , Tjitrosoemarto Bagus A
Published: February 2022

Since the implementation of the cabotage principle, the number of Indonesian flagged ships has been increasing significantly, due to the government’s incentive on importation tax for used ships. The fleet is dominated by old ships, which most of them will soon be sent for recycling. The ship recycling industry has a great opportunity for the economy of Indonesia, because of its contribution to the steel industry and job creation, but on the other hand it is also a very environmentally unfriendly industry. Currently there is no ship recycling yard complies with the requirements of international and national regulations, most of them are still implementing conventional method, and are not connected to the supporting industries. Based on these issues the study was aimed to design a concept of an integrated green and sustainable ship recycling industry estate, which has all necessary industries and facilities in it, and efficiently connected with each other. Block Plan program was used to optimize the arrangement. It is proposed that five ship recycling yards, large; medium; and smaller capacity, steel mill, waste treatment facility, electricity power plant, fresh water facility, training centre, workers accommodation, hospital, and bus terminal should be included in the estate.
Everyday Performance of Ship Officer: Qualitative Analysis based on Functional Resonance Analysis Method
Authors: Gde Manik Sukanegara Adhita I , Fuchi Masaki , Shoji Fujimoto , Konishi Tsukasa , Ino Anju
Published: February 2022

Uncertainty in a complex socio-technical system, such as ship, is given. Yet, surprisingly, most of the ship operations were done without any significant problem. In this case, the ship officer as the operator plays an important role in maintaining ship safety. Human performance is unpredictable and varies on the condition. However, variation in human performance is more likely to produce acceptable outcomes than adverse outcomes. Therefore, this study aimed to determine how human variability performance in specific officers onboard contributes to successful ship operation. Evaluation of officer variability performance for establishing safety in everyday ship operation has been done using Functional Resonance Analysis Method (FRAM) in this study. FRAM is Safety-II based tool that provides concepts and models for safety analysis that use terms called function to describe system activities. An essential feature of FRAM is the mean that is necessary to explain the activity of a system in which the functions are mutually dependent. System activities are modeled in terms of how the system works to ensure that it performs systematically. Key functions of officer activities onboard are generated through observation in training ship Fukae-maru owned by Kobe University. As a result, FRAM could define how officer variability performance contributes to system propagation and create a safe ship operation.
Analysis of The Effect of Pitch Angle on Propeller Modification by Considering Wake Distribution on Propeller Performance
Authors: Suranto Maful , Made Ariana I , Baidowi Achmad
Published: February 2022

The propeller is an important component of the ship’s propulsion system, and its design related to the safety and ship’s cost. The propeller is operated in an uneven flow field behind the ship so it has an important influence on the cavity, vibration and hydrodynamic performance. Therefore, optimization calculations are needed to get most economical in addition to meeting the provisions of the Energy Efficiency Design Index. Optimization software through polynomial regression values can be used for selecting propeller. However, when the propeller is installed on the hull, the Velocity Advance (Va) on the propeller will change from the distribution at the time of the open water test because of the shape of the hull. This reduces the performance of propeller. So it is necessary to calculate the engine propeller hull matching to get a match on each propulsion component. Blade element theory concept can be used in designing the propeller for the engine hull matching, with the hypothesis that if the pitch angle is greater than Va, cavitation will occur. This condition is not allowed and if the pitch angle is too small for Va, the thrust cannot be maximized against flow, then it must adjust to the Velocity Advance (Va) distribution on the ship’s hull, because increasing the thrust value will also increasing propeller’s relative rotative efficiency (ηR) and open water efficiency (ηO) and hull efficiency (ηH). This situation makes a proportional increase in the value of the propulsive coefficient. The simulations are carried out on the size of the model with a dual domain (single-hull) by turning the propeller while the ship is stationary and seeing the convergent speed generated by the ship. The simulation data that will be taken are propeller thrust and torque because these values are considered sufficient to compare the simulation results. It’s getting the thrust foil value that making model S_T, S_eta and S_KomL S_T model is done by looking at the highest thrust, S_eta model with highest efficiency method and on S_KomL with highest thrust and efficiency by looking at the streamlined model, the thrust and efficiency values are equal to or higher of the MP687. It is showed that open water efficiency value in the two modified models has decreased, namely S_T model of 0.341, S_KomL of 0.345 and S_eta of 0.301 with original MP687 model of 0.371. While the hull efficiency of S_T model has decreased to 1,449 and S_KomL model increased by 1,591 and S_eta model increased by 3.8 but in MP687 model was 1,526, and the relative rotate efficiency of S_T model increased to 1,096, S_KomL model also increased by 1,099 and also S_eta model of 1.08 which originally on the MP687 1,055 model. This will result in the Propulsive Coefficient (PC) value in S_T model of 0.543 with decreasing, S_KomL 0.604 and S_eta 1.25 with an increase from the original MP687 0.597
Implementing 3D Model LNG Tanker Ship Cargo Handling System Equipment for Training Using Augmented Reality
Authors: Herwisesa A , Zaman M B , Siswantoro N , Prastowo H , Pitana T , Priyanta D , Busse Wolfgang
Published: February 2022

