bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass-limited plasmas heated by laser-driven fast electrons as a powerful source of neutron and hard x-ray radiation
Authors: Gus’kov S Yu , Kuchugov P A , Murakami M , Yakhin R A
Published: September 2020

To create a plasma with extreme thermodynamic parameters, we propose to heat with a laser-accelerated fast electron beam a target of a size less than the mean free path of the heating particles. The effect of capture of fast electrons generated in an electrically neutral target due to the action of a self-consistent electrostatic field at its boundaries allows us to volumetrically heat a target over multiple flights of fast electrons through it. Using such a heating mode enables control of the target mass to be significantly less than the mass stopping range of the heating particles. Heating a mass-limited target by laser-driven relativistic electrons can produce a plasma with a temperature of ∼10’s keV and a density close to its initial solid-state density. Such plasma objects are expected to serve as powerful sources of neutron and hard x-ray radiation.
Development of robust metric based on cumulative electrical power for electromechanical impedance based structural health monitoring
Authors: Soman Rohan , Singh Shishir Kumar , Wandowski Tomasz , Malinowski Pawel
Published: September 2020

Electromechanical impedance (EMI) based techniques have been proposed for structural health monitoring due to their sensitivity to low levels of damage. Most of the work in the EMI technique depends on the change in the admittance signature of the structure in the healthy and damaged state. Several metrics have been proposed to quantify this difference in the signature. Most common being root-mean square difference (RMSD), mean absolute percentage deviation, correlation coefficient etc. As the admittance signatures has several troughs and peaks, the statistical metrics are not robust and often show false detection due to ambient changes and measurement noise.

Thus, this paper proposes a novel index for the damage detection using the EMI technique based on the cumulative electrical power. The frequency v/s resistance or conductance plot is used for calculating the normalized cumulative electrical power (NCP) of the system. The NCP curve is a monotonically increasing function and hence robust for statistical comparison. The cumulative power curve is then used to develop three different indices comparing the amplitude difference (RMSD of the NCP curves), difference in the area under the NCP curve as well as the modified Frechet distance between the NCP curves. The performance of these indices are compared with the RMSD index which has been commonly used. The comparison is carried out on four different structures and show very encouraging results. In addition to the experimental validation, sensitivity studies have been carried out on an analytical signal. It is seen that the Frechet distance based index is a robust indicator for damage detection and minimizes the false detection under variety of conditions affecting the EMI signature.
Topologically nontrivial interband plasmons in type-II Weyl semimetal MoTe2
Authors: Jia Xun , Wang Maoyuan , Yan Dayu , Xue Siwei , Zhang Shuyuan , Zhou Jianhui , Shi Youguo , Zhu Xuetao , Yao Yugui , Guo Jiandong
Published: September 2020

In many realistic topological materials, more than one kind of fermions contribute to the electronic bands crossing the Fermi level, leading to various novel phenomena. Here, using momentum-resolved inelastic electron scattering, we investigate the plasmons and their evolution across the phase transition in a type-II Weyl semimetal MoTe2, in which both Weyl fermions and trivial electrons contribute to the Fermi surface in the T
d phase. One plasmon mode in the 1T′ phase at high temperature and two plasmon modes in the topological T
d phase at low temperature are observed. Combining with first-principles calculations, we show that all the plasmon modes are dominated by the interband correlations between the inverted bands of MoTe2. Especially in the T
d phase, since the electronic bands split due to inversion symmetry breaking and spin–orbit coupling, the plasmon modes manifest the interband correlation between the topological Weyl fermions and the trivial electrons. Our work emphasizes the significance of the interplay between different kinds of carriers in plasmons of topological materials.
Investigation of TESPEL cloud dynamics in Wendelstein 7-X stellarator
Authors: Kocsis G. , Tamura N. , Bussiahn R. , McCarthy K.J. , Baldzuhn J. , Biedermann C. , Cseh G. , Damm H. , Kornejew P. , König R. , Panadero N. , Szepesi T.
Published: September 2020

Tracer-encapsulated solid pellet (TESPEL) was injected from the outboard midplane into Wendelstein 7-X (W7-X) plasmas. Viewing from behind the flight path, the distribution of the light emissions from the TESPEL cloud particles (H, C and C2+) was recorded using an ultrafast visible camera with a temporal resolution up to 2 µs, which allows resolving both the pellet cloud evolution and the detachment of the drifting cloud. It was observed that both the B┴ and the B║ aligned dimensions of the pellet cloud fluctuate quasi-periodically, this being associated with a vertical cloud movement and an eruption/ejection of part of the cloud. It is found that, first, the pellet cloud expands parallel to the magnetic field lines for about 10 µs. Then, when the cloud reaches a certain B║ size the ionized part of the cloud (plasmoid) moves vertically (typically upwards) and detaches itself from the pellet within 10 µs. One possible explanation for the upward movement of the pellet cloud is the presence of a vertical component of grad(B) pointing downward resulting in an upward cloud drift.
Cephalopod-inspired robot capable of cyclic jet propulsion through shape change
Authors: Christianson Caleb , Cui Yi , Ishida Michael , Bi Xiaobo , Zhu Qiang , Pawlak Geno , Tolley Michael T
Published: September 2020

