bluuebunny/crossref_metadata_2025 huggingface dataset:
The analysis strategies of catfish farming based on chicken manure utilized the cld model
Authors: Nisa K , Sunarto  , Rosariastuti R
Published: December 2022

Production of catfish farming increased every year. Cultivation of catfish by utilizing chicken manure as feed integrates in terms of the environment livestock, as well as soy milk dregs waste as organic probiotics. We require the right model in catfish farming by utilizing chicken manure as feed. This study aims to analyze the model of the catfish farming approach based on chicken manure, using the Causal Loop Diagram (CLD) method as system thinking by entering causal variables into a diagram using software Vensim®. This study utilized a descriptive method with a qualitative approach. Data collection techniques conducted interviews and observations in February-May 2022 by several actors, such as chicken breeders and catfish farmers, collectors of soy milk dregs, local residents, and village officials in Margosari Village, Kendal. The results obtained from the CLD model analysis showed the catfish farming strategies based on chicken manure is based on the variables of Environmental Problems, Knowledge, and Economic Potential.
Ecological Risk Assessment and Spatial Distribution of Heavy Metals of Agricultural Soils in Nganjuk Regency, Indonesia
Authors: Sukarjo  , Handayani C O , Zu’amah H
Published: December 2022

This research measures the lead, cadmium, copper, nickel, chromium, and arsenic in the paddy fields in Nganjuk Regency. Moreover, this research identifies the effect of these metals to the environment and their location. 105 topsoil samples were collected. The AAS was utilized to ascertain the elemental composition of the soil samples. Numerous soil pollution and ecological risk indices, such as Igeo, PI, IPI, PLI, and PERI, were used to analyze the situation. Spline interpolation with ArcGIS 10.2 was used to study metal distribution. The metal content (mg/kg) in Pb, Cd, Co, Ni, Cr, and As was 10.01, 0.77, 9.60, 5.46, 3.61, and 2.79, respectively. These pollutants had pollution index values of between 0.59 and 2.56 and 0.05 and 0.56 on the lower end of the scale. With an average of 1.10−6, the pollutant load index suggests that all samples are safe. The paddy fields in the research region have an average PERI score of 91.48, indicating a low ecological risk. Most metals researched under agriculturally safe levels will be highly valuable for establishing control and remediation measures in paddy fields.
Feasibility analysis of hybrid corn farming in Karanganyar Regency
Authors: Suswadi  , Prasetyo A , Mahananto  , Prasetyowati K , Purnomo Y
Published: December 2022

The productivity and price of hybrid corn in Karanganyar Regency are lower than the productivity and price of the surrounding districts, especially during the la Nina storm. This study aims to determine the feasibility of mixed corn farming in the Karanganyar Regency. Determining the location and sampling was done using the purposive sampling technique with 80 farmers as respondents. The data analysis method used was the farm Cost-income analysis, R/C ratio, BEP (Break-Even Point), Profitability-cost ratio, Labor productivity, and Sensitivity analysis. The average income was IDR 3,975,741 per farm or IDR 7,795,571 per hectare. The average cost calculated was IDR 1,930,362 per farm and 4,257,302 per hectare. The analysis of BEP, R/C ratio, the profitability-cost proportion, labour productivity and sensitivity showed that hybrid corn is feasiblethe profitability-cost proportion was more significant than the applicable bank interest. Labour productivity was greater than the prevailing labor wage. The sensitivity showed that hybrid corn farming was feasible under decreasing prices by up to 50%. Therefore, farmers still benefit from cultivating hybrid corn. However, the effect of La Nina will continue, so farmers must be more adaptive to excessive water and pest attacks on their land.
Effectiveness of community based-collaborative on forest management of the forest programme III in Central Sulawesi
Authors: Golar G , Muis H , Herman A , Simorangkir W S
Published: December 2022

