bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping the tree damage index: A case study on the green lane in the urban area of Banda Aceh City
Authors: Muslih A M , Hidayat N E , Arlita T , Farida A , Dewiyanti I , Sugara A
Published: June 2024

Climate change mitigation efforts implemented by the Government of Banda Aceh by building green lanes with trees. The level of the tree’s ability to absorb carbon is highly correlated with the vitality of the tree itself. The health status of a tree can be known by the tree’s damage level. The aim of the research is to provide information on how much damage to trees and the degree of severity. The research was carried out on green lanes on urban streets in Banda Aceh City as many as 8 lines. The object of research is vegetation with the tree growth phase category, and tree damage index assessment using the forest health monitoring method with indicators of tree damage conditions with parameters of damage location code, damage type code, and damage level code. Based on the results, most of the trees suffered light damage. Of the total number of trees observed, there were 1797 individuals, 252 trees were in good health, 1494 were lightly damaged, 40 trees were medium damaged and 11 trees were heavily damaged. The type of damage experienced was dominated by 46% open wound, 32% cancer, 11% brum (excessive branching) and 11% the rest with other kinds of damage.
The potential biomass, carbon stock and CO2 sequestration of forest litters at Sibolangit nature park
Authors: Ulfa M , Ritonga Y E , Zahirah A , Silalahi R R , Sitinjak A R
Published: June 2024

Several factors generated CO2 releasing into the atmosphere in large quantities and persist. The CO2 concentration is continuously increase (exceeding 400 ppm in 2019) leading to more negative impact of global warming and climate change. Biomass is a key parameter in estimating and predicting ecosystem productivity, carbon storage, nutrient sharing, and fuel accumulation in assessing an ecosystem. This study aims to analyze the biomass, carbon stock and carbon sequestration of forest litters at Sibolangit nature park. The research data was recorded at Sibolangit Tourism Park, located in Sibolangit, Deli Serdang, North Sumatera. 0.5 m x 0.5 m plot was placed based on the simple random sampling method to collect the litters. The 5% sampling intensity was applied resulting in total of 30 sampling plots. All litter in the sample plots was collected and weighed to determine the wet weight. 100 grams of sample was then placed in a sample plastic and labelled. The litter biomass was calculated using the formula according to SNI7724-2011. This research calculated the biomass, carbon stock, and carbon sequestration of litter at Sibolangit nature park, i.e., 86.92 ton ha−1, 40.85 ton ha−1, and 149.94 ton ha−1. The results support the role of Sibolangit nature park in climate change mitigation by reduction of carbon emission.
Forest composition and carbon reserves in Bukit Barisan Forest Park, Dolat Rayat Village, Karo District
Authors: Utomo B , Dalimunthe A , Hakim L , Tampubolon T H
Published: June 2024

Bukit Barisan Grand Forest Park Forest is a forest area formed from forests with protected forest status. In this forest area there is a main road connecting the cities of Medan and Berastagi, which is a tourist destination for people in North Sumatra. Therefore this area is very unique to study but is also vulnerable to logging disturbances, etc. Apart from that, tourist activities also put pressure on this area, especially during holiday periods. The aim of this research is to determine the composition of stands and the carbon content stored in Dolay Rayat Village, Karo Regency. The method used is a combination of stripes and plotted lines where the plots are placed using systematic sampling with random start. Meanwhile, allometric equations are used to estimate carbon stocks. The research used 50 sample plots (2 Ha) arranged in 10 transect lines. The results of the vegetation analysis that has been carried out show that there are 29 types of standing vegetation. The dominant species found at the seedling level are Eurya accuminata (IVI: 30.05), saplings are Altingia excelsa (IVI: 34.44), poles are Lithocarpus edulis (IVI: 44.61) and trees are Lithocarpus edulis (IVI: 30.82). This forest has moderate species diversity with an H’ value ranging from 2.41-2.76. Carbon reserves stored in forest areas in the administrative area of Dolat Rayat Village are quite high, namely 14,639.04 tons.
Reproductive biology of goldstripe sardinella (Sardinella gibbosa) landed at TPI Pantai Labu Deli Serdang, North Sumatra
Authors: Hasibuan J S , Waruwu B K , Susetya I E , Fadhilah A , Manurung V R
Published: June 2024

Goldstripe sardinella (Sardinella gibbosa) is a small pelagic fish found in Pantai Labu, Malacca Strait. Goldstripe sardinella has an important economic value and is in great demand by the local community because it has an affordable price so that it becomes the main target catch of fishermen. Increased fishing effort and demand are feared to have decreased population. This study aimed to determine the reproductive biology of Goldstripe sardinella (S. gibbosa) landed at the TPI Pantai Labu Deli Serdang, North Sumatra Province. This research was conducted from September to November 2022. The method used was a random purposive sampling method with an interval of one month. The number of fish samples was 209 fish with a total length of 134-208 mm and a total weight of 25.01-99.89 g. The sex ratio between males and females is 0.82:1 indicating the ratio is balanced. The GSI values were concurrent from GML I-GML IV with an overall GSI value of 2.39%, fecundity ranged from 1548-30858 grains with a partial spawning pattern.
Avian species and diversity on the campus of Universitas Sumatera Utara, Medan City
Authors: Jumilawaty E , Saragih J E , Nasution A L A
Published: June 2024