The learning system of the vessel is very important for a marine engineer to understand the characteristic of machinery system. This can be conducted by looking at the block diagram and seeing the 3D picture or directly observing the system on a vessel in order to get a complete understanding. It is difficult to do direct observation due to safety regulations and company confidentiality, especially for LNG tanker ship. To overcome this restriction, this study will propose a 3D drawing for training that can represent the real operational condition of cargo handling system equipment of an LNG tanker vessel. Augmented Reality 3D is used to recreate the system and put necessary information about the object along with the 3D drawing. The augmented reality 3D object and information showing with the android application by scanning the object augmented reality marker. In this research, the user is satisfied with the experience and interface based on user data collected from the questionnaire method with aspect of attractiveness, uses ability, effectiveness, user interface experience, and measure the understanding about the application with questionnaire value measurement.
Short Circuit Analysis on AHTS Ship Due To Use of Closed Circuit Electrical System
Authors: Sarwito Sardono , Kusuma Indra Ranu , Kurniawan Adi , Prananda Juniarko
Published: February 2022

Dynamic Positioning (DP) enables a ship to automatically maintain a vessel’s position and heading by using its own propellers and thrusters. The position can be kept optimally when the ship leans on the harbour with the assistance of the anchoring and mooring process. Under particular circumstances, when the ship is in the middle of the sea, both of the processes can’t be done optimally. To ensure the ships absolute position, the ship must have zero six degrees of motion: heave, sway, surge, roll, pitch and yaw, in which the vessel must be in absolute idle despite the wave effect. The DP is used to articulate wave force and against it by a work of mechanism and sensor in which prevents the ship’s standpoint deviates. The computer will proceed with the information, articulate a levelised thruster work, and avoid any degrees of motion from becoming non-zero. Ship equipped with this DP system generally uses split bus configuration in the electricity system, by allowing one load supplied by one independent generator to improve its reliability. However, this configuration was deficient with the efficient aspect and high emissions caused by the power supply. With the application of closed bus configuration electricity system, there is a high potential of excess current influx, which causes short circuit current. The analysis of how much short circuit current happened on the electricity system of AHTS ship is to revolve the short circuit current, and thus resulting in electrical system failure. Based on the analysis that has been done, the configuration electricity system with 1 generator supply power thruster and two diesel generator, also the load that used is two bow thruster and 60% shipload having short circuit based of the standard short circuit for low voltage electricity.
Design auto trajectory of passenger ship in variation of sea condition in line Ketapang - Gilimanuk of Bali strait, Indonesia
Authors: Aisjah Aulia Siti , Masroeri A A , Andika Made Widnyana , Arifin Syamsul , Bastian Ferry
Published: February 2022

The fleet of ferry ships crossing in the Bali Strait between Ketapang - Gilimanuk is relatively old, where when the waves are quite large and the current is strong enough the ships cannot go directly to Ketapang or vice versa. In order for the ship to reach its destination, it needs the right trajectory based on sea conditions. An automatic control system algorithm is proposed to perform an auto trajectory system. New trajectory is created base on the sea conditions. The auto trajectory system consists of steering and speed control system. The study was done by computer simulation and using of Matlab software. Simulations were carried out for various conditions of sea current speed of 3-7 knots and waves with in height of 1-1.5 meters. The auto trajectory system used of adaptive fuzzy control system to determine the proportional - integral and - derivatives (PID) gain controller. The rules in fuzzy control use the Sugeno type. The performances of control to meet IMO standards and produced 5 trajectory models for various current and wave heights, in both of the direction from the north (Java Sea) and from the south (Australian sea). The fuzzy control can keep the ship on its trajectory with the largest error of 3.93 meters when the sea current is 7 knots from the south and the sea wave height is 1.5 meters.
Numerical Simulation of Low Pressure Evaporator Modified with Vortex Generator for Improving the Heat Transfer Characteristics
Authors: Yudhatama A R , Safitra A G , Satrio D
Published: February 2022

