bluuebunny/crossref_metadata_2025 huggingface dataset:
Modal Test and Model Modification of the Rotating Parts of a Self-propelled Antiaircraft Gun
Authors: Huan Liu , Pengke Liu , Bianfang Ning , Faming Zhou , Fanfan Zhang , Jiaxing Li
Published: June 2023

The rotating parts of a self-propelled antiaircraft gun is taken as the research object, the single point excitation and multi-point response frequency response function method were used to test the experimental mode. At the same time, the finite element simulation model is established, and the frequency and mode of vibration are obtained. Combined with the modal test and analysis of the rotating parts, the stiffness of the connection between the rotating parts and the turret is selected as the optimization parameter. The numerical simulation model was optimized and modified by comparing the experimental and simulation modes and combining with the sensitivity analysis of the connection parameters, the correction variable with the higher sensitivity of the parameters to the results was selected. After optimization, the error between the first order calculation frequency and the test frequency is reduced from 8.61% to 1.13%, it is shown that the simulation model optimized by parameters can better reflect the physical characteristics of the real structure.
Study on the influence of helicopter rotor flow on projectile motion
Authors: Liu Z L , Dai J S , Lin S Y , He F
Published: June 2023

In this paper, the muzzle flow field generated during helicopter gun firing is numerically studied. Based on Navier-Stokes equation and Standard k − ε turbulence model, the projectile motion is realized by using overlapping mesh technology. The development of the muzzle flow field formed by complex wave systems such as Mach disk and shock wave under the influence of helicopter rotor flow at different speeds, as well as the force and motion state of the projectile in the flow field are analysed. The results show that the degree of asymmetry of the flow field, the force and offset of the projectile are positively correlated with the rotor flow velocity. The research will help to improve the understanding of the muzzle flow field of helicopter gun and provide a new idea for improving the firing accuracy of helicopter gun..
Scalar fields in the de Sitter spacetime
Authors: Kamenshchik Alexander Y , Starobinsky Alexei A , Vardanyan Tereza
Published: June 2023

We examine long-wavelength correlation functions of massive scalar fields in de Sitter spacetime. For the theory with a quartic self-interaction, the two-point function is calculated up to two loops. Comparing our results with the Hartree-Fock approximation and with the stochastic approach shows that the former resums only the cactus type diagrams, whereas the latter contains the sunset diagram as well and produces the correct result. We compare our results with the preceding results obtained for the massless scalar field.
Instantaneous vacuum and States of Low Energy for a scalar field in cosmological backgrounds
Authors: Ferreiro Antonio , Pla Silvia
Published: June 2023

We construct the instantaneous vacuum state for a quantum scalar field coupled to another classical scalar field as described in [1]. We then compare it with the state of low energy constructed for a particular solution. We show that under physically motivated conditions they become very similar.
Remarks on the Integral Form of D=11 Supergravity
Authors: Grassi Pietro Antonio
Published: June 2023

We make some considerations and remarks on D = 11 supergravity and its integral form. We start from the geometrical formulation of supergravity and by means of the integral form technique we provide a superspace action that reproduces (at the quadratic level) the recent formulation of supergravity in pure spinor framework. We also make some remarks on Chevalley-Eilenberg cocycles and their Hodge duals.
On the Resilience of Black Hole Evaporation: Gravitational Tunneling through Universal Horizons
Authors: Schneider M. , Del Porro F. , Herrero-Valea M. , Liberati S.
Published: June 2023

Using a quantum tunneling derivation, we show the resilience of Hawking radiation in Lorentz violating gravity. In particular, we show that the standard derivation of the Hawking effect in relativistic quantum field theory can be extended to Lorentz breaking situations thanks to the presence of universal horizons (causal boundaries for infinite speed signals) inside black hole solutions. Correcting previous studies, we find that such boundaries are characterized by a universal temperature governed by their surface gravity. We also show that within the tunneling framework, given the pole structure and the tunneling path, only a vacuum state set in the preferred frame provides a consistent picture. Our results strongly suggest that the robustness of black hole thermodynamics is ultimately linked to the consistency of quantum field theories across causal boundaries.
Quantum Chiral Superfields
Authors: Fioresi Rita , Lledó María A. , Razzaq Junaid
Published: June 2023

We define the ordinary Minkowski space inside the conformal space according to Penrose and Manin as homogeneous spaces for the Poincaré and conformal group respectively. We realize the supersymmetric (SUSY) generalizations of such homogeneous spaces over the complex and the real fields. We finally investigate chiral (antichiral) superfields, which are superfields on the super Grassmannian, Gr(2|1, 4|1), respectively on Gr(2|0, 4|1). They ultimately give the twistor coordinates necessary to describe the conformal superspace as the flag Fl(2|0, 2|1; 4|1) and the Minkowski superspace as its big cell.
ADENIUM — A demonstrator for a next-generation beam telescope at DESY
Authors: Liu Yi , Feng Changqing , Gregor Ingrid-Maria , Herkert Adrian , Huth Lennart , Stanitzki Marcel , Teng Yao , Yang Chenfei
Published: June 2023

High-resolution beam telescopes for charged particle tracking are one of the most
important and equally demanding infrastructure items at test beam facilities. The main purpose of
beam telescopes is to provide precise reference track information of beam particles to measure the
performance of a device under test (DUT). In this report the development of the ADENIUM beam
telescope (ALPIDE sensor based DESY Next test beam
 Instrument) as a demonstrator and prototype for a next-generation beam
telescope is presented. The ADENIUM beam telescope features up to six pixelated reference planes
framed by plastic scintillators for triggering. ADENIUM is capable of replacing the currently
used EUDET-type beam telescopes without impacting existing DUT implementations due to the
integration of the telescope DAQ into EUDAQ2.