Universitas Sumatera Utara (USU) is strategically situated for conducting investigations into the biodiversity of flora and fauna, serving as a source of genetic resources for educational purposes. USU, as a green campus, plays a multifunctional role in determining, protecting, and disseminating information regarding biodiversity, including avian diversity, to support environmentally sustainable development. The USU campus area essentially serves as an urban zone with a focus on species diversity and conservation, making it a key aspect of management. This study aims to identify bird species and diversity on the campus and analyze the diversity index and evenness of bird species on the campus. The methods employed involve direct observations using the line transect method combined with the point count method. We documented a total of 36 bird species, encompassing 22 families. The Avian Diversity Index value on the campus was calculated as 3.117, and the Avian Evenness Index was 0.870. The most prevalent families were Columbidae and Cisticolidae, constituting 3.8% of the total.
Public perception of the Sumatran elephant conflict in the village buffer region GLNP and economic loss consequence of the conflict
Authors: Zahrah M , Ras J S
Published: June 2024

The Sumatran Elephant (Elephas maximus sumatranus) is registered with IUCN Red List with status threatened extinct (endangered species). Conflict that occurs between humans and elephants is increasing from time to time. Change of forest land to agricultural land and settlements are the main causes of the occurrence conflict. This study aims to determine community perceptions, the effectiveness of mitigation and the value of losses economic response to the Sumatran elephant conflict. The method used in this study is by observation and interview through charging questionnaire to selected respondents. Respondents determined in a manner random from population at the estimated location as a distribution area elephant in the village GLNP Area Buffer Location studies shared into 24 grids, with wide each grid is 5x5 km. In each grid determined 3 respondents. Results study show 20% respondent experience conflict and 80% respondent No caught conflict. Mitigation conflict For drive away elephants considered the most effective by the community is with cannon spirit. Amount loss public in 3 year final reach IDR 58,000,000.00. Mark loss smallest i.e. as big Rp 500,000.00 on lemongrass.
The effect of drying temperature and material thickness on the drying characteristics and drying kinetics of curcuma drying using an oven
Authors: Rangkuti M T A , Hasibuan R , Haryanto B , Pramananda V
Published: June 2024

Curcuma is a plant that has medicinal, anti-bacterial, anti-diabetic, anti-hepatotoxic, anti-inflammatoryand anti-tumor properties. Curcuma sold in the market is still fresh rhizomes, so it is impractical and clean and can potentially decrease in quality if stored for a long time. One of the efforts to produce good quality curcuma is the drying process. This study aims to analyze the effect of drying temperature and material thickness on the drying characteristics and drying kinetics of curcuma drying using an oven. Based on this research, it is known that the initial moisture content of content at drying temperature variations of 50, 60 and 70°C is 8.59%, 8.82% and 6.28% (dry base) and after drying, it becomes 0.58%, 0.36% and 0.17% (dry base). The initial moisture content at thickness variations of 5, 10and 15 mm was 8.59%, 5.67% and 3.6% (dry base) and after drying, it became 0.58%, 0.25% and 0.12 % (dry base). Characteristics of curcuma drying using an oven consist of three stages of the drying period. The drying kinetics models suitable for this study are the Page, Logarithmic and Verma et al. models, with R2 values ranging from 0.9737 to 0.9988.
Synthesis and Characterization of Ruminant Feed Based on Palm Kernel Cake Using EM4 Fermentation Method
Authors: Hamid Muhammadin , Nasution Tulus Ikhsan , Syafrina Sherly , Isnaeni Isnaeni
Published: June 2024

The purpose of this study was to determine the effect of the addition of cassava as an adhesive and the use of palm kernel meal as a concentrate and the addition of other ingredients on the physical, mechanical and chemical properties of food ingredients in the form of pellets. The animal feed was made by mixing palm kernel meal, tofu dregs, rice bran, and cassava with a percentage of (68,5 : 15,75 : 5,25 : 10,5)% and mixing molasses and EM 4 in a ration 1 : 1. The test samples were made by going through the stages of weighing, chopping, mixing, fermentation, drying, and molding into pellets. The results showed that the animal feed mixture had a specific gravity of 1.70 gr/mL, porosity of 29.05%, water absorption of 72.62%, pellet hardness of 4.85%, and brittleness with 4.92%. Animal feed pellets have a brownish color and a normal smell like the smell of animal feed pellets in general. The fermentation process was carried out for 8 days until it reached a maturity temperature of 38.44°C. Based on the proximate analysis, it was found that the animal feed contained 10.50% protein, 2.30% total fat, 22.80% crude fiber, 28.50% carbohydrate, 3.00% ash content and 32.90% moisture content. This animal feed pellet with palm kernel meal concentrate and cassava adhesive can be used as an alternative to cattle feed as an energy source feed, because it has a protein content of less than 20%.
Initial vegetative growth and determination of the lethal dose of local rice arias putih at various doses of gamma irradiation
Authors: Siregar D S , Rosmayati  , Hanafiah D S , Lubis K
Published: June 2024

