bluuebunny/crossref_metadata_2025 huggingface dataset:
Harmful algal bloom of the three selected coastal bays in Indonesia
Authors: Sidabutar T , Srimariana E S , Cappenberg H A W , Wouthuyzen S
Published: December 2022

The occurrences of phytoplankton bloom have recently increased in some coastal bays in Indonesia. Harmful algal blooms are now a significant problem for several coastal bays, which causes problems and economic losses to the fishing industry, harm to aquatic ecosystems, fish mortalities, and other living organisms. The negative impact also affects the marine environment, tourism, and consumer health. The most frequent algal bloom occurrences are three coastal bays: Jakarta Bay, Lampung Bay, and Ambon Bay. In particular, those three bays are the most infected areas of harmful algal bloom in this country. Samples were taken using a 20 um net plankton and directly preserved with Lugol’s solution before being identified. Some bloom maker species were identified as toxic, mainly belonging to dinoflagellates, such asPyrodinium sp, Aleandrium sp, Gymnodinium sp, andCochlodinium sp. And the species that most frequently cause a bloom in those coastal waters areSkeletonema, Chaetoceros, Trichodesmium, andNoctiluca. The nutrients, mainly nitrate and phosphate, are the main driving factor resulting from anthropogenic activities on the land that make the coastal waters eutrophic. This paper discusses the recent distribution, causes, and impact of harmful algal blooms in the three coastal bays in this country.
Proximate and mineral compositions of the green seaweeds Caulerpa lentilifera and Caulerpa racemosa from South Sulawesi Coast, Indonesia
Authors: Kasmiati K , Syahrul S , Badraeni B , Rahmi M H
Published: December 2022

This study aimed to evaluate the nutritional and mineral composition of the green seaweeds Caulerpa lentilifera and Caulerpa racemosa collecting from Takalar Water, South Sulawesi, Indonesia. Test of proximate analysis of seaweeds observed was ash, protein, lipid, fiber, and carbohydrate. While the test mineral compositions were phosphorus, calcium, potassium, sodium, magnesium, cuprum, manganese, zinc, ferrum, iodine. The results of the analysis showed that the proximate composition, C. lentilifera had the highest ash content (63.83%) while C. racemosa had the highest carbohydrate content of 38.18%. The results of the mineral analysis showed that C. lentillifera and C. racemosa contained macro and microminerals. The highest macromineral content is Na (10.040% and 16.280%) and followed by K (3.958% and 2.195%), Mg (59.201 ppm and 519.201 ppm), Ca (0.521% and 0.466%) and P (0.270% and 0.335%). The highest microminerals in the two types of seaweed from the largest are Fe (756.1805 and 386.1202 ppm), Mn (59.201 ppm and 519.062 ppm), Zn (10.079 ppm and 3.366 ppm), and Cu (5.496 ppm only in C. racemosa). This study revealed that C. lentilifera and C. racemosa contain constituents with proximate and mineral composition as potential sources of plant foods and good sources of mineral supplements.
The potential of skipjack fish (Katsuwonus pelamis) in the Flores Sea of South Sulawesi
Authors: Baso Aris , Tahang Hamzah , Amiluddin  , Kasri  , Carda Muhammad Aldair Mukstofa
Published: December 2022

The purpose of this study is to analyze the marketing efficiency of skipjack fish in the Flores Sea of South Sulawesi. This research was carried out in September - December 2021 with due observance of the Covid-19 health protocol. The method of research used is a survey method. The sampling method used is stratified random sampling. Analysis of the data used is descriptive analysis, marketing margin, marketing cost and marketing efficiency. The results showed that the skipjack fish marketing channel in the Flores Sea, South Sulawesi is efficient with efficiency value of 0.03 for Selayar Islands Regency and 0.02 for Bulukumba Regency, which means that the skipjack marketing channel is efficient because it has a value smaller than one (<1).
The use of superior common carp for a better aquaculture
Authors: Ariyanto D
Published: December 2022

Fish farming is an economic business activity that has been carried out for a long time in Indonesia. One of the most popular commodities cultured is common carp. In 2001, common carp production was 418,910 MT, equivalent to 63.5% of Indonesia’s national production. However, the existence of obstacles in common carp culture, especially the outbreak of KHV in 2002 and the decrease of the genetic quality of fish, indicated by the slower growth of fish, resulted in a significant decrease in common carp production. The use of lower genetic quality fish causes the efficiency of the feed used is getting lower, as indicated by the high value of the FCR. In-efficient use of feed has an impact on increasing feed waste in the cultural environment. To increase common carp production, several varieties of superior common carp have been released for the farmer. Empirically, superior fish carp have a better growth rate and are more efficient in the use of feed. Culture of these superior varieties impacted to increase in the national production of common carp, by an average of 8.7%/year. On the other hand, the culture environment is kept clean due to up to 47.0±4.8% reduction in waste.
Impact of presidential decree number 44 of 2016 on sustainable fisheries at archipelago state
Authors: Mira  , Wardono B
Published: December 2022