The compliance and conformability of soft robots provide inherent advantages when working around delicate objects or in unstructured environments. However, rapid locomotion in soft robotics is challenging due to the slow propagation of motion in compliant structures, particularly underwater. Cephalopods overcome this challenge using jet propulsion and the added mass effect to achieve rapid, efficient propulsion underwater without a skeleton. Taking inspiration from cephalopods, here we present an underwater robot with a compliant body that can achieve repeatable jet propulsion by changing its internal volume and cross-sectional area to take advantage of jet propulsion as well as the added mass effect. The robot achieves a maximum average thrust of 0.19 N and maximum average and peak swimming speeds of 18.4 cm s−1 (0.54 body lengths/s) and 32.1 cm s−1 (0.94 BL/s), respectively. We also demonstrate the use of an onboard camera as a sensor for ocean discovery and environmental monitoring applications.
Identification of fire protection system availability in faculty of engineering, University of Teuku Umar
Authors: Salena I Y , Safriani M , Amin M A R
Published: September 2020

The objective of this study is to identify the availability and implementation of fire protection systems in the Engineering Faculty of Teuku Umar University. The fire protection components identified were the access and water supply component, the mean of egress, passive and active fire protection systems, by conducting direct observations to the field using a checklist form. The building identification refers to the Minister of Public Works Regulation No. 26/PRT/M/2008, and the collected data was analyzed using the Likert scale method, which shows the level of conformity to the regulations based on the generated data. The result shows that the access and water supply components obtain 2.75 of the Likert scale. The mean of egress obtains an average value of 2.24 of the Likert scale. The values mean these facilities do not fulfill the regulation. The passive protection system obtains 2.48 of the Likert scale; it means the facilities do not fulfill the regulation. Active protection systems get an average value of 1.4 of the Likert scale; it means the facilities do not fulfill the regulation. The results of the study show that the fire protection system in the Faculty Of Engineering Building did not meet regulation No. 26/PRT/M/2008 overall so that further improvement is needed to fulfill the requirement of fire protection systems to overcame the danger of fire.
The influence of occupational safety and health program on the manpower performance of construction company in Banda Aceh city
Authors: Jamil M , Maulina F , Fachurrazi  , Hasan M , Muslimsyah
Published: September 2020

The implementation of occupational safety and health program in Banda Aceh city is still not optimal, as indicated by a high rate of work accidents. The purpose of this research is to study the effect of the occupational safety and health program on the manpower performance of construction companies in Banda Aceh city. Three construction companies were studied and compared to each other. Data collection was carried out by observation, using questionnaires, and interviewing the respondents of the research, in this case, the foreman, chief workman, workman, and worker. Data processing is conducted by using descriptive statistical analysis, validity test, reliability test, and regression analysis. The results of the analysis show that the application of occupational safety and health program has a significant influence on manpower performance.
Level of importance and housing satisfaction of Jeulingke residence housing on-road aspect
Authors: Iqbal M
Published: September 2020

Jeulingke Residence is one of the subsidized housing located in Jeulingke Village, Syiah Kuala District, Banda Aceh City. Occupants after occupying, faced with problems regarding the performance of developers on aspects of roads. The road aspect has a bad condition because the road surface + 246 m towards the housing complex is currently not pavement. This study aims to identify the level of importance and satisfaction of residents of Jeulingke Residence Housing on-road aspects. This study uses qualitative methods through observation and interviews and quantitative methods through questionnaires. The total population of houses that have been occupied in Jeulingke Residence is 102 units, and no sampling is taken. Data analysis used Importance Performance Analysis (IPA) through Minitab software 16. The results of the study showed that the level of importance and satisfaction that requires priority in improving performance in the aspect of the road is the condition of the entrance pavement.
Characteristic of calcined diatomaceous earth from Aceh Besar District - Indonesia as cementitious binder
Authors: Hasan M , Saidi T , Muyasir A , Alkhaly Y R , Muslimsyah M
Published: September 2020

Diatomaceous earth is a naturally occurring, soft, siliceous sedimentary rock, which is easily crumbled into a fine powder. In this paper, the characteristic of calcined diatomaceous earth from Aceh Besar District – Indonesia as a cementitious binder is studied. The chunk of diatomaceous earth was burned in the brick burning furnace for 4 days, then ground so that it becomes a powder. The powder was sieved to form the binder having the particle sizes less than 250 μm. The binder then calcined at the temperature of 600°C for 5 hours in a laboratory furnace. The density, specific gravity, absorption, particle size analyzer, X-ray diffraction, X-ray fluorescence, and scanning electron microscopy tests were therefore performed. The test results show that the density, saturated surface dry specific gravity, and absorption of calcined diatomaceous earth binder are 767 kg/m3, 2.000, and 6.535 %, respectively. The particle sizes range from 0,107 μm to 231 μm. The main minerals of the particle are graphite, quartz, and lead-silver thallium antimony sulphide. The main chemical compositions of calcined diatomaceous earth are SiO2, 56.00 %; Fe2O3, 26.40 %; ZrO2, 7.20 %; and Al2O3, 6.50 %.
Risk analysis study on building projects in Pidie District
Authors: Fahmi F , Aulia T B , Isya M
Published: September 2020