Local rice cultivars that are resistant to biotic and abiotic stress, in fact, still have weaknesses in terms of longevity and idiotypes that causes farmers to rarely cultivate local rice cultivars commercially. One method of plant breeding that can be taken to correct deficiencies in a plant is a mutation program using gamma-ray irradiation. The use of gamma rays must be tested for the value of LD50 so that the right dose is obtained in an effort to increase diversity. One of the upland rice varieties, Arias Putih, was irradiated with gamma rays at the following doses, G0=0 Gy, G1=100 Gy, G2=200 Gy, G3=300 Gy, G4=400 Gy, G5=500 Gy, G6=600 Gy, G7=700 Gy, G8=800 Gy, G9=900 Gy, G10=1000 Gy, and G11=1100 Gy. This LD 50 was carried out with three repetitions per treatment dose, including control. Each dose of gamma-ray irradiation used 100 rice seeds and sown in the seedbed for three weeks. The parameters observed were germination percentage, seedling height and root length, crown and root fresh weight. LD50 was obtained from germination percentage data and was analyzed using Curve-Fit Analysis software. The results revealed a decrease in growth character as the irradiation dose increased. Increasing the irradiation dose up to 500 Gy caused the seeds to die. The LD50 value obtained from the study was 224.13 Gy.
Ethnobotany of Zingiberaceae in the Tamiang tribe, Aceh Province, Sumatra
Authors: Zumaidar  , Husna S , Amalia  , Asmilia N , Saudah
Published: June 2024

Tamiang is one of the unique tribes from Aceh Province because it is descended from the Sriwijaya Kingdom. This tribe is located in eastern Aceh. Research on the ethnobotany of Zingiberaceae plants in the Tamiang tribe aims to identify species, know the parts used, and classify uses. The method used in this research is Purposive Sampling and Participatory Rural Appraisal (PRA) methods. This research was conducted in 30 villages from seven selected sub-districts, namely Bendahara, Seruway, Karang Baru, Rantau, Kejuruan Muda, Bandar Pusaka, and Sekerak sub-districts. The respondents selected were the tribal elders, traditional leaders, owners of family medicinal plants, vegetable traders, and housewives. The results showed that there were 10 Zingiberaceae plant species utilized, namely Curcuma longa, Curcuma zanthorrhiza, Curcuma zedoaria, Zingiber officinale, Zingiber officinale var. rubrum, Zingiber cassumunar, Alpinia galanga, Alpinia purpurata, Kaempferia galanga, and Etlingera elatior. The most widely used part of the plant is the rhizome. Zingiberaceae plants are used as cooking spices, traditional medicines, traditional ceremonies, health drinks, food preparations, food fragrances, and in the beauty and economics fields. The ways to utilize and use Zingiberaceae plants are boiling, soaking, grinding or pounding, steaming, mixing in cooking, selling, consuming, and direct use.
Communities Interaction with Sumatran Tiger (Panthera tigris sumatrae) in the Buffer Zone of Batang Gadis National Park
Authors: Patana P , Fahma N , Purwoko A , Alikodra H S , Kuswanda W , Situmorang R O P , Suntornvongsagul K , Al Hilal M R
Published: June 2024

Bukit Barisan Grand Forest Park Forest is a forest area formed from forests with protected forest status. In this forest area there is a main road connecting the cities of Medan and Berastagi, which is a tourist destination for people in North Sumatra. Therefore this area is very unique to study but is also vulnerable to logging disturbances, etc. Apart from that, tourist activities also put pressure on this area, especially during holiday periods. The aim of this research is to determine the composition of stands and the carbon content stored in Dolay Rayat Village, Karo Regency. The method used is a combination of stripes and plotted lines where the plots are placed using systematic sampling with random start. Meanwhile, allometric equations are used to estimate carbon stocks. The research used 50 sample plots (2 Ha) arranged in 10 transect lines. The results of the vegetation analysis that has been carried out show that there are 29 types of standing vegetation. The dominant species found at the seedling level are Eurya accuminata (IVI: 30.05), saplings are Altingia excelsa (IVI: 34.44), poles are Lithocarpus edulis (IVI: 44.61) and trees are Lithocarpus edulis (IVI: 30.82). This forest has moderate species diversity with an H’ value ranging from 2.41-2.76. Carbon reserves stored in forest areas in the administrative area of Dolat Rayat Village are quite high, namely 14,639.04 tons.
Identifying users’ needs for cycle-transit facilities in MRT Jakarta
Authors: Ramadhanty Galuh Pasha Balqis , Nurlaela Siti
Published: June 2024

Cycle-transit is a multimodal alternative for motorized transportation. Cycle-transit provides a number of environmental and societal benefits that contribute to the SDG 11, which calls for cities and human settlements to be inclusive, safe, resilient, and sustainable. One of the modes of transportation in Indonesia that already supports cycle-transit activities is the MRT Jakarta. The cycle-transit facilities include bike on board, bike parking, bike lane, and bike sharing. MRT Jakarta continues to develop cycle-transit facilities, aiming to shift the travel behavior of Jakarta citizens. MRT Jakarta improvement is financed with public money, so the community should perceive the benefits as much as possible. It is necessary to know the users’ needs for cycle-transit facilities in MRT Jakarta. This article is a part of ongoing research to formulate recommendations for improving cycle-transit facilities in MRT Jakarta. This paper analyzed the improvement priority of four types of cycle-transit facilities at MRT Jakarta based on users’ needs using AHP. The analysis shows that the users need the addition of bike on board access and some improvements on its supporting infrastructure. These findings will be valuable to PT MRT Jakarta and DKI Jakarta Provincial Government as decision-makers to develop cycle-transit facilities in the future. This paper is also followed by formulating recommendations for improving cycle-transit facilities in MRT Jakarta.
Assessing the Waste and Sanitation Infrastructures toward COVID-19 Spreading in Surakarta City, Indonesia
Authors: Miladan N , Istanabi T , Putri A N A , Putripraja D P , Siota I
Published: June 2024