The purpose of this study is to analyze the impact of the Presidential Regulation (Perpres) Number 44 of 2016 on sustainable fisheries. Presidential Decree No. 44 of 2016 concerning business fields closed to foreign investment in Indonesia. In the results of the analysis using the models: linear trend, quadratic and exponential. Result analyzed indicated that the most suitable model is the quadratic model. The quadratic model is related to the nature of fish resources. The Gordon-Schaefer model states that fisheries with an open access management regime will lead to economic inefficiency. To prevent this economic inefficiency, several economic instruments must be applied, such as limiting efforts and quotas. One of the instruments for limiting fishing efforts is through Presidential Regulation no. 44 of 2016. Limiting efforts is positive impact for local fisherman. For example, since the foreign vessels banned from operating, small bitung fishermen, they could catch 3-6 tunas per day in 2019. In 2014, they had only been caught 1-3 tuna per day. Investment waste in a sector will eliminate the potential economic rents of fish resources. Investment waste in capture fisheries should be used for fish processing activities and aquaculture activities that will provide added value.
Performance growth and survival of Hemibagrus nemurus with probiotic application on aquaponics
Authors: Yosmaniar  , Taufik Imam , Setijaningsih Lies , Widyastuti Yohanna R
Published: December 2022

Hemibagrus nemurus is a freshwater catfish commodity that has high economi value and favored by the community. The purpose of study was to evaluate the growth and survival of Hemibagrus nemurus in aquaponics with the application of probiotics. The research was conducted in Sukawening Dramaga Bogor. Using 6 units of tarpaulin ponds measuring 20 x 3.0x 0.8 m filled with 3 M 3 of water, each pool is equipped with an aquaponics unit with an upstream system using lettuce and eggplant. The experiments, namely using probiotics and without using probiotics with 3 replication. The test fish used is 16.5 sd 0.2 g/individu The probiotics used at a dose of 10 ml/M3. Given every 5 days. Fish were given commercial feed of 4 % at 50 days rearing and then 3% until the end of the study with feeding times/day (morning and afternoon). The test parameters were SGR, survival, absolute weight, FCR and water quality. The result showed that the application of probiotic RIFA can increase the growth and survival of the fish, improve water quality and increase plant productivity.
The effect of various doses of vitomolt as a feed additive on meat quality and feed nutrient retention in mud crab fattening
Authors: Sari Nur Intan , Fujaya Yushinta , Aslamyah Siti
Published: December 2022

Vitomolt is a feed additive in fattening mud crabs (Scylla olivaceae). The study aimed to determine the best dose of vitomolt for meat quality and nutrient retention for fattening Scylla olivaceae. It was conducted at the Educational Farm of Universitas Hasanuddin, Barru Regency, Indonesia. The treatments were various doses of vitomolt in the feed, which 0, 200, 400, 600 mg kg−1 of feed. Rearing was held for 60 days and fed 5% body weight daily. The analysis showed that the dose of vitomolt in the feed affected the percentage of meat carcass weight, fat content, fat retention, and crab energy retention. However, it did not affect protein content, crude fiber, Nitrogen-Free Extract (NFE), ash content, and crab protein retention. The best percentage of meat carcass weight at a dose of vitomolt 400 mg kg−1 and same from a dose of 200 mg kg−1, while the best fat content, fat retention, and energy at a vitomolt dose of 600 mg kg−1 and different from a dose of 400 and 200 mg kg−1, but different from the control. Vitomolt with a 200 mg kg−1 of feed is the best dose to produce the highest meat quality and nutrient retention in fattening crabs.
Selection of prospective probiotic bacteria from the intestines of Rabbitfish, Siganus guttatus as a fermenter for fish feed raw materials
Authors: Kamaruddin  , Haryati  , Aslamyah Siti , Karim Yusri , Mulyaningrum Sri Rejeki Hesti , Tampangallo B.R.
Published: December 2022

Rabbitfish is classified as herbivorous fish by utilizing plants as a staple food, so it has the potential to contain microflora in the digestive tract. The study aimed to select bacteria from the intestines of Rabbitfish as probiotic candidates for degradation of feed ingredients. At the beginning of the study, microbial dissolution of the intestines of 10 Rabbitfish measured weight and body length 127 ±20.1 g and 191.4±1.17 cm, healthy and not deformed, obtained from the waters around the island of Salemo, Regency. Pangkep. At this stage, they have successfully isolated 72 isolates. Then make a selection of bacteria based on the activity of extracellular enzymes by testing the hydrolysis ability of starch using Zobel media adding 1% soluble starch, protein hydrolysis using Zobel media adding 1% skim milk, cellulose hydrolysis using Zobel media adding 1% CMC. The ability of the insulator to hydrolyze starch ranges from 0.4 cm; to protein to 2.4 cm; cellulose to 1.5 cm. Based on these results, 10 isolates were selected as probiotic candidates, namely 411; 413; 422; 427; 430; 434; 437; 452 and 455. The next stage of the pathogenicity test of 10 selected isolates. Each isolate with a density of 106 CFU/mL was injected into 5 juveniles of healthy Rabbitfish intramuscularly as much as 0.1 mL. Monitoring is carried out daily for 10 days after infection to evaluate clinical signs of the disease in test fish. The results obtained showed that no symptoms of pain, injury, or death were found, so it was concluded that the bacterial isolate was not pathogenic.
Tilapia aquaculture water quality in response to the addition of fermented herbal extract
Authors: Fujaya Yushinta , Azis Hasni Yulianty , Hidayani Andi Aliah , Badraeni  , Arifin Namiratul Hasanah , Khor Waiho , Fazhan Hanafiah , Nurhidayat  , Hardi Esti Handayani
Published: December 2022