In this report the concept and design of the ADENIUM telescope as well as its performance are
discussed. The telescope's pointing resolution is determined in different configurations. For an
optimal setup at a momentum of 5.6 GeV with an ALPIDE as DUT, a resolution better than
3 μm has been extracted. No rate limitations have been observed at the DESY II test beam.
The potency of soil bacteria on soil phosphorus solubilization and IAA production for innovation on sustainable Melon (Cucumis melo) production through biofilm biofertilizer
Authors: Amalina D D , Sudadi  , Pratama N M , Dewi W S
Published: June 2023

To fulfils the demand of melons (Cucumis melo), it requires intensive maintenance by agrochemical products. If this is done continuously, it will lead to soil degradation and disrupt the sustainable food supply. Therefore, an innovation is needed to maintain the sustainable food supply using biofilm biofertilizer technology. This study aims are to determine the potential of bacteria isolated from melon rhizosphere to solubilize phosphate and producing indole acetic acid (IAA) so that it can be developed into biofilm biofertilizer. Soil samples were taken from three melon gardens owned by farmers located in Sragen Regency, Karanganyar Regency and Wonogiri Regency, Central Java. In the laboratory, the soil bacteria then isolated from the soil using the dilution method. The isolates obtained then tested for their ability to solubilize phosphate and produce IAA. Phosphate is an essential nutrient for plant growth and IAA is plant growth promoting. The results showed that the highest phosphate solubilization potential was produced by bacterial isolate SRG 1A with a halo zone ratio of 1.957 and the highest concentration of IAA was produced by bacterial isolate WNG 1B with a value of 6.151 ppm. Based on the ability of the bacteria, indicates that the obtained bacterial isolates have the potential to be developed as a biofilm biofertilizer to help the growth of melon plants because it has the potency to solubilize soil nutrient and produce IAA.
The effect of differences in lactation period and milking time on milk production and quality of Saanen Etawa Crossbreed Goats (Sapera)
Authors: Pramono A , Altiara D N P , Cahyadi M
Published: June 2023

This research aims to analyze the effect of different lactation periods and milking time on milk production and quality in Sapera goats (Saanen Peranakan Etawa). The research was carried out from September 2021 to January 2022. The materials used were 8 Sapera goats in the II lactation period and 8 Sapera goats in the III lactation period by collecting milk samples in the morning and afternoon. Milk quality analysis of Sapera goats milk using Lactoscan SAP (Nova Zagora, Bulgaria). The following parameters observed were milk production, fat content, protein content, lactose content, and density. This study used the Nested Design method, namely the nested milking time in the lactation period. The research data were analyzed statistically using T Test. The results showed that the difference in lactation period in Sapera goats could affect the density of milk (p<0.05). Differences in milking time in Sapera goats can affect milk production, milk protein content, milk lactose content and density (p<0.05). The conclusion of this study was that Sapera goats milk in the III lactation period showed a higher density of milk than II lactation period. Sapera goat milk yield from morning milking associated higher milk production, lactose content and density than the afternoon milking, but the protein content in the afternoon milking time was higher than the morning milking time and was still in the normal range. Milk fat content and milk protein content have met the standard of SNI No. 01–3141–2011 and Thai Agricultural Standard (TAS) 6006-2008.
Effect of boiling time on the stability of the phenolic compounds in wedang uwuh after gastric digestion
Authors: Fauziah IN , Prangdimurti E , Palupi NS
Published: June 2023

Plant-based products are an excellent source of dietary phenolic compounds, such as herbal drinks, juices, dried fruits, etc. Wedang uwuh is one of the herbal drinks that is made from a mixture of herbal plants. In previous studies, it has been reported that the boiling time affects the total phenolic content and antioxidant capacity of wedang uwuh. However, there has been no research on the effects of digestion on the stability of the phenolic components in wedang uwuh. This study aims to evaluate the stability of phenolic compounds of wedang uwuh after gastric digestion simulation with different boiling times of 5, 10, and 15 minutes. This research used total phenolic content assay, and DPPH• radical scavenging capacity to determine the stability of phenolic compounds after gastric digestion simulation. We found that the boiling time affected the amount of extractable and stability of the phenolic compounds in wedang uwuh during gastric digestion. There was a degraded capacity of DPPH radical scavenging after gastric digestion. The total phenolic and antioxidant capacity before consumption did not indicate the quantity of bioaccessible. Further research using intestinal digestion simulation is needed to obtain the bioaccessibility of wedang uwuh.
Effect of Storage time on quality of Bebek Ungkep in retort pouch
Authors: Mardiana Nur Agustin , Kurniawan Hindra , Wirawantoro Aditya , Purnomo Panji , Prasetiyo Bagus
Published: June 2023