COVID-19 can spread rapidly in areas having high-density populations. The COVID-19 spreading in urban areas is higher than that in rural areas due to the population of urban areas being denser than that of rural areas. The existence of urban infrastructures is assumed to affect COVID-19 spreading in cities. The existence of waste and sanitation systems are the critical urban infrastructures relating to COVID-19 spreading. Surakarta is one of the cities in Indonesia having a high number of COVID-19 infection cases. Based on the Surakarta official website concerning COVID-19, it is known that COVID-19 infected about 37132 persons, or seven percent of the population until the end of the year 2022. This research seeks to reveal the correlation between the existence of waste and sanitation systems and COVID-19 spreading in Surakarta City. This research uses a quantitative approach supported by the statistical data which were retrieved from the Surakarta Statistics Agency, and the official website of the Surakarta Government concerning COVID-19 cases. The statistical data was processed by correlation analysis. The research result revealed that waste management correlates with the number of COVID-19 survivors’ cases. Meanwhile, the sanitation facilities even individually or communally do not correlate with the number of COVID-19 survivors’ cases. Furthermore, the factor of implementing health protocols has a low correlation with the number of COVID-19 survivors’ cases. The waste management is one of the important urban strategies for COVID-19 spreading. Furthermore, this study case describes that COVID-19 risk reduction relates more to urban management than urban planning.
Innovative Poorer areas Upgrading of Mojo Riverbank Settlement Surakarta
Authors: Astuti W , Rahayu P
Published: June 2024

Housing Policies to deal with poorer areas in lower-income countries have shifted from demolitions and evictions to resettlement and to in-situ upgrading and redevelopment. This paper explores the innovative operation of Mojo Poorer Area’s improvement, that integrating aspects of policy, financial, technical and environment, and their impact on economic, social, and health aspects. Using a case study method, this paper analyses qualitative and quantitative data from interviews, field observations, government documents, and a questionnaire survey of 56 households of program beneficiaries. The results show that the most unique approach in this case is the process of discretionary policy for transferring land right between authorities. In addition, the integrated approach can recognize and change marginalized communities’ capital to modern economic, through tourism activities.
Evaluation of Commuter Train User Mapping in the Sidoarjo – Indro Department
Authors: Susanti A , Zhain I
Published: June 2024

The mobility of people from Sidoarjo to Gresik for various purposes requires commuter train as an efficient transportation mode. There is a fundamental need to map the distribution of potential commuter train users whose destination is Gresik area. In this study, the researcher chose Sidoarjo - Indro commuter train route as it intersects with a road and its vehicular traffic. This research method examined the population, number of people using commuter service, vehicle mode selection, and problems encountered while travelling between Sidoarjo and Gresik. Data collection methods used were surveys and questionnaires. Data processing used was tabulation. The mapping results show that the purpose of the passengers’ trip is predominantly for work using motorbike which delivered access as far as 4 km (30%) and online motorbike taxi as far as 4 km (43%). It is known that the distribution of commuter train passengers is dominated by those who start from Gubeng Station and stop at Sidoarjo Station. The mapping of the distribution is important to create fundamental reference that is further used in transportation modelling for areas that are not yet served by Commuter Train services, considering that commuter train services are not evenly distributed throughout the region. It is also essential to evaluate based on commuter train travel behavior mapping.
Preservation of The Vastenburg Fort Site as a Historical Public Space in Surakarta City based on User Perception
Authors: Putra A R A , Ima D N , Akbar F M , Andhika R N , Baiti H N , Yusuf M
Published: June 2024

Social interaction and public space are interrelated and play crucial roles in human life. The Vastenburg Fort Site serves as an example of a public space still utilized by the community and holds historical value from the Dutch colonial era. However, inadequate management has led to a decline in quality and user interest. Thus, this research aims to formulate preservation efforts for it as a historical public space in Surakarta through the assessment of quality and preferences based on user perceptions. In general, this study employs a mixed-methods approach with a deductive perspective. Data were collected through questionnaires and interviews, followed by analyses using Likert scales, descriptive analysis, and content analysis. Consequently, the research reveals a deteriorating condition of the site, perceived as “Enough” by users. Additionally, revitalization efforts and the creation of better spaces with community involvement are deemed necessary by the local community around the Vastenburg Fort Site. Based on these findings, preservation recommendations are formulated, encompassing the strengthening of historical value, integrated management, improved accessibility, diversification of utilization, and community participation. It is hoped that these efforts will restore the Vastenburg Fort Site as a sustainable historical tourism destination and enhance the quality of life for the community.
Fundamental particles
Authors: Kragh Helge
Published: June 2024

The history of elementary particle physics is echoed in the names coined for these particles, including those which did not catch on and are now obsolete. ‘Meson’ lived on, ‘mesotron’ did not. ‘Oreston’ died almost instantly. Starting with the electron and the positron, the chapter ends with the modern era with quarks and gluons as the fundamental particles. While particle names were traditionally based on Greek, after World War II most new particles were given freely invented and often whimsical names. Examples are not only quark and gluon, but also hypothetical particles such as sneutrino, higgsino, and anyon.
The epistemic role of vividness
Authors: Myers Joshua
Published: June 2024