Heat Recovery Steam Generator (HRSG) is a crucial component in the combined cycle power plant, which utilises gas turbine exhaust gases to heat water into further hot steam. Research is needed to improve the heat transfer process in the LP Evaporator. One way to increase the heat transfer is by adding a Vortex Generator (VG) to the LP evaporator. The Vortex Generator itself is a vortex generator that aims to make the fluid flow from the gas turbine not only hit the tube banks in the HRSG but also between the tubes installed a Vortex Generator, which functions to make the fluid flow that was previously laminar into turbulent so that the heat transfer that occurs in LP Evaporator just got better. The analysis consists to velocity contour, temperature contour, local Nu, heat transfer (q), and pressure drop. To determine fluid flow using 2D simulation with Computational Fluid Dynamics (CFD). From the geometry type. Variations made are geometric shapes and the VG arrangement, namely rectangular common flow down, delta winglet common flow down, delta winglet common flow up, and rectangular common flow up. The heat transfer rate value is 2271.34 W, 2333.27 W, 3340.334 W, 3090.747 W. The highest heat transfer rate value occurs on the delta winglet with the common flow up arrangement, and the lowest heat transfer rate value occurs on rectangular with the common flow down arrangement.
Navigation Channel Capacity Modeling: A Case Study for Balikpapan Bay
Authors: Mustakim Achmad , Nur Hasan Iqbal , Yuliana Naning
Published: February 2022

Vessel traffic flow in Balikpapan Bay will increase to follow the nation’s new capital city planning development in East Kalimantan affects the demand for development on a large scale from all around Indonesia to the new area in East Kalimantan. This final project aims to determine the maximum number of vessels passing a particular channel per unit time. The discrete simulation method will use Anylogic software to determine the channel capacity with the channel length, vessel safety distance, and vessel velocity. The number of vessel arrival to Balikpapan Bay is estimated using the Forecasting Method and Moving Average Method. The results showed that the recommended channel capacity is 74 units/day or equal to 27.010 units/year with a utility rate of 80%. That maximum number of vessels entering the channel can guarantee the safety level of shipping activities and reduce queues that cause congestion and costs arising from long waiting times for channel services and the stability of port workload. Based on these conditions, Balikpapan Bay could accommodate vessel arrival during materials and heavy-duty equipment for the nation’s new capital city planning development until 2032. The total number of vessel arrival is 24.282 units and a utility rate of 72%.
Comparison of voltage harmonics in AC and DC shipboard electrical power distribution systems: A case study of 17,500 DWT tanker vessel
Authors: Budianto Firman , Kurniawan Adi , Kusuma Indra R. , Kurniawan Akhmad R. , Gumilang Ahlur R.N.
Published: February 2022

Recently, direct current (DC) shipboard electrical power distribution systems has begun to be looked at to replace conventional alternating current (AC) distribution systems. DC distribution systems has some technical advantages such as lower power losses and drop voltage across the distribution cables. However, there is a drawback in its high harmonics distortion due to the utilization of AC-DC rectifier in the generation side and DC-AC inverter in the load side. This study tries to investigate how much increase of voltage harmonics when a conventional AC shipboard electrical power distribution systems is replaced with equal DC systems. A 17,500 deadweight tonnage (DWT) shipboard systems is used as the case study. Both of AC and DC distribution systems are modelled with a same generation and load systems in a simulation software and the results are being compared. The comparison shows that DC distribution systems generate voltage harmonics are higher than AC distribution systems for the sample vessel.
LNG Distribution Optimization using Set Partitioning Problem Method
Authors: Adli AWS , Prastyasari FI , Handani DW , Artana KB
Published: February 2022