Bebek ungkep is highly commercialized in Indonesia, but it has a short shelf life. To overcome the problem, we used a retort pouch to prolong the shelf-life of the product. This study aimed to evaluate the effect of storage time on the quality of Bebek Ungkep in retort pouch packaging based on physicochemical, microbiological, and sensory analysis. The parameters were free fatty acid value, pH value, total plate counts of aerobic and anaerobic bacteria, and sensory. This study used a Randomized Block Design (RBD) with one experimental factor: the length of storage time. The storage time was 0, 2, 4, and 6 weeks. The data were evaluated by using one-way ANOVA (α= 95%) and followed by Fisher’s test. The results showed that storage time affected FFA and pH values of retorted Bebek ungkep. Meanwhile, total plate counts of aerobic and anaerobic bacteria were not significantly different. Based on sensory analysis, color, and aroma were not significantly different, while taste and texture were significantly different.
The extraction effect of the skin of dragon fruit (Hylocereus polyrhizus) to its phenolic compounds and its antioxidants: A review
Authors: Harni M. , Anggraini T. , Rini  , Suliansyah I.
Published: June 2023

Dragon fruit contains various nutrients and functional values both in the flesh and skin. The skin of dragon fruit contains 30-35% water. It has lots of phenolic compounds and antioxidants, of which the higher amount of antioxidants are in the skin. These compounds are very easily damaged due to the extraction process especially if done incorrectly. This article is written to be a guide in selecting the extraction process in order to preserve the compounds. Based on the review, it is found the modern UAE (Ultrasound Assisted Extraction) process provides better quality than the other various conventional and modern extraction processes. UAE is an extraction process that does not use a heating process in its extraction which can damage the phenolic compounds and antioxidants. The results of the analysis of phenolic compounds using the UAE system have found betacyanin 17.64 mg, phenolic compounds 65.16 mg, flavonoid compounds 195 mg and antioxidants 620 mol. Thus, the recommended treatment to do is to use UAE extraction.
Analysis of chili supply in Indonesia
Authors: Sundari Mei Tri , Darsono  , Sutisno Joko , Antriyandarti Ernoiz
Published: June 2023

This study aims to determine the supply factor of chili, the dominant factor, and the elasticity of supply in the Indonesian research location. Multiple linear regression was used to analyze the data. The results showed that the variable number of chili production in the previous year and chili area in year t significantly affected the supply of chili in Indonesia. In contrast, the price of chili in the previous year and the price of urea fertilizer in year t had no significant effect. A variable of chili area is the dominant factor in the supply of chili. The value of elasticity in the short and long term on the number of chili production in the previous year is inelastic. At the same time, the variable of chili area is elastic in the short and long term.
The efficiency of use of production factors for rice through mechanization in Sukoharjo
Authors: Suswadi  , Prasetyo Agung , Mahananto  , Astriyaningsih
Published: June 2023

Paddy was a staple food ingredient to produce rice. Rice contains nutrients for the human body as an energy source. Rice contains strengthening substances such as carbohydrates, protein, fat, crude fiber, ash, and vitamins. Sukoharjo Regency has implemented a corporate farming system since 2018. The level of use of the mechanization system of production factors was not yet known. The objective of this study was to know the level of efficiency of the use of the corporate farming system in the Sukoharjo Regency. The method of determining the location of the study uses a purposive. The method of determining the sample in this study is the purposive sampling method. That is, sampling from the population was done randomly without regard to the existing strata in the population. The results showed that The use of production factors in lowland rice farming had not reached the maximum efficiency level. The factors of production needed to increase their use were land area and organic fertilizer. In comparison, the inefficient factors were labor, seeds, urea fertilizer, sp36 fertilizer, spontaneous pesticides, and furadan pesticides, so their use does not need to be added.
Effect of packaging type on the quality of premix white bread based on modified rice flour
Authors: Duka Febby Suzanna , Rahman Andi Nur Faidah , Tahir Mulyati M , Langkong Jumriah , Jalaluddin
Published: June 2023

White bread premix flour based on modified rice flour is a practical food product that is safe, nutritious and has functional value. However, loss of nutritional components may occur during storage. In this study, premix flour was packaged in PP plastic, HDPE plastic and aluminum foil, and stored under controlled conditions at 30°C temperature and 75% relative humidity for 28 days. The content of carbohydrates, protein, fat, ash and water is regularly assessed. Flour packaged using aluminum foil showed the smallest percentage loss of nutritional components, namely 0.8% loss of carbohydrates, 75% protein loss, 13% fat loss, 4% loss of ash content and 49% increase in water content. Meanwhile, the highest percentage of nutrient loss in HDPE packaged premix flour is 10% carbohydrate loss, 91% protein loss, 45% fat loss, 8% loss of ash content and 56% increase in water content. This shows that the product quality is better maintained by using aluminum foil packaging.
The effect of stinky bean (Parkia speciosa) peel ethanolic extract to enhance superoxide dismutase (SOD) and reduce malondialdehyde (MDA) level of “jelantah” exposed rats
Authors: Nurdyansyah F , Widyastuti D A , Mandasari A A
Published: June 2023