The vividness of mental imagery is epistemically relevant. Intuitively, vivid and intense memories are epistemically better than weak and hazy memories, and using a clear and precise mental image in the service of spatial reasoning is epistemically better than using a blurry and imprecise mental image. But how is vividness epistemically relevant? I argue that vividness is higher-order evidence about one’s epistemic state, rather than first-order evidence about the world. More specifically, the vividness of a mental image is higher-order evidence about the amount of first-order information one has about its subject matter. When vividness is sufficiently low, it can give one reason to doubt the epistemic basis of the mental image and thereby act as a defeater. This account has important implications for theorizing about the epistemic roles of memory, imagination, mental imagery and phenomenal consciousness.
The genome assembly of Carex breviculmis provides evidence for its phylogenetic localization and environmental adaptation
Authors: Yuan Tao , Gao Xiaoman , Xiang Niyan , Wei Pei , Zhang Guiyu
Published: June 2024

Background and Aims

Carex breviculmis is a perennial herb with good resistance and is widely used for forage production and turf management. It is important in ecology, environmental protection and biodiversity conservation, but faces several challenges due to human activities. However, the absence of genome sequences has limited basic research and the improvement of wild plants.

Methods

We annotated the genome of C. breviculmis and conducted a systematic analysis to explore its resistance to harsh environments. We also conducted a comparative analysis of Achnatherum splendens, which is similarly tolerant to harsh environments.

Key Results

The assembled the genome comprises 469.01 Mb, revealing 37 372 genes with a BUSCO completeness score of 99.0 %. The genome has 52.03 % repetitive sequences, primarily influenced by recent LTR insertions that have contributed to its expansion. Phylogenetic analysis suggested that C. breviculmis diverged from C. littledalei ~6.61 million years ago. Investigation of repetitive sequences and expanded gene families highlighted a rapid expansion of tandem duplicate genes, particularly in areas related to sugar metabolism, synthesis of various amino acids, and phenylpropanoid biosynthesis. Additionally, our analysis identified crucial genes involved in secondary metabolic pathways, such as glycolysis, phenylpropanoid biosynthesis and amino acid metabolism, which have undergone positive selection. We reconstructed the sucrose metabolic pathway and identified significant gene expansions, including 16 invertase, 9 sucrose phosphate synthase and 12 sucrose synthase genes associated with sucrose metabolism, which showed varying levels of expansion.

Conclusions

The expansion of these genes, coupled with subsequent positive selection, contributed to the ability of C. breviculmis to adapt to environmental stressors. This study lays the foundation for future research on the evolution of Carex plants, their environmental adaptations, and potential genetic breeding.
Unity Without Truth? Contra Trueman’s Immodest Identity Theory
Authors: Dodd Julian
Published: June 2024

Robert Trueman (2022) sets out and defends an ‘immodest’ identity theory of truth: that is, an identity theory in which the facts with which true propositions are identical are things whose totality is the world: i.e. obtaining states of affairs. This brief reply argues that Truman’s theory falls foul of a perennial objection to such immodest identity theories: namely, that it cannot explain how a candidate proposition’s putative elements can be unified into a proposition proper without this proposition being true.
Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing
Authors: Suljič Alen , Zorec Tomaž Mark , Zakotnik Samo , Vlaj Doroteja , Kogoj Rok , Knap Nataša , Petrovec Miroslav , Poljak Mario , Avšič-Županc Tatjana , Korva Miša
Published: June 2024

The emergence and rapid spread of SARS-CoV-2 prompted the global community to identify innovative approaches to diagnose infection and sequence the viral genome because at several points in the pandemic positive case numbers exceeded the laboratory capacity to characterize sufficient samples to adequately respond to the spread of emerging variants. From week 10, 2020, to week 13, 2023, Slovenian routine complete genome sequencing (CGS) surveillance network yielded 41 537 complete genomes and revealed a typical molecular epidemiology with early lineages gradually being replaced by Alpha, Delta, and finally Omicron. We developed a targeted next-generation sequencing based variant surveillance strategy dubbed Spike Screen through sample pooling and selective SARS-CoV-2 spike gene amplification in conjunction with CGS of individual cases to increase throughput and cost-effectiveness. Spike Screen identifies variant of concern (VOC) and variant of interest (VOI) signature mutations, analyses their frequencies in sample pools, and calculates the number of VOCs/VOIs at the population level. The strategy was successfully applied for detection of specific VOC/VOI mutations prior to their confirmation by CGS. Spike Screen complemented CGS efforts with an additional 22 897 samples sequenced in two time periods: between week 42, 2020, and week 24, 2021, and between week 37, 2021, and week 2, 2022. The results showed that Spike Screen can be applied to monitor VOC/VOI mutations among large volumes of samples in settings with limited sequencing capacity through reliable and rapid detection of novel variants at the population level and can serve as a basis for public health policy planning.
NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach
Authors: Xue Zhengfa , Zhou Aifen , Zhu Xiaoyan , Li Linxuan , Zhu Huanhuan , Jin Xin , Wang Jiayin
Published: June 2024