This study aims to determine the dominant risk factors occurring during the implementation of building construction and to know how to control and handle the risk factors that occur. The methodology used is a quantitative method with a questionnaire as a research instrument. The number of samples used was 55 respondents from a population of 121 companies. Based on the analysis of frequency index (FI), there are dominant risk factors that occur in the implementation of building construction in Pidie District. The dominant risk factors are skills and expertise, weather, access to the project location, unequipped workers with protective equipment, wrong implementation method, the expensive material, incomplete design data, low quality of material, damage to the tool, and a lack of workers. Furthermore, the ways to control and handle risks that occur during the construction project are increasing the trust of the owner, having knowledgable company management and competent workforce, reducing security disturbances, increasing collaboration with local village officials, minimizing equipment damage, managing material purchases before the prices rise, and mastering the implementation method.
The effect of public space availability on children’s creativity (case study: Taman Sari kota Banda Aceh)
Authors: Fitri I , Aulia T B , Fuady M
Published: September 2020

The purpose of this study was to determine the effect of Taman Sari as a public space on children’s creativity, what factors were the most influential of public space facilities on children’s creativity, and how much the Taman Sari facility was structured for children. The research location was Taman Sari, a City Park, in Baiturrahman Sub-District, City of Banda Aceh. Primary data collection was done by dividing the questionnaire. This research was conducted by multiple linear regression analysis. The results showed that the existence of Taman Sari with its variables (accessibility, facilities, environment, and comfort), together, had a significant effect on children’s creativity. The factors that have the highest impact on children’s creativity were facilities and comfort. Taman Sari at present, 2019, has undergone improvements and handlings. There are many improvements in both quantity and quality facilities. The government has been performing marked improvement to make Taman Sari as a public space.
Performance of reinforced concrete columns strengthened with carbon fiber reinforced polymer (CFRP) - case study of an abandoned school project
Authors: Amin N M , Ahmad N A
Published: September 2020

This research presented a case study of an abandoned three-storey school building focusing on strengthening of Reinforced Concrete (RC) column with Carbon Fiber Reinforced Polymer (CFRP) jacketing. The constructed structural element of the building was assessed and evaluated by visual observation, destructive tests and non-destructive tests include carbonation tests, ferro scan tests, steel reinforcement verification, Ultrasonic Pulse Velocity (UPV), coring tests and rebound hammer tests. The modeling of the whole building was carried out using Orion 18, a structural analysis program based on the site test results in order to assess the structural integrity of the building. Based on the structural analysis conducted in Orion 18, a column at ground floor level was chosen to be strengthened with multilayer CFRP jacketing. This column has cross-section of 300mm x 300mm with 3600mm in height. Results were obtained through non-linear Finite Element simulation. The behavior of the column with and without CFRP jacketing was studied to observe its axial stress and strain behavior in ABAQUS Finite Element software. The result shows that increasing in number of CFRP layers has a significant effect on the behavior of such columns which was expected due to confinement effect.
Topographic change and sediment transport on Maeshima Tombolo tidal flat
Authors: Kato S , Kuritani I , Tabata T , Nakamura R , Okabe T
Published: September 2020

For the management of the tidal flat environment and the preservation of several important functions of the tidal flat, the accurate topographic monitoring is indispensable. However, the appropriate measurement of the tidal flat topography is very difficult because water level changes every moment due to tidal oscillation, and the accountable time for the measurement is limited within several hours under low tide condition. In this study, topographic measurement of tidal flat using Unmanned Aerial Vehicle (UAV) was conducted 5 times over a year, and Digital Elevation Model (DEM) obtained by UAV photogrammetry (UAV-DEM) of the tidal flat was constructed in each measurement. The area of 400m in the land-island (L-I) direction and 100m in the west-east (W-E) direction was set on the developed UAV-DEM to analyze the short-term topographical changes (2 weeks including typhoon events, half year and year). By the influence of typhoon passing, sand on the tidal flat was transported from east to west obviously within typhoon event. However, after the topographic change due to the typhoon event, the sand moved opposite direction. By the estimation of the sand volume on the tidal flat using UAV-DEM, it was found that the change of the volume was quite small in one year. These results indicate that the sand volume on this tidal flat is mostly preserved although active sand transport occurs on the tidal flat.
Numerical modeling of suspended sediment concentration (SSC) due to water surface fluctuations of the Krueng Langsa estuary, Aceh Province
Authors: Isma F , Ismida Y , Purwandito M , Fajri H
Published: September 2020

Krueng Langsa estuary is a meeting zone between the sea and the river that crosses the Langsa city. As a result, the Krueng Langsa estuary had a physical change due to tides and river discharge. The Indonesian Minister of Trade Regulation of Number 24 of 2019 has announced that the Krueng Langsa estuary will resume its activities as international shipping. This indeed becomes an important problem for the continuity of shipping activities. An initial study needs to be carried out related to changes in the physical waters of the estuary due to high and low tides. This study is focused on the estuary physical system—especially in water depth, tidal current, salinity, temperature, and SSC along the estuary due to tidal dynamics processes and river discharge runoff—which are modeled numerically. The influence of the Malacca Strait and the Langsa River flow on SSC at each measurement point have also been observed. In this study, the model results were evaluated using the in-situ measurements. The results show that numerical modeling is capable of providing useful information about the physical condition of the Krueng Langsa estuary and agree well with the measurement data.
Study of potential implementations for motorcycle lanes in Padang city
Authors: Kurniati T , Afyendo E , Putri E E
Published: September 2020