“Jelantah” is cooking palm oil which is used repeatedly. Its daily use leads to enhancement of free radical level in the body. Free radical level should be lowered by a compound named antioxidant, either synthetic or natural antioxidant. This study aims to analyze the effect of P. speciosa peel ethanolic extract (PSPE) to superoxide dismutase (SOD) and malondialdehyde (MDA) level of jelantah exposed Rattus norvegicus (rats). The rats were divided into four groups. There were group I as a negative control (without jelantah and PSPE treatment), group II with 1 ml jelantah 118 mek/kg + 100 mg/kg body weight PSPE treatment, group III with 1 ml jelantah 118 mek/kg + 200 mg/kg body weight PSPE treatment, and group IV is a positive control (with 1 ml jelantah 118 mek/kg). The results showed that range of SOD and MDA level are 20.63-79.06 U/ml and 1.75-9.34 nmol/ml, respectively, with significantly different at α: 0.05. The negative control showed the highest SOD level and lowest MDA level because it was not treated with jelantah. On the other hand, the positive control showed the opposite because it was only treated with jelantah without addition of PSPE. Furthermore, the group III showed higher SOD and lower MDA level than group II. Those indicate that the higher PSPE concentration, the higher SOD level and the lower MDA level. SOD as an antioxidant has contrary level to MDA as free radical. PSPE showed a significant effect to the enhancement of SOD level and the reduction of MDA level in jelantah exposed rats.
Understanding the sensory profile of a traditional snack of Indonesia: Serabi
Authors: Fauza G , Astuti I , Muhammad D R A , Ishartani D , Ariviani S , Affandi D R , Prasetyo H
Published: June 2023

Serabi is Indonesian traditional food and has been widely known in Surakarta. However, its sensory profile has not yet been described. This study aims to characterize the sensory attributes of serabi products in Surakarta by combining quantitative descriptive analysis (QDA) and principal component analysis (PCA) methods. Ten samples of serabi produced by small medium enterprises (SMEs) in Surakarta were collected and evaluated. The sensory profile is categorized based on aroma, taste and texture. The focus group discussion (FGD) of eleven trained panellist agreed that the attributes of aroma are eggs, coconut milk, sweet, burnt and pandan leaf. Meanwhile the attributes of taste are coconut milk, sweet and salty, and softness, solid and crunchy particle, hardness, softness and creamy are the attributes of texture. The PCA result showed that two samples, J and I, were described as serabi that have intense burnt and hardness attributes while more shredded coconut texture were represented by sample H and A. Moreover, samples D, G, F fall in a quadrant that describes having dominant egg and flour taste, while the rest samples, E, C and B have more intense salty, sweet and pandan leaf aroma. This result can be used as a reference for describing the basic profile of traditional serabis in Surakarta.
Health of shallot bulbs planted with mycorrhizal applications and several types of mulch in moler disease conducive land
Authors: Supyani  , Poromarto SH , Supriyadi  , Utaminingsih R , Hadiwiyono
Published: June 2023

Moler is one of the important diseases of shallots caused by Fusarium oxysporum f.sp. cepae. Recently, it is very detrimental to one of the shallot production centers in Indonesia, namely Brebes, Central Java. The intensity and yield loss of this pathogen attack can exceed 60% and 50% respectively. Efforts to develop sustainable control are urgently carried out, such as the use of biological control agents and environmental management by using mulch. This paper reports on the health of shallot bulbs grown with the application of mycorrhiza and mulch. This research was conducted on shallot land conducive to moler disease, in Sidamulya, Wanasari District, Brebes Regency, Central Java with alluvial soil type. The results showed that the health Index of bulbs in the mycorrhizal treatment was 98.89%. In the combination treatment of mycorrhizae with some organic mulch, reached health index of shallot bulbs by 100%.
Relationship of weather factors on the progress of shallot moler disease in Brebes, Central Java in the rainy and dry seasons: intensity increases in humid and warm air
Authors: Widono S , Poromarto S H , Supyani  , Noviantoro W , Hadiwiyono
Published: June 2023

Shallots are one of the important commodities in Indonesia. One of the obstacles in the production of shallots is the existence of moler disease caused by Fusarium oxysporum f.sp. cepae (FOCe). This pathogen is capable of causing damage to crops and causing losses to crop failure. Changes in weather and global warming can affect the progress of the disease. This manuscript reports the results of observing the progress of moler disease in Brebes, Central Java, in two planting seasons of shallots, dry and rainy, in 2021. The results show that the progress of moler disease intensity in the rainy season is more conducive than in the dry season. Presumably, the factors of temperature and relative humidity of the air show the most influence on the progress of moler disease intensity compared to other weather factors such as rainfall and light intensity.
Optical non-volatile correction of SERS wavelength using optical pumping
Authors: Shameli Mohammad Ali , Eskandari Mohammad Reza , Safian Reza
Published: June 2023