This study aims to find a suitable Fermented Herbal Extract (FHE) dose to reduce ammonia levels in tilapia cultivation. This research was carried out for one month, from August to September 2021, at Fish Hatchery Laboratory of Marine Sciences and Fisheries Faculty, Hasanuddin University. The study was conducted using a completely randomized design with six treatments and three replications. The treatments were various doses of FHE added to the cultivation water, including 0 ppm, two ppm, four ppm, six ppm, eight ppm, and ten ppm. The juvenile tilapia measuring about 5 cm body length stocked with five fish for each aquarium. Water quality like Dissolved Oxygen, Temperature, pH, Nitrate, Nitrite, and Ammonia content was measured in this study. The results showed that adding FHE to tilapia culture media affected the ammonia concentration. In this study, six ppm of FHE treatment resulted in the lowest ammonia concentration on the 10th and 12th days of observation.
Mapping beje pond as fish source in a tropical peat swamp using Landsat 8 OLI-TIRS imagery
Authors: Aguswan Y , Gumiri S , Sukarna R M , Permana I
Published: December 2022

Tropical peatlands in Indonesia are severely degraded due to unsustainable logging, conversion to plantations, poor drainage, and repeated fires. Traditional communities in Central Kalimantan used to build “beje” ponds for fishing and paludikulur farming system (agrosilvo fishery) in deep peatlands area that are frequently flooded. However, hardly reached spot in peat swamp makes areas suitable for beje difficult to find. This study aims to map the location suitable for beje using Normalized Difference Water Index (NDWI) from Landsat 8 OLI imagery. Canopy results from the NDWI were used as a reference for field investigations at nine sites from each NDWI class. The classification test results show that NDWI is able to distinguish dry and wet areas in tropical peatlands, with a manufacturer accuracy of 83.3% and user accuracy of 84.9%. As a result, the area suitable for beje ponds development is ±9,616 ha, or 6.2% of the total area studied.
Identification of potential areas for upwelling based on characteristics of eddies event in the Bone gulf
Authors: Hidayat R , Zainuddin M , Safruddin  , Wiyono E S
Published: December 2022

The Bone Gulf is one of the waters with massive potential for catching pelagic fish. The potential for catching fish is associated with oceanographic events in the waters. This study aims to see the potential for upwelling in the eddy occurrence areas. The spatial analysis method will be used to see the potential for upwelling in the area of the eddy occurrence and will be associated with sea surface temperature parameters and chlorophyll-a as a fertility variable. The results of this study indicate that eddy events occur every month in the Bone Gulf waters. In addition, it can be proven that every eddy occurrence is not a guarantee for the emergence of upwelling areas simultaneously. However, several eddy events with high current velocities were seen to cause a decrease in temperature in the middle of the eddy and increase the chlorophyll-a concentration in that area. In addition, the suitability of this event is also shown from the time of upwelling, which occurs several months before the peak month of fishing in the Bone Gulf. This research is expected to be the basis for the sustainable development of fisheries.
Water quality analysis in Tempe Lake Wajo Regency, South Sulawesi
Authors: Rahim Sri Wahyuni , Takhir Qina Amalia , Kudsiah Hadiratul , Rukminasari Nita , Suwarni  , Yanuarita Dewi
Published: December 2022

Tempe Lake is one of the largest lakes in South Sulawesi, with a 47.800 ha area and heavily utilized, leading to water quality degradation. This research aims to analyze water quality parameters using the NSF Water Quality Index. The research was conducted from June until August 2021. The sampling was done in three stations. Station I located in the middle of Tempe Lake; Station II, located close to the rice field area; and Station III, located close to the area of residence. The water quality analysis was done in the Laboratory of Water Quality, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar. There were eight water quality parameters measured: temperature, turbidity, pH, TSS, DO, BOD, phosphate and nitrate. The results showed that all parameters, except phosphate, still met the Standard of PP No. 22/2021 of Water Quality Management and Pollution Control. Based on the NSF Water Quality Index, the Lake Tempe is categories as medium.
Computational discovery of two-dimensional rare-earth iodides: promising ferrovalley materials for valleytronics
Authors: Sharan Abhishek , Lany Stephan , Singh Nirpendra
Published: December 2022

Two-dimensional Ferrovalley materials with intrinsic valley polarization are rare but highly promising for valley-based nonvolatile random access memory and valley filter devices. These ferromagnetic materials exhibit valleys at or near the Fermi level with intrinsic magnetism. The strong coupling between magnetism and spin–orbit coupling induces intrinsic valley polarization. Using Kinetically Limited Minimization, an unconstrained crystal structure prediction algorithm, and prototype sampling based on first-principles calculations, we have discovered new Ferrovalley materials, rare-earth iodides RI2, where R is a rare-earth element belonging to Sc, Y, or La-Lu, and I is Iodine. The rare-earth iodides are layered and demonstrate either 2H, 1T, or 1T
d
phase as the ground state in bulk, analogous to transition metal dichalcogenides (TMDCs). The calculated exfoliation energy of monolayers (MLs) is comparable to that of graphene and TMDCs, suggesting possible experimental synthesis. The MLs in the 2H phase exhibit ferromagnetism due to unpaired electrons in d and f orbitals. Throughout the rare-earth series, d bands have valley polarization at K and