The Indonesian government’s commitment to increase the use of gas for domestic demand, by issuing the Decree of the Minister of Energy and Mineral Resources Number 13K/13/MEM/2020 concerning the Assignment of the Implementation of the Supply and Development of LNG Infrastructure and the Gasification 52 power plants in Indonesia. Therefore, a study on the supply chain design that can support the gasification process of the 52 power plants is crucial. Power plant data is imperative to identify receiving terminals which are then grouped into 8 clusters using the K-Means method. The design will use operating LNG refineries, which will then go to the hub for each cluster. Considering the feasibility factor of the receiving terminal and using the center of gravity method carries the determination of the hub. Considering the investment and operational costs form the feasible route as the most optimal by using the Set Partitioning Problem (SPP) method. The optimization considers several types of ships with six different sizes. The total investment cost required was $107,815,749.11, and the operational cost was $68,993,709.11. The results of the economic analysis indicate the distribution will reach a payback period within 10 years if gas sales use a margin of 1,75 USD.
Prediction Performance of Two Stroke Semi Free Piston Diesel Engine with Dual Piston System
Authors: Fathallah Aguk Zuhdi Muhammad , Bimatara Ian , Bakar Rosli Abu
Published: February 2022

The design of the semi-free piston two-stroke diesel engines has been successfully implemented. Before the engine is built, it is necessary to predict its performance. Prediction is done by using the simulation method. This method is considered the most effective because it does not fabricate the machine first. Modelling and simulation are done using application software. Simulation modelling covers all parts of the engine, namely the intake system, block, injection system, and then exhaust system. Engine performance predictions are based on speed variations as well as load variations. Validation is done with a conventional machine. The difference between the two engines lies in friction losses, where the free piston concept is to reduce friction losses. The simulation results are engine performance such as torque, power, bsfc, bmep, and combustion processes such as heat release, pressure, and ignition delay. The difference in the performance of the semi-free piston compared to a conventional engine with the same combustion chamber size. Prediction results state that the difference in performance is very significant.
Optimalization of Smart Technologies in Improving Sustainable Maritime Transportation
Authors: Priadi Antoni Arif
Published: February 2022

The geographical constellation of Indonesia among Asia and Australia as well as among Indian and Pasific ocean has an important role in sea transportation internationally and domestically. This paper is aimed to elaborate the advantage of geographical constellation in relation with sea transportation, to discuss the Indonesia policies on sea transportation and to challenge the smart technology for answering the challenges. The discussion began with six areas of Indonesian policies such as: competitive sea transportation, connectivity, seperti infrastructure, compliance on safety and security, law enforcement and integration in organizational management. The paper also gave example on how currently information technology applied on Inaportnet, National Logistic Ecosystem, Sitolaut and harzadous and harmful substances management system. Further research to support each of six areas on the context of smart technology need to be developed.
Planar representations of group actions on surfaces
Authors: Bozlee Sebastian , Lippert Samuel , Wootton Aaron
Published: February 2022

The space of skeletal signatures was introduced as a simple but generally much coarser two-dimensional representation of the space of all signatures with which a group can act on a compact oriented surface. In this paper, we provide a complete characterization of the groups for which the skeletal signature space provides a complete and accurate picture of the structure of the full space of signatures. We show that such groups fall into three distinct families, and for two of these families, we show that for sufficiently large genus, the skeletal signature space depends essentially only on group order, and we explicitly describe these spaces. For the third family, we show that the skeletal signature space depends much more strongly upon group structure and provide some partial analysis of the structure of this space.
Reduction of superelliptic Riemann surfaces
Authors: Shaska Tanush
Published: February 2022

For a superelliptic curveX\mathcal {X}, defined overQ\mathbb {Q}, letp\mathfrak {p}denote the corresponding moduli point in the weighted moduli space. We describe a method how to determine a minimal integral model ofX\mathcal {X}such that: i) the corresponding moduli pointp\mathfrak {p}has minimal weighted height, ii) the equation of the curve has minimal coefficients. Part i) is accomplished by reduction of the moduli point which is equivalent with obtaining a representation of the moduli pointp\mathfrak {p}with minimal weighted height, as defined in \cite{b-g-sh}, and part ii) by the classical reduction of the binary forms.
Dessins d’enfants with a given bipartite graph
Authors: Hidalgo Ruben
Published: February 2022

Let

G

\mathcal {G}

be a finite connected bipartite graph. We describe the set

D

e
s
s

G

{ \mathcal Dess}_{\mathcal G}

consisting of all the isomorphism classes of the dessins d’enfants whose underlying bipartite graph is isomorphic to

G

\mathcal {G}

. Such a description is explicit and it permits, for each dessin, to provide some of its Galois invariants, such as its passport, its automorphism group, its monodromy group and its Z-orientability property.
On the Riemann-Hurwitz formula for regular graph coverings
Authors: Mednykh Alexander
Published: February 2022