In this paper, we propose a reconfigurable two-dimensional photonic crystal (PC) made from a new ultralow loss phase change material for detecting and imaging applications of surface-enhanced Raman scattering (SERS). The proposed all-dielectric structure is composed of identical holes periodically distributed on Sb2S3 as a substrate, tuned by optical pumping. The proposed PC is investigated using full-wave simulation of the CST with the finite-difference frequency domain method over a wide bandwidth of optical wavelengths. In this study, compensation for the error of the Fano resonance wavelength due to the fabrication process is realized through tuning optical pumping applied to the configuration. Also, the numerical results show the designed PC supports two high-quality Fano resonance modes, leading to uniform and high field enhancement with a SERS enhancement factor of 1.23 × 1012, which is significant for the application of SERS enhancement.
Engineering spatiotemporal patterns: information encoding, processing, and controllability in oscillator ensembles
Authors: Bomela Walter , Singhal Bharat , Li Jr-Shin
Published: June 2023

The ability to finely manipulate spatiotemporal patterns displayed in neuronal populations is critical for understanding and influencing brain functions, sleep cycles, and neurological pathologies. However, such control tasks are challenged not only by the immense scale but also by the lack of real-time state measurements of neurons in the population, which deteriorates the control performance. In this paper, we formulate the control of dynamic structures in an ensemble of neuron oscillators as a tracking problem and propose a principled control technique for designing optimal stimuli that produce desired spatiotemporal patterns in a network of interacting neurons without requiring feedback information. We further reveal an interesting presentation of information encoding and processing in a neuron ensemble in terms of its controllability property. The performance of the presented technique in creating complex spatiotemporal spiking patterns is demonstrated on neural populations described by mathematically ideal and biophysical models, including the Kuramoto and Hodgkin-Huxley models, as well as real-time experiments on Wein bridge oscillators.
Study on lubrication characteristics of rotary combination seals under stress relaxation
Authors: Zhang Yi , Zhong Sipeng , Xiong Siyang , Xiong Zijie
Published: June 2023

Temperatures in the drilling environment can reach 150 °C and pressures up to 30 MPa, all of which can cause oil film rupture and even seal failure. In addition, under high pressure, viscosity changes can lead to stress relaxation, which may eventually cause seal failure as well. In order to study the influence of high temperature and high pressure conditions on seal performance during stress relaxation, the pressure permeation loading method on both sides is used in the finite element model to simulate the fluid pressure on both sides of the seal interface, and the TEHL (thermo-elastohydrodynamic lubrication) model of the rotary combination seal is also established. On this basis, the TEHL characteristics of the rotary combination seal under different working conditions were analyzed. The results show that: Firstly, the contact pressure and von Mises stress of the seal tend to increase at high temperature, and the higher the temperature, the faster the growth rate, while the increase of the seal area temperature leads to the thinning of the oil film thickness and the high oil film pressure. Secondly, at high fluid pressure, the contact pressure of the rotary combination seal gradually increases, and its peak is close to the peak oil-side contact pressure. Thirdly, with the increase of the linear speed (or rotational speed), the oil film pressure and thickness increase. Fourthly, the larger the rotational speed, the larger the volume leakage and friction, and the larger the compression ratio, the larger the contact pressure.
Structural design and analytical study of a new polysilicon tunable microactuator for measurement of different resonance frequencies
Authors: Taherian Sina , Gholinataj-Jelodar Ehsan
Published: June 2023

This paper presents a novel MEMS tunable resonator that draws inspiration from the folded beam structure in its comb drive resonator design. Conventional electrostatic comb-drive resonators commonly employ folded-beam suspensions to achieve linearity and reduce system stiffness. The proposed design incorporates eight zigzag-shaped meander springs to support the comb finger structure, featuring two central anchors. The objective of this design is to introduce zigzag-shaped nested-folded beam suspensions to the comb parts, thereby reducing the tuning voltage and sensor size. The governing equations are provided to calculate the support springs’ stiffness, and a comparative analysis is conducted to evaluate the stiffness of the proposed design against other parameters. The mathematical analysis demonstrates that Zigzag Nested-Folded beams result in a decreased resonance frequency and a softened electrostatic spring under applied DC voltage. The integration of zigzag-shaped nested-folded beam flexures enables MEMS resonator devices to exhibit reduced stiffness, leading to a lower pull-in voltage. The resonator design and simulation are performed using Intellisuite and SolidWorks software. Results indicate that the resonant frequency of the proposed tunable comb-drive resonator, equipped with 26 finger pairs and a movable part displacement of 21 μm, is reduced by 66% from the original frequency of 2.420 kHz when a tuning voltage of 59 V is applied. Simultaneously, the corresponding effective stiffness decreases by 66% from the initial value of 0.72 N m−1. This compact resonator occupies an area of approximately 1.058×278 (μm)2, demonstrating a smaller size compared to previous works.
Effects of epigallocatechin gallate, caffeine, and their combination on fat accumulation in high-glucose diet-fed Caenorhabditis elegans
Authors: Guo Cheng , Shen Wangyang , Jin Weiping , Jia Xiwu , Ji Zhili , Jinling Li , Bin Li
Published: June 2023