Non-invasive prenatal testing (NIPT) is a quite popular approach for detecting fetal genomic aneuploidies. However, due to the limitations on sequencing read length and coverage, NIPT suffers a bottleneck on further improving performance and conducting earlier detection. The errors mainly come from reference biases and population polymorphism. To break this bottleneck, we proposed NIPT-PG, which enables the NIPT algorithm to learn from population data. A pan-genome model is introduced to incorporate variant and polymorphic loci information from tested population. Subsequently, we proposed a sequence-to-graph alignment method, which considers the read mis-match rates during the mapping process, and an indexing method using hash indexing and adjacency lists to accelerate the read alignment process. Finally, by integrating multi-source aligned read and polymorphic sites across the pan-genome, NIPT-PG obtains a more accurate z-score, thereby improving the accuracy of chromosomal aneuploidy detection. We tested NIPT-PG on two simulated datasets and 745 real-world cell-free DNA sequencing data sets from pregnant women. Results demonstrate that NIPT-PG outperforms the standard z-score test. Furthermore, combining experimental and theoretical analyses, we demonstrate the probably approximately correct learnability of NIPT-PG. In summary, NIPT-PG provides a new perspective for fetal chromosomal aneuploidies detection. NIPT-PG may have broad applications in clinical testing, and its detection results can serve as a reference for false positive samples approaching the critical threshold.
FOXL2 regulates RhoA expression to change actin cytoskeleton rearrangement in granulosa cells of chicken pre-ovulatory follicles
Authors: Li Xuelian , Du Hongting , Zhou Haobo , Huang Ying , Tang Shuixin , Yu Chengzhi , Guo Yan , Luo Wei , Gong Yanzhang
Published: June 2024

Forkhead box L2 (FOXL2) is an indispensable key regulator of female follicular development, and it plays important roles in the morphogenesis, proliferation, and differentiation of follicle granulosa cells, such as establishing normal estradiol signaling and regulating steroid hormone synthesis. Nevertheless, the effects of FOXL2 on granulosa cell morphology and the underlying mechanism remain unknown. Using FOXL2 ChIP-seq analysis, we found that FOXL2 target genes were significantly enriched in the actin cytoskeleton-related pathways. We confirmed that FOXL2 inhibited the expression of RhoA, a key gene for actin cytoskeleton rearrangement, by binding to TCATCCATCTCT in RhoA promoter region. In addition, FOXL2 overexpression in granulosa cells induced the depolymerization of F-actin and disordered the actin filaments, resulting in a slowdown in the expansion of granulosa cells, while FOXL2 silencing inhibited F-actin depolymerization and stabilized the actin filaments, thereby accelerating granulosa cell expansion. RhoA/ROCK pathway inhibitor Y-27632 exhibited similar effects to FOXL2 overexpression, even reversed the actin polymerization in FOXL2 silencing granulosa cells. This study revealed for the first time that FOXL2 regulated granulosa cell actin cytoskeleton by RhoA/ROCK pathway, thus affecting granulosa cell expansion. Our findings provide new insights for constructing the regulatory network of FOXL2 and propose a potential mechanism for facilitating rapid follicle expansion, thereby laying a foundation for further understanding follicular development.
PPARG is dispensable for bovine embryo development up to tubular stages
Authors: Pérez-Gómez Alba , González-Brusi Leopoldo , Flores-Borobia Inés , Martínez De Los Reyes Nuria , Toledano-Díaz Adolfo , López-Sebastián Antonio , Santiago Moreno Julián , Ramos-Ibeas Priscila , Bermejo-Álvarez Pablo
Published: June 2024

Following blastocyst hatching, ungulate embryos undergo a prolonged preimplantation period termed conceptus elongation. Conceptus elongation constitutes a highly susceptible period for embryonic loss, and the embryonic requirements during this process are largely unknown, but multiple lipid compounds have been identified in the fluid nourishing the elongating conceptuses. Peroxisome proliferator-activated receptors mediate the signaling actions of prostaglandins and other lipids, and, between them, PPARG has been pointed out to play a relevant role in conceptus elongation by a functional study that depleted PPARG in both uterus and conceptus. The objective of this study has been to determine if embryonic PPARG is required for bovine embryo development. To that aim, we have generated bovine PPARG knock-out embryos in vitro using two independent gene ablation strategies and assessed their developmental ability. In vitro development to Day 8 blastocyst was unaffected by PPARG ablation, as total, inner cell mass, and trophectoderm cell numbers were similar between wild-type and knock-out D8 embryos. In vitro post-hatching development to D12 was also comparable between different genotypes, as embryo diameter, epiblast cell number, embryonic disk formation, and hypoblast migration rates were unaffected by the ablation. The development of tubular stages equivalent to E14 was assessed in vivo, following a heterologous embryo transfer experiment, observing that the development of extra-embryonic membranes and of the embryonic disk was not altered by PPARG ablation. In conclusion, PPARG ablation did not impaired bovine embryo development up to tubular stages.
Enhancement of excimer formation ability by modulating the length of Side-chains in polyhedral oligomeric silsesquioxane (POSS) and application for fluorescence sensors for metal cations
Authors: Narikiyo Hayato , Gon Masayuki , Tanaka Kazuo , Chujo Yoshiki
Published: June 2024