Currently, two-wheeled vehicles or motorcycle dominate more than 80% of motorized vehicles in Indonesia. In addition to low prices, these motorized vehicles are fuel efficient, have easier and faster mobilization. However, the large number of motorcycles results in complicated traffic operations and reduced levels of safety. Lanes separation is the best engineering solution to overcome this problem. The purpose of this study was to review the potential application of motorcycle lanes in the city of Padang, a case study on the Raya Ampang and By Pass roads. Collecting the primary data were conducted by Video Image Processor. Each road was carried out recording for 1 day during peak hours in the morning, afternoon, and evening. Analysis of road performance is based on the Highway Capacity Manual of Indonesia (MKJI) 1997 with the degree of saturation (DS) parameter. Road performance analysis is reviewed by comparing the existing conditions and the conditions in which the inclusive motorcycle lanes are applied. The results of the study show that both the Raya Ampang and By Pass streets is feasible to provide an inclusive lane or shared lanes for motorcycles—with a lane width of 3 meters. With motorcycle lane application scenarios, on the Raya Ampang street for non-motorcycles lanes, there is a 10.7% increase in road performance, while for By Pass road, the increase in road performance is 31.5%.
Numerical simulation of groyne placement in minimising Krueng Aceh river bank erosion
Authors: Fatimah E , Fauzi A , Rezeki S , Suryati S
Published: September 2020

This paper presents the prediction of the flow velocity in a 575 meters-long reach of the Krueng Aceh river. It focused on the part of the riverbank where erosion occurred due to the pillars and bridge abutments. One alternative to reduce erosion is using groynes for regulation. The simulations were conducted using the Surface Water Modelling System program (SMS 11.2). The effects of the groynes on the flow changes causing erosion were determined by mathematical simulation of two-dimensional flow using RMA2. The calibration of RMA2 was undertaken by determining the Root-Mean-Square (RMS) error between the measured and mathematical model velocities. Nine scenarios of simulations have been done to investigate the effect of the groyne installation in reducing erosion in the river bend, in term of its length (L), and angle (α), according to river condition. From the simulation results, it can be concluded that the distribution of flow velocities towards the outer river bend for the perpendicular groyne of 9.0m long was smaller compared to the 7.0m one. The groyne with the angle of 10° and length of 7.0m was better in reducing the velocities at the outer riverbank than the 9.0m one. Whereas the groyne with 30° orientation and 9.0m long is better in reducing the eddy than that of the 7.0 m.
The feasibility construction of Alas-Pedesi bridge in Kuta Cane Southeast Aceh district based on the analysis of the transportation economic value
Authors: Harja J , Isya M , Sugiarto S
Published: September 2020

Kutacane is a city located in Southeast Aceh district, the majority of the community’s economic income comes from agricultural and plantation products, the production of corn and cocoa is distributed to the city center from several sub-districts located across the Alas river which is a river that separates some of these districts from the city center. Therefore, the Lawe Alas-Pedesi bridge was built, to facilitate the distribution of production results by reducing distance and travel time. The purpose of this study was to determine the effect of the Alas-Pedesi Lawe bridge, on the operational costs of vehicles, agricultural production, plantations based on producer surpluses, and calculate the economic viability of development including Benefit Cost Ratio (BCR), Net Present Value (NPV), Economic Internal Rate of Return (EIRR). The results of this study get a total time difference of IDR 68,583, - / vehicle, a total difference in vehicle operating costs (BOK) of IDR.4,441, / vehicle, the profit of farmers (corn) for 10 years can be as much as IDR200.567.937.375, - / planting season, the total difference for the benefit of farmers (cocoa) for 10 years can be as much as IDR 3.919.484.400 / planting season. The economic feasibility of the construction of the Lawe Alas-Pedesi bridge obtained in 2030 has met the eligibility standards for all discount rates. In the BCR obtained a 10% discount rate is 1.74, a 12% discount rate is 1.46 and at a 15% discount rate is 1.12, and at the Net Present Value 10% discount rate is obtained NPV IDR 23,422,534,229, - discount 12% rate is obtained NPV IDR. 13,491,749,019, and at a 15% discount rate is obtained NPV IDR. 3,243,265,869. While the value of EIRR obtained at a discount rate of 16, 33 %, this shows the bridge Lawe Alas-Pedesi feasible to build the bank lending rate at 16.33%.
Geophysical investigation of road failure the case of the main street of Alue Naga, Banda Aceh, Indonesia
Authors: Syukri M , Taib A M , Fadhli Z , Safitri R
Published: September 2020