Epigallocatechin gallate (EGCG) and caffeine are inevitable to be ingested together in the process of drinking green tea. This study used Caenorhabditis elegans as an organism model to examine whether the binding of EGCG and caffeine could influence the fat-reduction effect. The results revealed that EGCG significantly reduced the Nile Red fluorescence intensity and the triglyceride/protein ratio of the C. elegans obesity model by 14.7% and 16.5%, respectively, while the effect of caffeine was not significant. Moreover, the degree of reduction in fluorescence intensity and triglyceride/protein ratio by EGCG + caffeine was comparable to that of EGCG. In the exploration of underlying mechanism, we found that EGCG and EGCG + caffeine treatments had no influence on food intake and energy expenditure of C. elegans. Their fat-reduction effects were dependent on the regulation of lipogenesis, as shown by the decreased expression of the sbp-1, fat-7, and daf-16 genes.
Network integration and protein structural binding analysis of neurodegeneration-related interactome
Authors: Chen Hongjun , Zhou Yekai , Liu Yongjing , Zhang Peijing , Chen Ming
Published: June 2023

Neurodegenerative diseases (NDs) usually connect with aggregation and molecular interactions of pathological proteins. The integration of accumulative data from clinical and biomedical research will allow for the excavation of pathological proteins and related interactors. It is also important to systematically study their interacting proteins in order to find more related proteins and potential therapeutic targets. Understanding binding regions in protein interactions will help functional proteomics and provide an alternative method for predicting novel interactions. This study integrated data from biomedical research to achieve systematic mining and analysis of pathogenic proteins and their interaction network.

A workflow has been built as a solution for the collective information of proteins involved in NDs, related protein–protein interactions (PPIs) and interactive visualizations. It also included protein isoforms and mapped them in a disease-related PPI network to illuminate the impact of alternative splicing on protein binding. The interacting proteins enriched by diseases and biological processes (BPs) revealed possible regulatory modules. A high-resolution network with structural affinity information was generated. Finally, Neurodegenerative Disease Atlas (NDAtlas) was constructed with an interactive and intuitive view of protein docking with 3D molecular graphics beyond the traditional 2D network. NDAtlas is available at http://bis.zju.edu.cn/ndatlas.
JTK: targeted diploid genome assembler
Authors: Masutani Bansho , Suzuki Yoshihiko , Suzuki Yuta , Morishita Shinichi
Published: June 2023

Motivation

Diploid assembly, or determining sequences of homologous chromosomes separately, is essential to elucidate genetic differences between haplotypes. One approach is to call and phase single nucleotide variants (SNVs) on a reference sequence. However, this approach becomes unstable on large segmental duplications (SDs) or structural variations (SVs) because the alignments of reads deriving from these regions tend to be unreliable. Another approach is to use highly accurate PacBio HiFi reads to output diploid assembly directly. Nonetheless, HiFi reads cannot phase homozygous regions longer than their length and require oxford nanopore technology (ONT) reads or Hi-C to produce a fully phased assembly. Is a single long-read sequencing technology sufficient to create an accurate diploid assembly?

Results

Here, we present JTK, a megabase-scale diploid genome assembler. It first randomly samples kilobase-scale sequences (called ‘chunks’) from the long reads, phases variants found on them, and produces two haplotypes. The novel idea of JTK is to utilize chunks to capture SNVs and SVs simultaneously. From 60-fold ONT reads on the HG002 and a Japanese sample, it fully assembled two haplotypes with approximately 99.9% accuracy on the histocompatibility complex (MHC) and the leukocyte receptor complex (LRC) regions, which was impossible by the reference-based approach. In addition, in the LRC region on a Japanese sample, JTK output an assembly of better contiguity than those built from high-coverage HiFi+Hi-C. In the coming age of pan-genomics, JTK would complement the reference-based phasing method to assemble the difficult-to-assemble but medically important regions.

Availability and implementation

JTK is available at https://github.com/ban-m/jtk, and the datasets are available at https://doi.org/10.5281/zenodo.7790310 or JGAS000580 in DDBJ.
Large-scale rare variant burden testing in Parkinson's disease
Authors: Makarious Mary B , Lake Julie , Pitz Vanessa , Ye Fu Allen , Guidubaldi Joseph L , Solsberg Caroline Warly , Bandres-Ciga Sara , Leonard Hampton L , Kim Jonggeol Jeffrey , Billingsley Kimberley J , Grenn Francis P , Jerez Pilar Alvarez , Alvarado Chelsea X , Iwaki Hirotaka , Ta Michael , Vitale Dan , Hernandez Dena , Torkamani Ali , Ryten Mina , Hardy John ,   UK Brain Expression Consortium (UKBEC),, Scholz Sonja W , Traynor Bryan J , Dalgard Clifton L , Ehrlich Debra J , Tanaka Toshiko , Ferrucci Luigi , Beach Thomas G , Serrano Geidy E , Real Raquel , Morris Huw R , Ding Jinhui , Gibbs J Raphael , Singleton Andrew B , Nalls Mike A , Bhangale Tushar , Blauwendraat Cornelis
Published: June 2023

Parkinson’s disease has a large heritable component and genome-wide association studies have identified over 90 variants with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for Parkinson’s disease.