Indonesia is moving quickly to ratify the Paris Agreement as stipulated in Constitution Number 16/2016 as a total commitment and contribution to reducing global carbon emissions. For this action, Indonesia received a cooperation grant, one of which was the Forest Programme (FP) III Sulawesi. FP III aims to contribute to implementing forest conservation and rehabilitation strategies, as a form of adaptation and mitigation of climate change, through support for improving the livelihoods of the rural poor. This program was conducted with multi-stakeholder management in the Lore Lindu landscape. This study attempted to examine the effectiveness of the project on collaborative community-based forest management with an explanatory approach. The results showed that interconnectivity between programs in each PIU had not gone optimally. Although the village facilitators have carried out their job, the indicator results have not followed the community’s needs. In addition, the role of FMUs as the holder of the regional authority at the site level has not been directly involved. It has strategic value for the national interest, ensuring that the forest and land rehabilitation program’s implementation will be in the right location on the target because FMUs have detailed data and information at the field level.
Upland rice growth on giving of biochar and organic fertilizer
Authors: Rahayu M , Nurmalasari AI , Aprilya K
Published: December 2022

Upland rice is a food crop commodity that can be cultivated on dry land. Increasing soil fertility on dry land can be through the addition of organic materials in the form of biochar and organic fertilizers. The aim of this research was to examine the growth of upland rice on the application of several types of biochar and organic fertilizers. The research was conducted in Sukosari Jumantono Village, Karanganyar in March-June 2022. The research used completely randomized block design. The first factor was type of biochar (without biochar, coconut shell biochar, rice husk biochar, strobilanthes biochar) and the second factor was type of organic fertilizer (without organic fertilizer, chicken manure, goat manure, cow manure) with three replications. Data analysis using Analysis of Variance and Duncan’s Multiple Range Test. The results showed that the application of biochar and organic fertilizers was not able to increase plant height, fresh weight of biomass, dry weight of biomass and leaf area of upland rice. The application of biochar can increase the leaves number and tiller number of upland rice at 4-6 weeks after planting (WAP). Coconut shell biochar produced the highest leaves number and tillers numbers than rice husk biochar and strobilanthes biochar.
Genetic variability, correlation and path coefficient among agronomic characters of soybeans [Glycine max (L.) Merr.] lines
Authors: Kuswantoro Heru , Santoso Juli , Suryanto Agus
Published: December 2022

Genetic variability and relationship among characters plays important roles in development of plants varieties. The aim of the research was to study genetic variability and relationship among characters. Fifty soybean lines were grown in randomized complete block design with three replicates. The number of branches and seed yield that had broad genetic variability. The maturity, branches, and 100-seed weight had high heritability. Seed weight per plant and seed yield showed significant genotypic correlations. The phenotypic correlation among characters was found between seed yield with number of filled pods, 100 seeds weight and seed weight per plant, branches with productive node and filled pods, and productive nodes with filled pods. Phenotypic path coefficient revealed that flowering, branches, 100-seed weight, and seed weight per plant contributed directly to seed yield per plot. Despite having high heritability and broad genetic variability, branches per plant showed negative indirect effect through number of nodes and seed weight per plant, while seed weight per plant showed positive indirect effect through number of branches per plant. Direct selection should be based on seed yield, while indirect selection should be based on seed weight per plant.
Diversity of agarwood-inducing fungi from Gyrinops versteegii tree
Authors: Roswanjaya Y P , Rosdayanti H , Nawfetrias W
Published: December 2022

Gyrinops versteegii is a tropical tree of the Thymelaeaceae family. Under special conditions, G. versteegii tree can produce agarwood (Gaharu), a high economic commodity in the world yielding aromatic resin. Agarwood can be used for incense, perfume, addition to herbal medicine, food ingredients, and ornamental functions. It also contains phenolic compounds and feruly glycerides, which exhibit anti-cancer activity. It is apparently an induced resinous product due to subsequent infection by facultative fungal pathogens. In this study, we aim to investigate the diversity of agarwood-inducing fungi by isolating fungi from the infected trunk of G. versteegii. The pure fungi isolates were identified microscopically and then reconfirmed by molecular techniques. The identification method included genomic DNA isolation, DNA amplification of Internal Transcribed Spacer (ITS) genes by a specific primer, direct ITS gene sequencing and molecular analysis of fungi species. The investigated fungi that resulted from this research are Fusarium sp. Gv1, Aspergillus sp. Gv2 and Fusarium sp. Gv3. Three different fungi found in the same infection site show that the diversity of agarwood-inducing fungi from the G. versteegii tree is relatively high.
Effect of moringa leaf extract and cow-manure on soya bean growth and yield
Authors: Haryuni H , Atmaja I Y , Supriyadi T , Priyadi S , Rumaningsih M
Published: December 2022