K
‾

points in the Brillouin zone in the vicinity of the Fermi level. Large intrinsic valley polarization in the range of 15–143 meV without external stimuli is observed in these Ferrovalley materials, which can be enhanced further by applying an in-plane bi-axial strain. These valleys can selectively be probed and manipulated for information storage and processing, potentially offering superior performance beyond conventional electronics and spintronics. We further show that the 2H ferromagnetic phase of RI2 MLs possesses non-zero Berry curvature and exhibits anomalous valley Hall effect with considerable anomalous Hall conductivity. Our work will incite exploratory synthesis of the predicted Ferrovalley materials and their application in valleytronics and beyond.
Imaging current control of magnetization in Fe3GeTe2 with a widefield nitrogen-vacancy microscope
Authors: Robertson Islay O , Tan Cheng , Scholten Sam C , Healey Alexander J , Abrahams Gabriel J , Zheng Guolin , Manchon Aurélien , Wang Lan , Tetienne Jean-Philippe
Published: December 2022

Van der Waals (vdW) magnets are appealing candidates for realising spintronic devices that exploit current control of magnetization (e.g. switching or domain wall motion), but so far experimental demonstrations have been sparse, in part because of challenges associated with imaging the magnetization in these systems. Widefield nitrogen-vacancy (NV) microscopy allows rapid, quantitative magnetic imaging across entire vdW flakes, ideal for capturing changes in the micromagnetic structure due to an electric current. Here we use a widefield NV microscope to study the effect of current injection in thin flakes (∼10 nm) of the vdW ferromagnet Fe3GeTe2 (FGT). We first observe current-reduced coercivity on an individual domain level, where current injection in FGT causes substantial reduction in the magnetic field required to locally reverse the magnetisation. We then explore the possibility of current-induced domain-wall motion, and provide preliminary evidence for such a motion under relatively low current densities, suggesting the existence of strong current-induced torques in our devices. Our results illustrate the applicability of widefield NV microscopy to imaging spintronic phenomena in vdW magnets, highlight the possibility of efficient magnetization control by direct current injection without assistance from an adjacent conductor, and motivate further investigations of the effect of currents in FGT and other vdW magnets.
Wavelength dependence of polarization-resolved second harmonic generation from ferroelectric SnS few layers
Authors: Moqbel Redhwan , Chang Yih-Ren , Li Zi-Yi , Kung Sheng-Hsun , Cheng Hao-Yu , Lee Chi-Cheng , Nagashio Kosuke , Lin Kung-Hsuan
Published: December 2022

Two-dimensional group-IV monochalcogenides such as GeS, GeSe, SnS, and SnSe were theoretically predicted as multiferroic materials with two or more ferroic properties. However, most of their bulk crystals are stacked layer by layer with an antiferroelectric manner, which lose the macroscopic in-plane ferroelectricity. In this work, we studied SnS in which the layers are stacked in a ferroelectric manner both experimentally and theoretically. We utilized polarization-resolved second harmonic generation (SHG) microscopy to investigate numerous flakes of ferroelectric SnS few layers on mica substrates. We found the SHG polar patterns dramatically varied in the range of 800 nm and 1000 nm due to the frequency-dependent SHG susceptibilities. First-principles calculations have been performed to study the frequency-dependent and layer-dependent SHG susceptibilities in the ferroelectric SnS with AA and AC stacking orders. The variation trend of calculated SHG polar patterns as a function of frequency agrees well with that of the experimental results. Since polarization-resolved SHG is a noncontact and nondestructive technique to determine the crystal orientation, understanding of its properties is important, especially for monitoring the transition of different ferroic phases.
Preparation and mechanism of silicate-based sintering material from large amount of steel slag
Authors: Ma Minglong , Yang He , Bai Bing , Xie Guiquan
Published: December 2022

In this paper, silicate-based sintering materials (SBSM) were prepared by high-temperature sintering process with steel slag as the main raw material. By strictly controlling the particle gradation of steel slag, the content of steel slag in SBSM was increased to 70%, to realize the efficient resource utilization of steel slag. The phase composition and micro-morphology of the SBSM were characterized by X-ray diffraction (XRD) and scanning electron microscope (SEM), respectively. The flexural and compressive strength of the SBSM were tested by the full-automatic compression and folding machine. The results show that the main phases of the SBSM are anorthite and quartz, and the existence of anorthite is benefit to improve the mechanical properties of the SBSM. An appropriate proportion of small-size steel slag (more than 100 mesh) can promote the reaction process, and improve the flexural and compression strength of the samples. However, excessive small-size particles of steel slag lead to a large amount of liquid phase in the reaction process, which makes the aggregate react with the matrix. The strength of the sample decreases with the decrease of its resistance to external forces. The water absorption of the samples decreases with the increase of the steel slag with small-size particles.
Mechanism of color change of flexible metafilm with structural parameters and stretching methods
Authors: Huang Zizhen , Long Linshuang , Yang Wei , Wu Yu , Ye Hong , Liu Minghou
Published: December 2022