The aim of this paper is to present a few versions of the Riemann-Hurwitz formula for a regular branched covering of graphs. By a graph, we mean a finite connected multigraph. The genus of a graph is defined as the rank of the first homology group. We consider a finite group acting on a graph, possibly with fixed and invertible edges, and the respective factor graph. Then, the obtained Riemann-Hurwitz formula relates genus of the graph with genus of the factor graph and orders of the vertex and edge stabilizers.
Efficient privacy-preserving whole-genome variant queries
Authors: Akgün Mete , Pfeifer Nico , Kohlbacher Oliver
Published: February 2022

Motivation

Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease–gene association studies are of great importance. However, genomic data are very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data.

Results

We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3 000 000 variants with five genomic query predicates under 400 ms. Querying 1 048 576 genomes, each containing 1 000 000 variants, for the presence of five different query variants can be achieved approximately in 6 min with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data.

Availability and implementation

https://gitlab.com/DIFUTURE/privacy-preserving-variant-queries.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cognitive flexibility, OCD and the brain
Authors: Robbins Trevor.W.
Published: February 2022

This scientific commentary refers to ‘Unbalanced fronto-pallidal neurocircuit underlying set shifting in obsessive-compulsive disorder’ by Kim et al. (https://doi.org/10.1093/brain/awab483).
Different saccadic profile in bulbar versus spinal-onset amyotrophic lateral sclerosis
Authors: Zaino Domenica , Serchi Valeria , Giannini Fabio , Pucci Barbara , Veneri Giacomo , Pretegiani Elena , Rosini Francesca , Monti Lucia , Rufa Alessandra
Published: February 2022

Two clinical phenotypes characterize the onset of amyotrophic lateral sclerosis (ALS): the spinal variant, with symptoms beginning in the limbs, and the bulbar variant, affecting firstly speech and swallowing. The two variants show some distinct features in the histopathology, localization and prognosis, but to which extent they really differ clinically and pathologically remains to be clarified. Recent neuropathological and neuroimaging studies have suggested a broader spreading of the neurodegenerative process in ALS, extending beyond the motor areas, toward other cortical and deep grey matter regions, many of which are involved in visual processing and saccadic control. Indeed, a wide range of eye movement deficits have been reported in ALS, but they have never been used to distinguish the two ALS variants.

Since quantifying eye movements is a very sensitive and specific method for the study of brain networks, we compared different saccadic and visual search behaviours across spinal ALS patients (n = 12), bulbar ALS patients (n = 6) and healthy control subjects (n = 13), along with cognitive and MRI measures, with the aim to define more accurately the two patients subgroups and possibly clarify a different underlying neural impairment.

We found separate profiles of visually-guided saccades between spinal (short saccades) and bulbar (slow saccades) ALS, which could result from the pathologic involvement of different pathways.

We suggest an early involvement of the parieto-collicular-cerebellar network in spinal ALS and the fronto-brainstem circuit in bulbar ALS. Overall, our data confirm the diagnostic value of the eye movements analysis in ALS and add new insight on the involved neural networks.
Sex-related brain connectivity correlates of compensation in adults with autism: insights into female protection
Authors: Walsh Melissa J M , Pagni Broc , Monahan Leanna , Delaney Shanna , Smith Christopher J , Baxter Leslie , Braden B Blair
Published: February 2022

The male preponderance in autism spectrum disorder (ASD) led to the hypothesis that aspects of female biology are protective against ASD. Females with ASD (ASD-F) report more compensatory behaviors (i.e. “camouflaging”) to overcome ASD-related social differences, which may be a mechanism of protection. No studies have examined sex-related brain pathways supporting camouflaging in ASD-F, despite its potential to inform mechanisms underlying the ASD sex bias. We used functional connectivity (FC) to investigate “sex-atypical” and “sex-typical” FC patterns linked to camouflaging in adults with ASD and examined multimodal coherence of findings via structural connectometry. Exploratory associations with cognitive/emotional functioning examined the adaptive nature of FC patterns. We found (i) “sex-atypical” FC patterns linked to camouflaging in the hypothalamus and precuneus and (ii) “sex-typical” patterns in the right anterior cingulate and anterior parahippocampus. Higher hypothalamic FC with a limbic reward cluster also correlated with better cognitive control/emotion recognition. Structural connectometry validated FC results with consistent brain pathways/effect patterns implicated in ASD-F. In summary, “male-typical” and “female-typical” brain connectivity patterns support camouflaging in ASD-F in circuits implicated in reward, emotion, and memory retrieval. “Sex-atypical” results are consistent with fetal steroidogenic/neuroinflammatory hypotheses. However, female genetics/biology may contribute to “female-typical” patterns implicated in camouflaging.
Evolution of Imipenem-Relebactam Resistance Following Treatment of Multidrug-Resistant Pseudomonas aeruginosa Pneumonia
Authors: Shields Ryan K , Stellfox Madison E , Kline Ellen G , Samanta Palash , Van Tyne Daria
Published: February 2022