A geophysical investigation has been conducted on the road to assess the subsurface soil characteristics. The study investigates the causes of road failure around the body of the damaged roads in the main street of Alue Naga, Syiah Kuala, Banda Aceh to determine the variations of rocks charge ability and resistivity value of the subsurface of the study area. The method employed for this study was 2D Electrical Resistivity and Induced Polarization (IP) method with using Wenner-Schlumberger array. Two profiles covering a distance of 100 meters each were established parallel to the road pavement along the stable and unstable sections of the road. Data were collected along the two profiles using ABEM Terra meter SAS 4000. The observed field data were processed and inverted using 2-D modelling inversion algorithm (RES2DINV Software). The result shows the presence of low resistivity and charge ability value at several parts of both line 1 and line 2. Both lines observed the 0-1.73 msec of charge ability value and <1 ohm.m of resistivity value; those values were interpreted as alluvium. In conclusion, the low resistivity and charge ability value present that the area investigation was a layer of permeable, especially in the central part which was cohesive, and led to the instability and weakness of the load-carrying capacity.
Rapid (FLASH-FLIM) imaging of protoporphyrin IX in a lipid mixture using a CMOS based widefield fluorescence lifetime imaging camera in real time for margin demarcation applications
Authors: Sagoo Kulwinder , Cumberbatch Nathan , Holland Adam , Hungerford Graham
Published: September 2020

The fluorescence from protoporphyrin IX (PpIX) has been employed to characterise cellular activity and assist in the visualisation of tumour cells. Its formation can be induced by 5-aminolevulonic acid (5-ALA) which is metabolised by tumour cells to form PpIX. The PpIX is localised within the cells, rather than spreading into the vascular system. This, plus its photophysics, exhibits potential in photodynamic therapy. Hence its study and the ability to rapidly image its localisation is of importance, especially in the field of fluorescence guided surgery. This has led to investigations using tissue phantoms and widefield intensity imaging. Aggregation or the presence of photoproducts can alter PpIX emission, which has implications using widefield imaging and a broad wavelength range detection. The use of the fluorescence lifetime imaging (FLIM) is therefore advantageous as it can distinguish between the emissive species as they exhibit different fluorescence lifetimes. Here we use PpIX in a construct consisting of lipid mixture (Intralipid), employed to simulate fat content and optical scattering, in a gellan gum matrix. PpIX in intralipid in aqueous solution was injected into the gellan host to form inclusions. The samples are imaged using commercial widefield TCSPC camera based on a sensor chip with 192 × 128 pixels. Each pixel contains both detection and photon timing enabling the Fluorescence Lifetime Acquisition by Simultaneous Histogramming (FLASH). This ‘FLASH-FLIM’ approach enables widefield fluorescence lifetime images, displayed in real time to be acquired, which has potential for use in visualising tumour boundaries.
Influence of surface modification of carbon fiber based on magnetron sputtering technology on mechanical properties of carbon fiber composites
Authors: Yang Li , Xia Hong , Xu Zhenzhen , Lihua Zou , Ni Qingqing
Published: September 2020

To improve the interfacial performance of carbon fiber (CF) and epoxy resin, the surface of CF was modified using magnetron sputtering technology, and a CF epoxy resin (CFER) composite was prepared using injection molding technology. The influence of magnetron sputtering technology on the surface properties of CF was investigated by scanning electron microscopy (SEM), atomic force microscopy (AFM), and dynamic contact angle analysis (DCAA). The influence of the surface modification of the CFs by magnetron sputtering on the mechanical and interfacial properties of CF composites was analyzed by testing the tensile and bending properties of the CFER composites. The results indicated that the surface morphology of CF can be modified by magnetron sputtering, and a nano sized carbon film was deposited on the surface of the CFs. The morphology of the carbon film on the surface of the CFs was different from that on the silicon pellet. The surface roughness of the CF increased after it was modified by magnetron sputtering. The surface wettability of the CFs may be improved by increasing the surface free energy of the fiber owing to the deposition of the carbon film. Tests of the tensile and bending properties of the CFER composites showed that the surface modification of CFs by magnetron sputtering can effectively improve the mechanical properties of the CFER composites, which not only improves the tensile strength and bending strength, but also increases the tensile modulus and bending modulus. The SEM images showed that the interfacial adhesion between the modified CF and the epoxy resin was significantly improved. The stress–strain curves showed that the failure mode of the CFER composite modified by magnetron sputtering CF surface changed, and a stress yield phenomenon was observed.
su(2)

spin s representations via

CP2s

sigma models*
Authors: Goldstein Piotr P , Grundland A Michel , Escobar-Ruiz Adrian M
Published: September 2020

We establish and analyze a new relationship between the matrix functions describing spin fields of a spin s, where

2
s
∈

Z

+

, and

C

P

2
s

two-dimensional Euclidean sigma models. The spin matrices are constructed from the rank-1 Hermitian projectors of the sigma models or from the anti-Hermitian immersion functions of their soliton surfaces in the

su
(
2
s
+
1
)

algebra. We provide a geometric interpretation of this construction. For the spin fields which can be represented as linear combinations of the generalized Pauli matrices, we find the dynamics equation satisfied by their coefficients. This equation is identical to the stationary equation of a two-dimensional Heisenberg model. We show that the same holds for matrices congruent to the generalized Pauli matrices through any coordinate-independent unitary linear transformation. These properties allow for new interpretations of the spins as compositions of more elementary objects. They also open up the possibility of future applications of the sigma models to the situations which depend on spin behaviour, including spintronics, spin glasses and quantum computing.
Electronic properties of one-dimensional pentacene crystals
Authors: Nappi C , Romeo F , Sarnelli E
Published: September 2020