Polyhedral oligomeric silsesquioxane (POSS) is a molecule with an inorganic cubic structure and organic side chains which has attracted great attention for its potential to modify luminophores with applications to luminescent materials. In this study, pyrenes-integrated POSSs with various lengths of side chains were synthesized and the effect of the length on luminescent properties was evaluated. In optical measurements, highly efficient excimer emission was observed under dilute solution conditions. Higher values of intensity ratios of excimer to monomer emissions were detected in the shortest side chains. It is likely that shorter side chains of POSS lead to more efficient intramolecular interaction. Interestingly, we also found that the luminescence changed in response to metal cations in the dilute solutions. From this mechanistic study, we found that metal cations such as Cu2+ can accelerate hydrolysis at the linker moiety. As a result, highly sensitive luminescent sensors were obtained. These data show that POSS can work as a reaction field where chemical reactions are accelerated through the accumulation of reactive species.
Increasing community prevalence of extended-spectrum beta-lactamase-producing Escherichia coli in urine is associated with increasing district-level antibiotic consumption
Authors: Nunes Larissa Hermann de Souza , Ribeiro Victoria Stadler Tasca , Salviato Rafael Buttini , de Andrade Ana Paula , Suss Paula Hansen , Vicenzi Fernando José , Hino Adriano Akira Ferreira , Telles João Paulo , Tuon Felipe Francisco
Published: June 2024

This study aimed to analyze ESBL-producing Escherichia coli prevalence in urine samples collected between 2011–2019 in Curitiba, a large city in Brazil, and relating it to antibiotic consumption and sanitary conditions. This is a longitudinal study correlating prevalence of ESBL-producing E. coli isolates from urine samples with district-level antibiotic consumption and sociodemographic data during 2011–2019. E. coli isolates were tested for antibiotic susceptibility and ESBL by an automated method. Statistical analysis applied linear regressions, pooled ordinary least squares, and fixed effects models for districts or years. The Chow and Hausman tests indicated that the fixed effects model for individual districts fitted best. Chi-square test was used for qualitative variables (statistical significance was set when P < 0.05). Among the 886 535 urine sample cultures, 9.9% of isolates were ESBL-producing E. coli. Their prevalence increased from 4.7% in 2012 to 19.3% in 2019 (P < 0.0001; R2 = 0.922). This progressive increase correlated with age (P = 0.007; R2 = 0.8725) and male gender (P < 0.001) and increased antibiotic consumption (P = 0.0386; R2 = 0.47). The fixed effects model showed that district influences ESBL prevalence and that antibiotic consumption explains 20%–30% of this variation, with an increase of one defined daily dose accounting for an increase of 0.02084 percentage points of ESBL. The increasing prevalence of ESBL-producing E. coli can, to a considerable extent, be explained by increasing antibiotic consumption.
Association of Frailty With Risk of Incident Hospital-Treated Infections in Middle-Aged and Older Adults: A Large-Scale Prospective Cohort Study
Authors: Xu Minzhi , Gong Yanhong , Yin Xiaoxv
Published: June 2024

Background

Although frailty is associated with a range of adverse health outcomes, its association with the risk of hospital-treated infections is uncertain.

Methods

A total of 416 220 participants from the UK Biobank were included in this prospective cohort study. Fried phenotype was adopted to evaluate frailty, which included 5 aspects (gait speed, physical activity, grip strength, exhaustion, and weight). More than 800 infectious diseases were identified based on electronic health records. Cox proportional models were used to estimate the associations.

Results

During a median 12.3 years (interquartile range 11.4–13.2) of follow-up (4 747 345 person-years), there occurred 77 988 (18.7%) hospital-treated infections cases. In the fully adjusted model, compared with participants with nonfrail, the hazard ratios (HRs) (95% confidence intervals [CIs]) of those with prefrail and frail for overall hospital-treated infections were 1.22 (1.20, 1.24) and 1.78 (1.72–1.84), respectively. The attributable risk proportion of prefrail and frail were 18.03% and 43.82%. Similarly, compared to those without frailty, the HRs (95% CIs) of those with frailty for bacterial infections were 1.76 (1.70–1.83), for viral infections were 1.62 (1.44–1.82), and for fungal infections were 1.75 (1.47–2.08). No association was found between frailty and parasitic infections (HR: 1.17; 95% CI: 0.62–2.20).

Conclusions

Frailty was significantly associated with a higher risk of hospital-treated infections, except for parasitic infections. Studies evaluating the effectiveness of implementing frailty assessments are needed to confirm our results.
Racial–Ethnic Gaps in Pandemic-Related Economic Hardship: Age Differences Among Older Adults
Authors: Wiemers Emily E , Lin I-Fen , Wiersma Strauss Anna , Chin Janecca A , Hotz V Joseph , Seltzer Judith A
Published: June 2024

Objectives

Racial–ethnic disparities in experiences of economic hardship during the pandemic are well documented in the population overall and among older adults. Existing research shows that this economic hardship was much less common at older than younger ages. Little is known about the intersection of racial–ethnic and age disparities in pandemic-related hardship in later life. This research report investigated racial–ethnic gaps in economic hardship by age group among older adults.