We report the emergence of imipenem-relebactam nonsusceptible Pseudomonas aeruginosa in 5 patients treated for nosocomial pneumonia for 10–28 days. Genome sequence analysis identified treatment-emergent mutations in MexAB-OprM and/or MexEF-OprN efflux operons that arose independently in each patient across distinct P. aeruginosa sequence types. Testing with efflux-inhibitor PAβN restored imipenem-relebactam susceptibility.
Bariatric surgery and cardiovascular disease: a systematic review and meta-analysis
Authors: van Veldhuisen Sophie L , Gorter Thomas M , van Woerden Gijs , de Boer Rudolf A , Rienstra Michiel , Hazebroek Eric J , van Veldhuisen Dirk J
Published: February 2022

Aims

Obesity is a global health problem, associated with significant morbidity and mortality, often due to cardiovascular (CV) diseases. While bariatric surgery is increasingly performed in patients with obesity and reduces CV risk factors, its effect on CV disease is not established. We conducted a systematic review and meta-analysis to evaluate the effect of bariatric surgery on CV outcomes, in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline.

Methods and results

PubMed and Embase were searched for literature until August 2021 which compared bariatric surgery patients to non-surgical controls. Outcomes of interest were all-cause and CV mortality, atrial fibrillation (AF), heart failure (HF), myocardial infarction, and stroke. We included 39 studies, all prospective or retrospective cohort studies, but randomized outcome trials were not available. Bariatric surgery was associated with a beneficial effect on all-cause mortality [pooled hazard ratio (HR) of 0.55; 95% confidence interval (CI) 0.49–0.62, P < 0.001 vs. controls], and CV mortality (HR 0.59, 95% CI 0.47–0.73, P < 0.001). In addition, bariatric surgery was also associated with a reduced incidence of HF (HR 0.50, 95% CI 0.38–0.66, P < 0.001), myocardial infarction (HR 0.58, 95% CI 0.43–0.76, P < 0.001), and stroke (HR 0.64, 95% CI 0.53–0.77, P < 0.001), while its association with AF was not statistically significant (HR 0.82, 95% CI 0.64–1.06, P = 0.12).

Conclusion

The present systematic review and meta-analysis suggests that bariatric surgery is associated with reduced all-cause and CV mortality, and lowered incidence of several CV diseases in patients with obesity. Bariatric surgery should therefore be considered in these patients.
Impact of oral anticoagulation on the association between frailty and clinical outcomes in people with atrial fibrillation: nationwide primary care records on treatment analysis
Authors: Wilkinson Chris , Wu Jianhua , Clegg Andrew , Nadarajah Ramesh , Rockwood Kenneth , Todd Oliver , Gale Chris P
Published: February 2022

Aims

People with atrial fibrillation (AF) frequently live with frailty, which increases the risk of mortality and stroke. This study reports the association between oral anticoagulation (OAC) and outcomes for people with frailty, and whether there is overall net benefit from treatment in people with AF.

Methods and results

Retrospective open cohort electronic records study. Frailty was identified using the electronic frailty index. Primary care electronic health records of 89 996 adults with AF and CHA2DS2-Vasc score of ≥2 were linked with secondary care and mortality data in the Clinical Practice Research Database (CPRD) from 1 January 1998 to 30 November 2018. The primary outcome was a composite of death, stroke, systemic embolism, or major bleeding. Secondary outcomes were stroke, major bleeding, all-cause mortality, transient ischaemic attack, and falls. Of 89 996 participants, 71 256 (79.2%) were living with frailty. The prescription of OAC increased with degree of frailty. For patients not prescribed OAC, rates of the primary outcome increased alongside frailty category. Prescription of OAC was associated with a reduction in the primary outcome for each frailty category [adjusted hazard ratio, 95% confidence interval, no OAC as reference; fit: vitamin K antagonist (VKA) 0.69, 0.64–0.75, direct oral anticoagulant (DOAC) 0.42, 0.33–0.53; mild frailty: VKA 0.52, 0.50–0.54, DOAC 0.57, 0.52–0.63; moderate: VKA 0.54, 0.52–0.56, DOAC 0.57, 0.52–0.63; severe: VKA 0.48, 0.45–0.51, DOAC 0.58, 0.52–0.65], with cumulative incidence function effects greater for DOAC than VKA.