To address this gap, we investigated the rare genetic component of Parkinson’s disease at minor allele frequencies <1%, using whole genome and whole exome sequencing data from 7184 Parkinson’s disease cases, 6701 proxy cases and 51 650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact.

Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for Parkinson’s disease, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10 and TREML1 but were unable to replicate the observed associations across independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in Parkinson’s disease. To date, this is the largest analysis of rare genetic variants in Parkinson’s disease.
Albuminuria and the risk of cancer: the Stockholm CREAtinine Measurements (SCREAM) project
Authors: Luo Li , Yang Yuanhang , Kieneker Lyanne M , Janse Roemer J , Bosi Alessandro , Mazhar Faizan , de Boer Rudolf A , de Bock Geertruida H , Gansevoort Ron T , Carrero Juan-Jesus
Published: June 2023

Background

Studies investigating the association of chronic kidney disease and cancer have focused on estimated glomerular filtration (eGFR) rather than on albuminuria. This study aimed to examine whether albuminuria is associated with cancer incidence, and whether this association is independent of eGFR.

Methods

We included subjects of the Stockholm Creatinine Measurements (SCREAM) project without a history of cancer—250 768 subjects with at least one urine albumin–creatinine ratio (ACR) test (primary cohort) and 433 850 subjects with at least one dipstick albuminuria test (secondary cohort). Albuminuria was quantified as KDIGO albuminuria stages. The primary outcome was overall cancer incidence. Secondary outcomes were site-specific cancer incidence rates. Multivariable Cox proportional hazards regression models adjusted for confounders including eGFR to calculate hazard ratios and 95% confidence intervals (HRs, 95% CIs).

Results

During a median follow-up of 4.3 (interquartile range 2.0–8.2) years, 21 901 subjects of the ACR cohort developed de novo cancer. In multivariable analyses, adjusting among others for eGFR, subjects with an ACR of 30–299 mg/g or ≥300 mg/g had a 23% (HR 1.23; 95% CI 1.19–1.28) and 40% (HR 1.40; 95% CI 1.31–1.50) higher risk of developing cancer, respectively, when compared with subjects with an ACR <30 mg/g. This graded, independent association was also observed for urinary tract, gastrointestinal tract, lung and hematological cancer incidence (all P < .05). Results were similar in the dipstick albuminuria cohort.

Conclusions

Albuminuria was associated with the risk of cancer independent of eGFR. This association was primarily driven by a higher risk of urinary tract, gastrointestinal tract, lung and hematological cancers.
T-next: a new custom-made Thoraflex graft to simplify proximal and distal aortic reinterventions
Authors: Di Eusanio Marco , Gatta Emanuele
Published: June 2023

Secondary root and distal thoraco-abdominal endovascular aortic re-interventions can be challenging after frozen elephant trunk. We obtained from the TERUMO Aortic custom-made platform a Thoraflex graft with a modified disposition of the arch branches that facilitate secondary proximal and distal reinterventions. Here we describe the graft and our first implant.
Whole genome sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine clade
Authors: Marr R Alexander , Moore Jackson , Formby Sean , Martiniuk Jonathan T , Hamilton Jonah , Ralli Sneha , Konwar Kishori , Rajasundaram Nisha , Hahn Aria , Measday Vivien
Published: June 2023

Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavor and aroma compounds in wine. Wineries place a high-value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite-typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired-end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into 4 clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin, and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine-making environment. The “wine circle/Region B”, a cluster of 5 genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to nonvineyard North American Oak strains from spontaneous wine fermentations.
Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants
Authors: Einson Jonah , Glinos Dafni , Boerwinkle Eric , Castaldi Peter , Darbar Dawood , de Andrade Mariza , Ellinor Patrick , Fornage Myriam , Gabriel Stacey , Germer Soren , Gibbs Richard , Hersh Craig P , Johnsen Jill , Kaplan Robert , Konkle Barbara A , Kooperberg Charles , Nassir Rami , Loos Ruth J F , Meyers Deborah A , Mitchell Braxton D , Psaty Bruce , Vasan Ramachandran S , Rich Stephen S , Rienstra Michael , Rotter Jerome I , Saferali Aabida , Shoemaker Moore Benjamin , Silverman Edwin , Smith Albert Vernon ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi Pejman , Castel Stephane E , Iossifov Ivan , Lappalainen Tuuli
Published: June 2023