Glycine max. L. Merril. is one of Indonesia’s strategic commodities, whose productivity can be increased by using moringa leaf extract (Simplicia extract) and cow manure. This research aims to determine the effect of the dose of Simplicia extract and cow manure on the growth and yield of soya beans. The research was carried out from October to December 2020. The soil type was regosol in Jagalan Village, Karangnongko District, Klaten Regency, Central Java. The research design used the factorial method with a completely randomized design (CRD) which consisted of 2 factors; the first factor was dose variations of Simplicia extract (M) were 0, 10, 20, 30, 40, and 50 ml./L (M0, M1, M2, M3, M4, and M5), the second factor is cow manure (C) which is 30 and 60 g/polybag (P1 and P2). The results showed that the combination treatment of M5P2 at a dose of 50 ml/L of Simplicia extract and 60g/polybag of cow manure had the highest growth and yield compared to other treatments. This research provides information on appropriate doses of Simplicia extract and cow manure on soya bean yield and growth.
Analysis of bacterial community from the rhizosphere of shallots (Allium ascalonicum L.) in Brebes, Central Java, using Next Generation Sequencing (NGS) approach
Authors: Rosariastuti R , Sutami  , Sumani  , Hartati S
Published: December 2022

Brebes is the largest shallot center in Indonesia. This area contributes 18.5 % of national or 57 % of production in Central Java. Farmers regularly spray about 63-93% of pesticides every 3-7 days in their maintenance. It is necessary to improve technology and the use of bacteria in it. This study aimed to determine the diversity of soil bacteria in two types of land use as initial information to optimize its role in overcoming pesticide pollution and increasing the productivity of shallots in the future. Sampling using the purposive sampling method. The bacteria community in the shallot field (KB2) and secondary forest (KB4) using the Next Generation Sequencing technique. Identification using FLASH (V1.2.7) and QIIME (V1.7.0) analysis. The results showed that the soil bacterial community in KB4 was higher than in KB2. The soil bacterial communities in KB2 were seven phyla, while in KB4 were eight phyla. In order of largest to the smallest relative abundance in KB2, including Proteobacteria (0.970%), Actinobacteria (0.015%), Firmicutes (0.014%), Fusobacteriota (0.001%), Desulfobacterota (0.0003%), Bacteroidota (0.0001%), and others (0.011%). In KB4, there are 8 phyla, namely Elusimicrobiota (6.385%), Cyanobacteria (3.192%), Proteobacteria (0.9861%), Actinobacteria (0.0041%), Firmicutes (0.0089%), Desulfobacterota (0.0001%), Bacteroidota (0.0002%), and others (0.0003%).
The Effect of Empty Fruit Bunch (EFB) Compost and Trichoderma Biofertilizer on Growth and Yield Performance of Chili (Capsicum annuum L. Var. Kulai)
Authors: Tangga C K , Mohidin H , Abdullah S
Published: December 2022

Chili Kulai (Capsicum annuum L) is a typical and popular chili that utilized by Malaysians as a spice in their daily food, emphasize its economic value. The objectives of this study were to evaluate the effect of empty fruit bunch (EFB) compost and Trichoderma biofertilizer on the growth and yield performance of chili production, as well as to determine physicochemical properties of soil and to evaluate N, P, K content of chili plant tissue. The experimental design used was Randomized Completely Block Design (RCBD) with four treatments replicated four (4) times with four plants giving a total of 64 experimental units. The treatments involved were: T1 (Control), T2 (100% EFB compost), T3 (100% Trichoderma biofertilizer) and T4 (50% EFB compost + 50% Trichoderma biofertilizer). The results revealed, there was a significant difference (p<0.05) for growth and yield performance of chili production. As for the nutrient content (%) in both soil and plant, T4 showed the highest NPK content with N (1.98%), P (0.76%) and K (0.69%). In conclusion, this study proved that the use of organic based EFB compost enriched with Trichoderma biofertilizer has increased the yield of chili plant, thus reducing the use of chemical fertilizer.
The Growth Response and Nutritional Status of Eggplant (Solanum melongena L.) Planted in Soil Incorporated with Oyster Mushroom Waste
Authors: Bisop W , Hashim M M , Mohidin H
Published: December 2022