Conclusion

Frailty among people with AF is common. The OAC was associated with a reduction in the primary endpoint across all degrees of frailty.
High Stability of the Epigenome inDrosophilaInterspecific Hybrids
Authors: Bodelón Alejandra , Fablet Marie , Veber Philippe , Vieira Cristina , García Guerreiro Maria Pilar
Published: February 2022

Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F1 hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis–trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.
Spectral element numerical simulation of the 2009 L’Aquila earthquake on a detailed reconstructed domain
Authors: Di Michele F , May J , Pera D , Kastelic V , Carafa M , Smerzini C , Mazzieri I , Rubino B , Antonietti P F , Quarteroni A , Aloisio R , Marcati P
Published: February 2022

In this paper, we simulate the earthquake that hit the city of L’Aquila on 2009 April 6 using SPEED (SPectral Elements in Elastodynamics with Discontinuous Galerkin), an open-source code able to simulate the propagation of seismic waves in complex 3-D domains. Our model includes an accurate 3-D reconstruction of the Quaternary deposits, according to the most up-to-date data obtained from the Microzonation studies in Central Italy and a detailed model of the topography incorporated using a newly developed tool. The sensitivity of our results with respect to different kinematic seismic sources is investigated. The results obtained are in good agreement with the recordings at the available seismic stations at epicentral distances within a range of 20 km. Finally, a blind source prediction scenario application shows that a reasonably good agreement between simulations and recordings can be obtained by simulating stochastic rupture realizations with basic input data. These results, although limited to nine simulated scenarios, demonstrate that it is possible to obtain a satisfactory reconstruction of a ground shaking scenario employing a stochastic source constrained on a limited amount of ex-ante information. A similar approach can be used to model future and past earthquakes for which little or no information is typically available, with potential relevant implications for seismic risk assessment.
Blocking EP4 down-regulates tumor metabolism and synergizes with anti-PD-1 therapy to activate natural killer cells in a lung adenocarcinoma model
Authors: Tokumasu Miho , Nishida Mikako , Kawaguchi Takamasa , Kudo Ikuru , Kotani Tohru , Takeda Kazuhiko , Yoshida Takao , Udono Heiichiro
Published: February 2022

Prostaglandin E2 (PGE2), a product of the cyclooxygenase (COX) pathway, is produced by tumors and surrounding stromal cells. It stimulates tumor progression, promotes angiogenesis and suppresses the anti-tumor response. Pharmacological inhibition of PGE2 synthesis has been shown to suppress tumor initiation and growth in vivo. In the current study, we demonstrated that the growth of the Ptgs2-deficient 3LL lung adenocarcinoma cell line was down-regulated in vivo through natural killer (NK) cell activation and a reduction in the population of polymorphonuclear leukocyte-myeloid-derived suppressor cells (PMN-MDSCs) and tumor-associated macrophages (TAMs). On the basis of these results, the therapeutic effect of ONO-AE3-208 (EP4i), an inhibitor of EP4 (a PGE2 receptor), combined with anti-PD-1 antibody was evaluated. EP4i, but not anti-PD-1 antibody, decreased tumor metabolism including glycolysis, fatty acid oxidation and oxidative phosphorylation. EP4i induced IFNγ production from only NK cells (not from T cells) and a shift from M2-like to M1-like macrophages in TAMs. These effects were further enhanced by anti-PD-1 antibody treatment. Although CD8 T-cell infiltration was increased, IFNγ production was not significantly altered, even with combination therapy. Tumor hypoxia was ameliorated by either EP4i or anti-PD-1 antibody treatment, which was further affected by the combination. Normalization of tumor vessels was significant only for the combination therapy. The results indicated a novel effect of EP4i for the metabolic reprogramming of tumors and revealed unique features of EP4i that can synergize with anti-PD-1 antibody to promote IFNγ production by NK cells, polarize TAMs into the M1 phenotype, and reduce hypoxia through normalization of the tumor vasculature.