Color change metafilm is promising for the color printing of displays and imaging. A metallic array on an elastic film can realize dynamic color change by mechanical extensions, such as uniaxial or biaxial stretching. In this study, an electromagnetic model of a flexible metafilm composed of a microscale Al cylindrical array on a polydimethylsiloxane elastic film was constructed to study the underlying optical mechanism of color change, especially brightness and saturation changes, of the flexible metafilm with structural parameters (diameter and height of the Al cylinders) and stretching methods (uniaxial or biaxial stretching). The 3D finite time domain difference method was used to simulate the propagation behavior of electromagnetic waves through metafilm. With increasing diameter, the lightness increases while the saturation decreases, which is due to the change of surface plasmon resonance from local surface plasmon resonance (LSPR) to propagation surface plasmon (PSP) and Wood Anomaly (WA) and finally to magnetic polariton excitation. With increasing height, lightness first decreases and then increases, while the change in saturation is opposite, which is due to the first increasing and then decreasing of the intensities of PSP and WA. By comparing the dynamic color changes of metafilm under uniaxial stretching and biaxial stretching, it is found that uniaxial stretching achieves lower lightness and saturation under small strain and higher lightness and saturation under large strain, which is caused by the enhanced WA and PSP on the Al-air interface at short wavelengths and the weakened LSPR on the Al-PDMS interface at long wavelengths. This discovery paves the way for practical applications of structural color display with high saturation and brightness.
Simulation of wall materials with isotope concentration gradient for corrosion degree calibration in ITER
Authors: Chen Yong , He Yang , Shuai Bincai , Qiu Changjun , Zheng Pengfei
Published: December 2022

In the ITER reactor, the degree of corrosion of the wall is monitored by detecting the concentration of the isotope injected into the wall to ensure safe operation. Therefore, a wall material with an isotope concentration gradient that can be easily monitored must be developed. In this study, we adopted TRIM, Monte Carlo (M-C), and N (X) to predict the concentration distribution of isotopes injected into wall materials. The concentration peak and depth range of the isotope concentration distribution curve calculated by the TRIM program were very different, and the deviation was as high as 2.70%. Combined with the Monte Carlo (M-C) calculation method and the modified longitudinal static stability theory (LSS), the simulated isotope concentration distribution curve was in good agreement with the actual detection curve. However, the result was discontinuous, so the deviation could not be calculated. The N (X) simulation calculation exhibited a high degree of agreement, and the deviation was only 0.67%, so it may be considered suitable for the simulation of the concentration distribution of ion implantation in wall materials under various conditions.
Carbon nanotubes enhanced bimorph effect of U-shaped flexure cantilever beam actuators made from polyethylene terephthalate and polymethyl methacrylate
Authors: Tsai Hsin-Jung , Chang Huang-Chao , Yang Yung-Kai , Hsu Wen-Kuang
Published: December 2022

U-shaped cantilever actuators made from PET and PMMA exhibit a bimorph effect upon radiation heating and beam always moves toward PMMA side with maximum displacement and displacing rate measured to be 2100 μm and 35 μm s−1. This number increases to 3300 μm and 55 μm s−1 while PET surfaces are coated with single-walled carbon nanotubes acting as heat reservoir. Actuations can be further improved by carbon nanotube resistive heating and improvement reaches two-fold (4100 μm and 68.3 μm s−1). Coated beam actuators exhibit an excellent stability over 2 h intermittent operations where the maximum displacement varies only in ±1%.
Impact of the anode tilt on photon emission spectrum and temperature rise in an x-ray tube
Authors: Ou hadda Hassan , Zerfaoui Mustapha , Bahhous Karim , Aboulbanine Zakaria , Didi Samir , Rrhioua Abdeslem , Bakari Dikra
Published: December 2022

In radiology, the photon fluence and the energy spectrum generated from an x-ray tube may depend on the anode tilt angle. In this contribution, a Monte Carlo investigation is performed to quantify this effect by modeling an x-ray tube based on published data Bujila R. et al (2020 Physica. Med. 75 44–54). The GATE simulation code is used for this purpose. The calculations have moreover confirmed this dependence; the tilt of the anode could be used to increase the photon fluence. The thermal analysis has shown that the hot spot size is dependent as well on the anode tilt angle. The thermal focus temperature (ΔT) decreases when the anode tilt angle increases. Finally, by moving the acquisition angle from 293°–337° to 248°–292° and changing the anode tilt angle from 8° to 28°, the photon fluence can be increased by 55%.
Entangling mechanical vibrations of two massive ferrimagnets by fully exploiting the nonlinearity of magnetostriction
Authors: Qian Hang , Fan Zhi-Yuan , Li Jie
Published: December 2022