The electronic properties of an infinite row of freestanding, aligned side-by-side, pentacene molecules are derived as a function of the intermolecular overlap integral and the chemical potential shift. We use a semiclassical approximation and a first principles tight binding method to obtain conductance and mobility of this one-dimensional crystal as a function of temperature and gate voltage. For two values of the intermolecular overlap, energy bands show a metallic behavior. For all the other values, a bandgap is present and evolves with the intermolecular overlap following a typical modulation. The magnitude of the scattering parameters estimated by the observed conductivity is coherent with the existing literature values. These findings could be relevant for the implementation of organic-based sensors.
Novel t(1;8)(p31.3;q21.3) NFIA-RUNX1T1 Translocation in an Infant Erythroblastic Sarcoma
Authors: King Rebecca L , Siaghani Parwiz J , Wong Katy , Edlefsen Kerstin , Shane Lisa , Howard Matthew T , Reichard Kaaren K , Mai Ming , Viswanatha David S , Greipp Patricia T , Goble Tony A , Ruiz Maritza , Hara Harneet
Published: September 2020

Objectives

Pure erythroid leukemia (PEL) is exceptionally rare in the pediatric setting. Four pediatric PEL cases with t(1;16)(p31;q24) NFIA-CBFA2T3 were reported previously. We present a case of an infant with PEL presenting with erythroblastic sarcoma and harboring a novel t(1;8)(p31.3;q21.3) NFIA-RUNX1T1 fusion detected by RNA sequencing and conventional karyotype.

Methods

Bone marrow (BM) and abdominal mass biopsies from the patient were evaluated with extensive immunohistochemical, flow cytometric, cytogenetic, and molecular studies.

Results

The patient was a female infant who presented between 2 and 5 months of age with cytopenias and an enlarging abdominal mass. Blasts in the BM and abdominal mass expressed CD71 and CD117 with focal expression of CD43, E-cadherin, epithelial membrane antigen, and hemoglobin A. They were negative for additional myeloid, lymphoid, and nonhematolymphoid markers. These findings were most consistent with PEL and erythroblastic sarcoma. RNA sequencing revealed the novel NFIA-RUNX1T1 fusion.

Conclusions

Along with the previously reported PELs with NFIA-CBFA2T3 fusions, we describe a subset of PELs that occur in children, that frequently display extramedullary disease, and that harbor rearrangements of NFIA with core binding factor genes. We hypothesize that, together, these cases represent a rare but distinct clinicopathologic group of pediatric PELs with recurrent genetic abnormality.
Strengthening Laboratory Diagnostic Capacity to Support Cancer Care in Uganda
Authors: Niyonzima Nixon , Wannume Henry , Kadhumbula Sylivestor , Wasswa Hassan , Osinde Godfrey , Mulumba Yusuf , Tusabe Tobias , Kalungi Samuel , Orem Jackson
Published: September 2020

Objectives

An accurate cancer diagnosis is critical to providing quality care to patients with cancer. We describe the results of a laboratory improvement process that started in 2017 to improve access to cancer diagnostics at the Uganda Cancer Institute (UCI). The overall objective of the project was to build capacity for the provision of quality and timely laboratory diagnostics to support cancer care in Uganda.

Methods

A phased multistep approach was used to improve laboratory capacity, including staff training, additional staff recruitment, equipment overhaul, and optimization of the supply chain.

Results

The program led to the establishment of a pathology laboratory that handled 5,700 tissue diagnoses in 2019. Immunohistochemistry services are now offered routinely. Turnaround time for histopathology has also reduced from an average of 7 to 14 days to 5.4 days. The main clinical laboratory has also increased both the test volume and the test capacity, with the additional establishment of a molecular diagnostics laboratory.

Conclusions

Our project shows a pathway to the improvement of laboratory diagnostic capacity in cancer care centers in sub-Saharan Africa (SSA). Improved laboratory diagnostic capacity is critical to improving cancer care in SSA and more rational use of targeted therapies.
General Practice Patients’ Readiness to be Treated With Brief Intervention to Reduce Alcohol Consumption: A Cross-Sectional Study With Between-Subject Design
Authors: Fankhaenel Thomas , Mueller Anna-Maria , Frese Thomas
Published: September 2020

Aims

To treat excessive alcohol consumption, general practices (GPs) are recommended to use non-directive implementation strategies. Directive implementation, however, may be perceived by general practice patients as something positive because of possibly indicating higher GP engagement and a more consistent treatment. In our study, we aimed to assess the readiness of patients to be treated with BI in the hypothetical event of excessive alcohol consumption either by a GP using non-directive recommendations according to WHO or by a GP using directive instructions. Additionally, we assessed the patients’ dispositional readiness to disclose alcohol-associated personal information, termed alcohol consumption self-disclosure, in order to analyze its influence on their readiness to be treated with brief intervention (BI).