Methods

Data were from the 2018 and 2020 U.S. Health and Retirement Study (HRS) including the 2020 coronavirus disease 2019 module. We estimated Heckman-corrected linear probability models to examine differences in experiences of pandemic-related economic hardship in the 2020 HRS by race–ethnicity (non-Hispanic White, non-Hispanic Black, U.S.-born Hispanic, foreign-born Hispanic) across age groups (55–64, 65–74, 75+). In the multivariable analysis, we controlled for sociodemographic characteristics, participation in social programs, pre-existing health conditions and behaviors, and economic resources from the 2018 HRS.

Results

Experiences of economic hardship declined with age within each racial–ethnic group. Racial–ethnic gaps in hardship remained at older ages without any controls. However, when all controls were added, racial–ethnic gaps in economic hardship were eliminated for those ages 75+. Individual characteristics prior to the pandemic explained racial–ethnic differences in hardship for the oldest adults (75+) but did not explain gaps for those ages 55–74.

Discussion

Results point to structural factors generating new racial–ethnic gaps in pandemic-related economic hardship among those approaching retirement (ages 55–74) that did not affect the oldest adults (ages 75+).
Digital Skills, STEM Occupation, and Job Automation Risks Among the Older Workers in the United States
Authors: Yamashita Takashi , Narine Donnette , Chidebe Runcie C W , Kramer Jenna W , Karam Rita , Cummins Phyllis A , Smith Thomas J
Published: June 2024

Background and Objectives

Advancing automation technologies are replacing certain occupations such as those involving simple food preparation more than occupations such as those in STEM fields (e.g., engineering and health care). Older workers generally face higher job automation risks in part due to their lower levels of digital skills. A better understanding of the associations between job automation risk, digital skills, and type of occupation (e.g., STEM vs non-STEM) can facilitate preparations for job automation and workforce population aging.

Research Design and Methods

We analyzed a nationally representative sample (N = 1,560) of middle-aged and older U.S. workers aged 50–74 years from the 2012/2014/2017 Program for International Assessment of Adult Competencies (PIAAC) restricted-use file. The estimated job automation risks (i.e., percentage of jobs to be automated in the next decades) were derived from the previous studies. PIAAC digital problem-solving skills proficiency (measured on a scale of 0–500 points) was assessed based on a series of practical digital tasks (e.g., finding a job research website that does not require registration).

Results

Linear regression analysis showed that greater digital skill proficiency (b = −0.04, p < .05) and STEM occupations (b = −17.78, p < .001) each were associated with lower job automation risks, even after adjusting for a series of demographic, socioeconomic, and civic engagement characteristics.

Discussion and Implications

Education and labor policy interventions to promote digital skills among older workers and non-STEM workers may better prepare an aging workforce for the dynamic labor market needs in the United States.
Clutch Size, but Not Egg Volume, Increases with Rainfall in an Arid-Dwelling Bird
Authors: Liebl Andrea L , Steen Andrew J , O'Neill Louis G , Savage James L , Russell Andrew F
Published: June 2024

Synopsis

Understanding how animals maximize reproductive success in variable environments is important in determining how populations will respond to increasingly extreme weather events predicted in the face of changing climates. Although temperature is generally considered a key factor in reproductive decisions, rainfall is also an important predictor of prey availability in arid environments. Here, we test the impact of weather (i.e., rainfall and temperature) on female reproductive investment in an arid-dwelling bird (i.e., clutch size and egg volume) and tradeoffs between the two. We predicted that female chestnut-crowned babblers (Pomatostomus ruficeps), endemic to the arid region of Australia, would increase clutch size at the expense of egg volume in response to variation in rainfall and temperature. We found that over 14 breeding seasons, clutch size decreased with increasing temperature, but increased following more rain. Egg volume, on the other hand, became larger as temperatures increased and, although not related to the amount of rain, was related to the number of days since the last rainfall. Finally, egg size decreased as clutch size increased, indicating a tradeoff between the two reproductive parameters. Our results suggest that chestnut-crowned babblers breed reactively in response to variable environments. We expect that clutch size variation in response to rain may reflect the impact of rain on arthropod abundance, whereas the effect of temperature may represent an established decline in clutch size observed in other seasonal breeders. As the tradeoff between clutch size and egg volume was modest and clutch sizes were modified to a greater extent than egg volumes in response to rainfall, we suggest selection is more likely to increase offspring number than quality, at least in favorable years. Our results support the idea that reproductive investment is variable in fluctuating environments, which has implications for species living in habitats experiencing more extreme and less predictable weather as the global climate changes.
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression
Authors: Coolen Silvia , Rogowska-van der Molen Magda A , Kwakernaak Ineke , van Pelt Johan A , Postma Jelle L , van Alen Theo , Jansen Robert S , Welte Cornelia U
Published: June 2024

The Southern green shield bug, Nezara viridula, is an invasive piercing and sucking pest insect that feeds on crop plants and poses a threat to global food production. Given that insects are known to live in a close relationship with microorganisms, our study provides insights into the community composition and function of the N. viridula-associated microbiota and its effect on host–plant interactions. We discovered that N. viridula hosts both vertically and horizontally transmitted microbiota throughout different developmental stages and their salivary glands harbor a thriving microbial community that is transmitted to the plant while feeding. The N. viridula microbiota was shown to aid its host with the detoxification of a plant metabolite, namely 3-nitropropionic acid, and repression of host plant defenses. Our results demonstrate that the N. viridula-associated microbiota plays an important role in interactions between insects and plants and could therefore be considered a valuable target for the development of sustainable pest control strategies.