Quantum entanglement in the motion of macroscopic objects is of significance to both fundamental studies and quantum technologies. Here we show how to entangle the mechanical vibration modes of two massive ferrimagnets that are placed in the same microwave cavity. Each ferrimagnet supports a magnon mode and a low-frequency vibration mode coupled by the magnetostrictive force. The two magnon modes are, respectively, coupled to the microwave cavity by the magnetic dipole interaction. We first generate a stationary nonlocal entangled state between the vibration mode of the ferrimagnet-1 and the magnon mode of the ferrimagnet-2. This is realized by continuously driving the ferrimagnet-1 with a strong red-detuned microwave field and the entanglement is achieved by exploiting the magnomechanical parametric down-conversion and the cavity–magnon state-swap interaction. We then switch off the pump on the ferrimagnet-1 and, simultaneously, turn on a red-detuned pulsed drive on the ferrimagnet-2. The latter drive is used to activate the magnomechanical beamsplitter interaction, which swaps the magnonic and mechanical states of the ferrimagnet-2. Consequently, the previously generated phonon–magnon entanglement is transferred to the mechanical modes of two ferrimagnets. The work provides a scheme to prepare entangled states of mechanical motion of two massive objects, which may find applications in various studies exploiting macroscopic entangled states.
A note on exotic families of 4-manifolds
Authors: Kato Tsuyoshi , Konno Hokuto , Nakamura Nobuhiro
Published: December 2022

We present a pair of smooth fiber bundles over the circle with a common

4
4

-dimensional fiber with the following properties: (1) their total spaces are diffeomorphic to each other; (2) they are isomorphic to each other as topological fiber bundles; (3) they are not isomorphic to each other as smooth fiber bundles. In particular, we exhibit an example with non-simply-connected fiber.
Vir2Drug: a drug repurposing framework based on protein similarities between pathogens
Authors: Minadakis George , Tomazou Marios , Dietis Nikolas , Spyrou George M
Published: December 2022

We draw from the assumption that similarities between pathogens at both pathogen protein and host protein level, may provide the appropriate framework to identify and rank candidate drugs to be used against a specific pathogen. Vir2Drug is a drug repurposing tool that uses network-based approaches to identify and rank candidate drugs for a specific pathogen, combining information obtained from: (a) ranked pathogen-to-pathogen networks based on protein similarities between pathogens, (b) taxonomy distance between pathogens and (c) drugs targeting specific pathogen’s and host proteins. The underlying pathogen networks are used to screen drugs by means of specific methodologies that account for either the host or pathogen’s protein targets. Vir2Drug is a useful and yet informative tool for drug repurposing against known or unknown pathogens especially in periods where the emergence for repurposed drugs plays significant role in handling viral outbreaks, until reaching a vaccine. The web tool is available at: https://bioinformatics.cing.ac.cy/vir2drug, https://vir2drug.cing-big.hpcf.cyi.ac.cy
Incomplete time-series gene expression in integrative study for islet autoimmunity prediction
Authors: Tanvir Ahmed Khandakar , Cheng Sze , Li Qian , Yong Jeongsik , Zhang Wei
Published: December 2022

Type 1 diabetes (T1D) outcome prediction plays a vital role in identifying novel risk factors, ensuring early patient care and designing cohort studies. TEDDY is a longitudinal cohort study that collects a vast amount of multi-omics and clinical data from its participants to explore the progression and markers of T1D. However, missing data in the omics profiles make the outcome prediction a difficult task. TEDDY collected time series gene expression for less than 6% of enrolled participants. Additionally, for the participants whose gene expressions are collected, 79% time steps are missing. This study introduces an advanced bioinformatics framework for gene expression imputation and islet autoimmunity (IA) prediction. The imputation model generates synthetic data for participants with partially or entirely missing gene expression. The prediction model integrates the synthetic gene expression with other risk factors to achieve better predictive performance. Comprehensive experiments on TEDDY datasets show that: (1) Our pipeline can effectively integrate synthetic gene expression with family history, HLA genotype and SNPs to better predict IA status at 2 years (sensitivity 0.622, AUC 0.715) compared with the individual datasets and state-of-the-art results in the literature (AUC 0.682). (2) The synthetic gene expression contains predictive signals as strong as the true gene expression, reducing reliance on expensive and long-term longitudinal data collection. (3) Time series gene expression is crucial to the proposed improvement and shows significantly better predictive ability than cross-sectional gene expression. (4) Our pipeline is robust to limited data availability. Availability: Code is available at https://github.com/compbiolabucf/TEDDY
Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile
Authors: Patiyal Sumeet , Dhall Anjali , Bajaj Khushboo , Sahu Harshita , Raghava Gajendra P S
Published: December 2022

This paper describes a method Pprint2, which is an improved version of Pprint developed for predicting RNA-interacting residues in a protein. Training and independent/validation datasets used in this study comprises of 545 and 161 non-redundant RNA-binding proteins, respectively. All models were trained on training dataset and evaluated on the validation dataset. The preliminary analysis reveals that positively charged amino acids such as H, R and K, are more prominent in the RNA-interacting residues. Initially, machine learning based models have been developed using binary profile and obtain maximum area under curve (AUC) 0.68 on validation dataset. The performance of this model improved significantly from AUC 0.68 to 0.76, when evolutionary profile is used instead of binary profile. The performance of our evolutionary profile-based model improved further from AUC 0.76 to 0.82, when convolutional neural network has been used for developing model. Our final model based on convolutional neural network using evolutionary information achieved AUC 0.82 with Matthews correlation coefficient of 0.49 on the validation dataset. Our best model outperforms existing methods when evaluated on the independent/validation dataset. A user-friendly standalone software and web-based server named ‘Pprint2’ has been developed for predicting RNA-interacting residues (https://webs.iiitd.edu.in/raghava/pprint2 and https://github.com/raghavagps/pprint2).
A data processing pipeline for the AACR project GENIE biopharma collaborative data with the {genieBPC} R package
Authors: Lavery Jessica A , Brown Samantha , Curry Michael A , Martin Axel , Sjoberg Daniel D , Whiting Karissa
Published: December 2022