Methods

When consulting their GP, a convenience sample of general practice patients was asked by questionnaire. By means of a between-subject design, they were asked for the readiness to be treated either with non-directive BI or with directive BI. Repeated-measure ANCOVA was used to analyze the main- and interaction effects.

Results

A sample of 442 general practice patients preferred the non-directive BI, F(1, 423) = 5.56, P < 0.05. We found moreover a two-way interaction between implementation and alcohol consumption self-disclosure, F(1, 423) = 18.89, P < 0.001, showing that only patients with low self-disclosure preferred the non-directive BI, t(428) = 3.99, P < 0.001.

Conclusions

Future research should investigate the reasons for the patients’ preference for the non-directive BI and may develop strategies to overcome the possibly low readiness of general practice patients to be treated with BI.
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS
Authors: Strayer Nick , Shirey-Rice Jana K , Shyr Yu , Denny Joshua C , Pulley Jill M , Xu Yaomin
Published: September 2020

Electronic health records (EHRs) linked with a DNA biobank provide unprecedented opportunities for biomedical research in precision medicine. The Phenome-wide association study (PheWAS) is a widely used technique for the evaluation of relationships between genetic variants and a large collection of clinical phenotypes recorded in EHRs. PheWAS analyses are typically presented as static tables and charts of summary statistics obtained from statistical tests of association between a genetic variant and individual phenotypes. Comorbidities are common and typically lead to complex, multivariate gene–disease association signals that are challenging to interpret. Discovering and interrogating multimorbidity patterns and their influence in PheWAS is difficult and time-consuming. We present PheWAS-ME: an interactive dashboard to visualize individual-level genotype and phenotype data side-by-side with PheWAS analysis results, allowing researchers to explore multimorbidity patterns and their associations with a genetic variant of interest. We expect this application to enrich PheWAS analyses by illuminating clinical multimorbidity patterns present in the data.

Availability and implementation

A demo PheWAS-ME application is publicly available at https://prod.tbilab.org/phewas_me/. Sample datasets are provided for exploration with the option to upload custom PheWAS results and corresponding individual-level data. Online versions of the appendices are available at https://prod.tbilab.org/phewas_me_info/. The source code is available as an R package on GitHub (https://github.com/tbilab/multimorbidity_explorer).

Supplementary information

Supplementary data are available at Bioinformatics online.
Learning graph representations of biochemical networks and its application to enzymatic link prediction
Authors: Jiang Julie , Liu Li-Ping , Hassoun Soha
Published: September 2020

Motivation

The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, enzymatic link prediction (ELP), for predicting the likelihood of an enzymatic transformation between two molecules. ELP models enzymatic reactions cataloged in the KEGG database as a graph. ELP is innovative over prior works in using graph embedding to learn molecular representations that capture not only molecular and enzymatic attributes but also graph connectivity.

Results

We explore transductive (test nodes included in the training graph) and inductive (test nodes not part of the training graph) learning models. We show that ELP achieves high AUC when learning node embeddings using both graph connectivity and node attributes. Further, we show that graph embedding improves link prediction by 30% in area under curve over fingerprint-based similarity approaches and by 8% over support vector machines. We compare ELP against rule-based methods. We also evaluate ELP for predicting links in pathway maps and for reconstruction of edges in reaction networks of four common gut microbiota phyla: actinobacteria, bacteroidetes, firmicutes and proteobacteria. To emphasize the importance of graph embedding in the context of biochemical networks, we illustrate how graph embedding can guide visualization.

Availability and implementation

The code and datasets are available through https://github.com/HassounLab/ELP.
Social Policy and State–Community Relationships: Storm over Forest Rights in India
Authors: Sengupta Sohini , Jha Manish K
Published: September 2020

Social Policy is concerned with minimising poverty and inequality through redistribution of goods and services. In the twentieth century, after the Second World War, European parliamentary democracies enlarged its ambit by making social policy an important instrument to create equality setting the benchmark for other countries. For the new independent countries in the global South, such as India, social policy followed different trajectories. In the aftermath of independence, India relied on preventive instruments to address the effects of famine, de-industrialisation and high levels of deprivation. Despite achieving high economic growth and rapid poverty reduction in the following decades, its dependence on targeted poverty reduction programme has remained. Recently, there has been some attempt to replace these strategies by rights-based programmes supported by legal framework advocated by civil society groups. Through a case study of The Scheduled Tribes and Other Traditional Forest Dwellers (Recognition of Forest Rights) Act, 2006 (referred to as FRA 2006), this article analyses the successes and failures in realising the goal of linking welfare provisions with the ideas of social citizenship and democratic rights. The article finds widening gulf in the interests of state actors and local community arising from the compromised interpretation of the social justice vision enshrined in FRA.
BACE inhibition causes rapid, regional, and non-progressive volume reduction in Alzheimer’s disease brain
Authors: Sur Cyrille , Kost James , Scott David , Adamczuk Katarzyna , Fox Nick C , Cummings Jeffrey L , Tariot Pierre N , Aisen Paul S , Vellas Bruno , Voss Tiffini , Mahoney Erin , Mukai Yuki , Kennedy Matthew E , Lines Christopher , Michelson David , Egan Michael F
Published: September 2020