Exonic variants present some of the strongest links between genotype and phenotype. However, these variants can have significant inter-individual pathogenicity differences, known as variable penetrance. In this study, we propose a model where genetically controlled mRNA splicing modulates the pathogenicity of exonic variants. By first cataloging exonic inclusion from RNA-sequencing data in GTEx V8, we find that pathogenic alleles are depleted on highly included exons. Using a large-scale phased whole genome sequencing data from the TOPMed consortium, we observe that this effect may be driven by common splice-regulatory genetic variants, and that natural selection acts on haplotype configurations that reduce the transcript inclusion of putatively pathogenic variants, especially when limiting to haploinsufficient genes. Finally, we test if this effect may be relevant for autism risk using families from the Simons Simplex Collection, but find that splicing of pathogenic alleles has a penetrance reducing effect here as well. Overall, our results indicate that common splice-regulatory variants may play a role in reducing the damaging effects of rare exonic variants.
A Randomized Clinical Trial of Online Social Intelligence Training With Custodial Grandmothers
Authors: Smith Gregory C , Infurna Frank J , Dolbin-MacNab Megan , Webster Britney , Castro Saul , Crowley Daniel M , Musil Carol , Hu Luxin , Hancock Gregory R
Published: June 2023

Background and Objectives

In this study, we investigated the efficacy of a self-administered, online Social Intelligence Training (SIT) program aimed at enhancing psychological and relational well-being among a nationwide U.S. sample of custodial grandmothers.

Research Design and Methods

A two-arm randomized clinical trial (RCT) was conducted, where 349 grandmothers raising grandchildren aged 11–18 years were assigned to either SIT or an attention control condition (ACC). Participants self-completed online surveys at baseline and immediately postintervention, in addition to follow-ups at 3-, 6-, and 9-month postintervention. First-order latent difference score models were used to compare SIT to ACC, across all times of measurement, along key indicators of psychological and relational well-being on an intent-to-treat basis.

Results

Although SIT was largely superior to ACC at yielding positive results, it appears that it attenuated longitudinal declines that occurred among ACC participants. SIT also exerted stronger effects on relational than psychological outcomes, with perceived relations with grandchildren being the most positively affected.

Discussion and Implications

Given that the historical time of this RCT unpredictably corresponded with the coronavirus disease 2019 pandemic, we suspect that SIT helped offset declines in psychological and relational well-being that are widely documented to have resulted from the pandemic. Our overall positive findings support future use of the inexpensive and easily delivered SIT program under normal environmental conditions, with the vulnerable and geographically disperse population of custodial grandmothers.

Clinical Trials Registration Number

NCT03239977
Comparing the peri-implantation endometrial T-bet/GATA3 ratio between control fertile women and patients with recurrent miscarriage: establishment and application of a reference range
Authors: Yu Shuyi , Diao Lianghui , Lian Ruochun , Chen Cong , Huang Chunyu , Li Xinyuan , Li Yuye , Zeng Yong
Published: June 2023

STUDY QUESTION

Is the ratio of endometrial T-box expressed in T cell (T-bet) and GATA-binding protein 3 (GATA3) changed in patients with recurrent miscarriage (RM) compared to fertile controls?

SUMMARY ANSWER

Our study showed a significantly higher T-bet/GATA3 ratio in patients with RM compared with fertile controls.

WHAT IS KNOWN ALREADY

The endometrial T-bet (Th1 lineage-committed transcription factor)/GATA3 (Th2 lineage-committed transcription factor) ratio could represent the Th1/Th2 balance, which is particularly important for healthy pregnancy. However, a reliable reference range for the T-bet/GATA3 ratio during the peri-implantation period has not yet been established for use in clinical practice.

STUDY DESIGN, SIZE, DURATION

This was a retrospective study carried out in a private fertility center. The control group included 120 women in couples undergoing IVF treatment for male infertility, who had experienced a live-birth baby following the first IVF cycle. The study group included 93 women diagnosed with RM that experienced at least two consecutive clinically spontaneous miscarriages before gestational week 12. The ratio of T-bet/GATA3 was calculated in the control group and RM group.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Endometrium samples were collected at mid-luteal phase of the menstrual cycle prior to IVF treatment or pregnancy. The percentage of T-bet+ and GATA3+ cells in total endometrial cells was analyzed using immunohistochemical staining and quantitative analysis.

MAIN RESULTS AND THE ROLE OF CHANCE

Using the 95th percentile to define the upper limits of the endometrial T-bet/GATA3 ratio during the mid-luteal phase, the reference range of control fertile women was ≤0.22. Compared with the control group, the RM group exhibited a significantly higher T-bet/GATA3 ratio (P = 0.02), and 19.4% (18/93) women with RM exhibited a T-bet/GATA3 ratio above the reference range in the mid-luteal phase.

LIMITATIONS, REASONS FOR CAUTION

All patients were recruited from a single center. The stability and clinical value of the endometrial T-bet/GATA3 ratio require further investigation.

WIDER IMPLICATIONS OF THE FINDINGS

The present study suggests that an abnormal endometrial T-bet/GATA3 ratio may be one of the risk factors of RM. Further studies are needed to follow up the pregnancy outcomes in patients with RM with normal and abnormal endometrial T-bet/GATA3 ratio according to the reference range.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by Shenzhen Fundamental Research Program (JCYJ20180228164631121, JCYJ20190813161203606, JCYJ20220530172817039). There are no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER

N/A.