Motivation

Data from the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE BPC) represent comprehensive clinical data linked to high-throughput sequencing data, providing a multi-institution, pan-cancer, publicly available data repository. GENIE BPC data provide detailed demographic, clinical, treatment, genomic and outcome data for patients with cancer. These data result in a unique observational database of molecularly characterized tumors with comprehensive clinical annotation that can be used for health outcomes and precision medicine research in oncology. Due to the inherently complex structure of the multiple phenomic and genomic datasets, the use of these data requires a robust process for data integration and preparation in order to build analytic models.

Results

We present the {genieBPC} package, a user-friendly data processing pipeline to facilitate the creation of analytic cohorts from the GENIE BPC data that are ready for clinico-genomic modeling and analyses.

Availability and implementation

{genieBPC} is available on CRAN and GitHub.
Impaired ribosome-associated quality control of C9orf72 arginine-rich dipeptide-repeat proteins
Authors: Viera Ortiz Ashley P , Cajka Gregory , Olatunji Olamide A , Mikytuck Bailey , Shalem Ophir , Lee Edward B
Published: December 2022

Protein quality control pathways have evolved to ensure the fidelity of protein synthesis and efficiently clear potentially toxic protein species. Defects in ribosome-associated quality control and its associated factors have been implicated in the accumulation of aberrant proteins and neurodegeneration. C9orf72 repeat-associated non-AUG translation has been suggested to involve inefficient translation elongation, lead to ribosomal pausing and activation of ribosome-associated quality control pathways. However, the role of the ribosome-associated quality control complex in the processing of proteins generated through this non-canonical translation is not well understood. Here we use reporter constructs containing the C9orf72-associated hexanucleotide repeat, ribosome-associated quality control complex deficient cell models and stain for ribosome-associated quality control markers in C9orf72-expansion carrier human tissue to understand its role in dipeptide-repeat protein pathology.

Our studies show that canonical ribosome-associated quality control substrates products are efficiently cleared by the ribosome-associated quality control complex in mammalian cells. Furthermore, using stalling reporter constructs, we show that repeats associated with the C9orf72-expansion induce ribosomal stalling when arginine (R)-rich dipeptide-repeat proteins are synthesized in a length-dependent manner. However, despite triggering this pathway, these arginine-rich dipeptide-repeat proteins are not efficiently processed by the core components of the ribosome-associated quality control complex (listerin, nuclear-export mediator factor and valosin containing protein) partly due to lack of lysine residues, which precludes ubiquitination. Deficient processing by this complex may be implicated in C9orf72-expansion associated disease as dipeptide-repeat protein inclusions were observed to be predominantly devoid of ubiquitin and co-localize with nuclear-export mediator factor in mutation carriers’ frontal cortex and cerebellum tissue. These findings suggest that impaired processing of these arginine-rich dipeptide-repeat proteins derived from repeat-associated non-AUG translation by the ribosome-associated quality control complex may contribute to protein homeostasis dysregulation observed in C9orf72-expansion amyotrophic lateral sclerosis and frontotemporal degeneration neuropathogenesis.
Weight and Metabolic Changes After Switching From Tenofovir Alafenamide/Emtricitabine (FTC)+Dolutegravir (DTG), Tenofovir Disoproxil Fumarate (TDF)/FTC + DTG, and TDF/FTC/Efavirenz to TDF/Lamivudine/DTG
Authors: Bosch Bronwyn , Akpomiemie Godspower , Chandiwana Nomathemba , Sokhela Simiso , Hill Andrew , McCann Kaitlyn , Qavi Ambar , Mirchandani Manya , Venter Willem Daniel Francois
Published: December 2022

Participants randomized to first-line tenofovir alafenamide (TAF)/emtricitabine (FTC)+dolutegravir (DTG), tenofovir disoproxil fumarate (TDF)/FTC + DTG, or TDF/FTC/efavirenz (EFV) for 192 weeks were then switched to TDF/lamivudine (3TC)/DTG for 52 weeks. Participants switching either TAF/FTC + DTG or TDF/FTC/EFV to TDF/3TC/DTG showed statistically significant reductions in weight, low-density lipoprotein, triglycerides, glucose and glycated hemoglobin.
A Revised Perspective on the Evolution of Troponin I and Troponin T Gene Families in Vertebrates
Authors: Joyce William , Ripley Daniel M , Gillis Todd , Black Amanda Coward , Shiels Holly A , Hoffmann Federico G
Published: December 2022