In the phase 3 EPOCH trial (Clinicaltrials.gov; NCT01739348), treatment with the BACE inhibitor verubecestat failed to improve cognition in patients with mild-to-moderate Alzheimer’s disease, but was associated with reduced hippocampal volume after 78 weeks as assessed by MRI. The aims of the present exploratory analyses were to: (i) characterize the effect of verubecestat on brain volume by evaluating the time course of volumetric MRI changes for a variety of brain regions; and (ii) understand the mechanism through which verubecestat might cause hippocampal (and other brain region) volume loss by assessing its relationship to measures of amyloid, neurodegeneration, and cognition. Participants were aged 55–85 years with probable Alzheimer’s disease dementia and a Mini Mental State Examination score ≥15 and ≤26. MRIs were obtained at baseline and at Weeks 13, 26, 52 and 78 of treatment. MRIs were segmented using Freesurfer and analysed using a tensor-based morphometry method. PET amyloid data were obtained with 18F-flutemetamol (Vizamyl®) at baseline and Week 78. Standardized uptake value ratios were generated with subcortical white matter as a reference region. Neurofilament light chain in the CSF was assessed as a biomarker of neurodegeneration. Compared with placebo, verubecestat showed increased MRI brain volume loss at Week 13 with no evidence of additional loss through Week 78. The verubecestat-related volumetric MRI loss occurred predominantly in amyloid-rich brain regions. Correlations between amyloid burden at baseline and verubecestat-related volumetric MRI reductions were not significant (r = 0.05 to 0.26, P-values > 0.27). There were no significant differences between verubecestat and placebo in changes from baseline in CSF levels of neurofilament light chain at Week 78 (increases of 7.2 and 14.6 pg/ml for verubecestat versus 19.7 pg/ml for placebo, P-values ≥ 0.1). There was a moderate correlation between volumetric MRI changes and cognitive decline in all groups including placebo at Week 78 (e.g. r = −0.45 to −0.55, P < 0.001 for whole brain), but the correlations were smaller at Week 13 and significant only for the verubecestat groups (e.g. r = −0.15 and −0.11, P < 0.04 for whole brain). Our results suggest that the verubecestat-associated MRI brain volume loss is not due to generalized, progressive neurodegeneration, but may be mediated by specific effects on BACE-related amyloid processes.
Electrophysiology of the Human Superior Temporal Sulcus during Speech Processing
Authors: Nourski Kirill V , Steinschneider Mitchell , Rhone Ariane E , Kovach Christopher K , Banks Matthew I , Krause Bryan M , Kawasaki Hiroto , Howard Matthew A
Published: September 2020

The superior temporal sulcus (STS) is a crucial hub for speech perception and can be studied with high spatiotemporal resolution using electrodes targeting mesial temporal structures in epilepsy patients. Goals of the current study were to clarify functional distinctions between the upper (STSU) and the lower (STSL) bank, hemispheric asymmetries, and activity during self-initiated speech. Electrophysiologic properties were characterized using semantic categorization and dialog-based tasks. Gamma-band activity and alpha-band suppression were used as complementary measures of STS activation. Gamma responses to auditory stimuli were weaker in STSL compared with STSU and had longer onset latencies. Activity in anterior STS was larger during speaking than listening; the opposite pattern was observed more posteriorly. Opposite hemispheric asymmetries were found for alpha suppression in STSU and STSL. Alpha suppression in the STS emerged earlier than in core auditory cortex, suggesting feedback signaling within the auditory cortical hierarchy. STSL was the only region where gamma responses to words presented in the semantic categorization tasks were larger in subjects with superior task performance. More pronounced alpha suppression was associated with better task performance in Heschl’s gyrus, superior temporal gyrus, and STS. Functional differences between STSU and STSL warrant their separate assessment in future studies.
Network Dynamics in the Developing Piriform Cortex of Unanesthetized Rats
Authors: Zhang Zihao , Collins Donald Chad , Maier Joost X
Published: September 2020

The time course of changes in functional cortical activity during early development has been extensively studied in the rodent visual system. A key period in this process is the time of eye opening, which marks the onset of patterned visual input and active vision. However, vision differs from other systems in that it receives limited patterned sensory input before eye opening, and it remains unclear how findings from vision relate to other systems. Here, we focus on the development of cortical network activity in the olfactory system—which is crucial for survival at birth—by recording field potential and spiking activity from piriform cortex of unanesthetized rat pups from birth (P0) to P21. Our results demonstrate that odors evoke stable 10–15 Hz oscillations in piriform cortex from birth to P15, after which cortical responses undergo rapid changes. This transition is coincident with the emergence of gamma oscillations and fast sniffing behavior and preceded by an increase in spontaneous activity. Neonatal network oscillations and their developmental dynamics exhibit striking similarities with those previously observed in the visual, auditory, and somatosensory systems, providing insight into the network-level mechanisms underlying the development of sensory cortex in general and olfactory processing in particular.