The troponin (Tn) complex, responsible for the Ca2+ activation of striated muscle, is composed of three interacting protein subunits: TnC, TnI, and TnT, encoded by TNNC, TNNI, and TNNT genes. TNNI and TNNT are sister gene families, and in mammals the three TNNI paralogs (TNNI1, TNNI2, TNNI3), which encode proteins with tissue-specific expression, are each in close genomic proximity with one of the three TNNT paralogs (TNNT2, TNNT3, TNNT1, respectively). It has been widely presumed that all vertebrates broadly possess genes of these same three classes, although earlier work has overlooked jawless fishes (cyclostomes) and cartilaginous fishes (chimeras, rays, and sharks), which are distantly related to other jawed vertebrates. With a new phylogenetic and synteny analysis of a diverse array of vertebrates including these taxonomic groups, we define five distinct TNNI classes (TNNI1-5), with TNNI4 and TNNI5 being only present in non-amniote vertebrates and typically found in tandem, and four classes of TNNT (TNNT1-4). These genes are located in four genomic loci that were generated by the 2R whole-genome duplications. TNNI3, encoding “cardiac TnI” in tetrapods, was independently lost in cartilaginous and ray-finned fishes. Instead, ray-finned fishes predominantly express TNNI1 in the heart. TNNI5 is highly expressed in shark hearts and contains a N-terminal extension similar to that of TNNI3 found in tetrapod hearts. Given that TNNI3 and TNNI5 are distantly related, this supports the hypothesis that the N-terminal extension may be an ancestral feature of vertebrate TNNI and not an innovation unique to TNNI3, as has been commonly believed.
A Narrative Inquiry Into the Lived Experiences of the Oldest-Old Caregivers and How These Are Shaped by Age and Aging
Authors: Arbel Ifah , Cameron Jill I , Trentham Barry , Dawson Deirdre R
Published: December 2022

Background and Objectives

Oldest-old (80+) spousal caregivers of people with dementia are a fast-growing, highly vulnerable, and poorly understood population. As oldest-old individuals, these caregivers have a high likelihood of experiencing aging-related changes (e.g., frailty and multimorbidity) that result in unique caregiving experiences and support needs. Specialized interventions, sensitive to caregivers’ age- and aging-related experiences and needs, may be required to provide adequate support to this group. To date, this group has received limited attention in the literature. Thus, the purpose of this study was to elucidate how age and aging shape the experiences of oldest-old spousal caregivers of people with dementia.

Research Design and Methods

We used a narrative gerontology approach, with 2–3 semistructured interviews with 11 caregivers ages 80–89 (25 interviews in total). We analyzed narrative data thematically.

Results

We identified 4 main themes representing caregivers’ perceptions of age or aging: aging as decline, aging as life experience, doings in older age, and older age as perceived by others. Our results illustrate a breadth of age- and aging-related caregiving experiences stemming from each perception.

Discussion and Implications

This study provides insight into the particular experiences of oldest-old spousal caregivers of people with dementia and provides a foundation for critical future research that will continue to explore the experiences of this unique and fast-growing caregiving group. A more nuanced understanding of this caregiving subgroup is needed to develop age-sensitive health and social care services to meet their needs and, ultimately, improve their well-being and that of their spouses.
‘It bringeth them into dangerous perill’: management of and recovery after miscarriage in early modern England, c.1600–1750
Authors: Evans Jennifer
Published: December 2022

Early modern medical literature described miscarriage as an especially dangerous process for women’s health. Recipe books, diary entries and personal correspondence show that some women experienced significant pain and complications, including retention of the foetus and placenta, fevers, haemorrhaging, headaches, and fertility issues. This article illuminates the management of the bodily process of miscarriage and the means used to promote women’s recovery after the event. It considers the interventions that were necessary to combat the complications associated with pregnancy loss allowing the two-stage process of recovery to take place. In doing so it underlines the gendered nature of treatment in this area. It also reveals that married women who desired pregnancies configured even early miscarriages as losses and emphasized the need for the body to recover.
Dietary patterns and risk of colorectal cancer: a comparative analysis
Authors: Wang Peilu , Song Mingyang , Eliassen A Heather , Wang Molin , Giovannucci Edward L
Published: December 2022

Background

Although several dietary patterns have been associated with incident colorectal cancer (CRC), it is unclear which diet is optimal.

Methods

Participants included 48 409 men and 169 772 women from three USA-based prospective cohort studies. We compared the associations of 18 dietary patterns with CRC risk, including two reference scores. The reference scores were derived based on the dietary recommendations for cancer prevention and CRC-specific dietary risk factors mentioned in the 2018 World Cancer Research Fund/American Institute of Cancer Research (WCRF/AICR) Third Expert Report. Multivariable Cox proportional hazards models were fitted to estimate hazard ratios (HRs) and 95% CIs.

Results

Most dietary patterns showed moderate correlations with the WCRF dietary score (absolute values of Spearman correlation coefficients: 0.45–0.63), except the Plant-based diet index, low-carbohydrate diets, the Empirical dietary index for hyperinsulinemia (EDIH) and Empirical dietary inflammation pattern (EDIP). HR for the 10th–90th percentile difference in the score was 0.86 (95% CI: 0.78–0.94) for the Dietary Approaches to Stop Hypertension score (DASH), 1.15 (1.06–1.26) for Western dietary pattern, 1.20 (1.10–1.31) for EDIH and 1.23 (1.13–1.34) for EDIP. These associations between patterns and CRC risk persisted after adjusting for the two reference scores.

Conclusions

Although further research is needed to improve the WCRF/AICR dietary recommendations, our comprehensive assessment of dietary patterns revealed that the DASH, Western dietary pattern, EDIH and EDIP may be the most relevant diets for preventing CRC.