Waste disposal has become primary concern in mushroom industry as it can lead to various environmental issues without proper waste management. Most of the mushroom grower are unaware of the utilization of organic waste as soil amendment which have been proven to improve the soil properties, growth performances and yield of various crops if conducted properly. This study intended to determine the growth response and nutritional status of eggplant by utilizing the oyster mushroom waste (OMW) as part of the growing medium. The experiment design used was Randomized Complete Block Design (RCBD) and the treatments involved were: T1 (100% Topsoil), T2 (90% Topsoil + 10% OMW), T3 (70% Topsoil + 30% OMW) and T4 (50% Topsoil + 50% OMW). The study showed that there was a significant difference on soil properties which is determined by the soil moisture content and soil pH value between treatment where p<0.0.5. The utilization of OMW in treatment showed to had a higher nutrient content (%) in both soil and plant and recorded to had better yield performances in eggplant cultivation, as it increases the eggplant yield by 30%-50%. Thus, mushroom waste can potentially be reutilized to avoid environmental problems while improving the growth and yield of eggplant.
Factors influencing biological asset disclosures in agricultural companies in Indonesia
Authors: Ika S R , Susetyo R , Pribadi A , Dwiwinarno T , Widagdo A K
Published: December 2022

This study examines to what extent biological asset reporting is corresponding to the Indonesian Statement of Financial Accounting Standard 69 (PSAK 69) among Indonesia Stock Exchange-listed agricultural firms. In their annual report, such companies should report how they recognize and measure the fair value of the living plants or animals’ assets. This study also examines factors that might impact the extent of disclosure of biological assets. The examined factors are biological asset intensity, concentrated ownership, audit committee effectiveness, profitability, and size. Biological asset disclosures were measured by a checklist derived from PSAK 69 and International Accounting Standard (IAS) 41 on Agriculture. This study uses 53 firm-year observations of the listed agriculture companies from 2017 to 2020. Multiple regression analysis findings indicate that biological asset intensity and firm size affect favorably the amount of biological asset disclosures. The results indicate that the greater the living plants or animals owned by a company and the larger the firm, the greater the commitment of a company to disclose its biological assets in its annual report. The study sheds light on the capital market authority agency’s current policy to strengthen factors that may impact agricultural companies’ disclosure of their biological assets.
The role of local leader on food security campaign toward sustainable goals of agriculture in Simeulue Island
Authors: Abus A F , Lubis T , Abus A A , Saputra N , Abus N A A
Published: December 2022

This study describes the relationship between food security and the role of the local leader in motivating his community to maintain their typical plants as the sources of their main food. This qualitative study used ethnography to describe humans’ role in making their life and environment harmonious, especially food security. From the recording and the interview result, it is known that the role of the chief as the informal leader has more opportunity and power to listen. It is known that in the past, the role of the local chief succeeded in influencing and convincing his community to consume rice as the main food and affected the community to grow rice even though their environment was not supported enough. The ‘rice standardization’ as a welfare area is not appropriate to be settled in all places in Indonesia. Formerly, Simeuluenese already knew and consumed other main food except for rice, namely sago and taeb, as their main food. However, the policy changed their mind to consuming rice as their main food instead of sago. Consequently, the local chief’s role is essential to campaign again to convince his community of food security toward sustainable goals based on local wisdom.
Organic materials and fish emulsion on shoot multiplication of Cavendish banana (Musa paradisiaca ‘Cavendish’)
Authors: Charantika J W , Samanhudi  , Sakya A T
Published: December 2022

This study aims to investigate the effect of combining organic matter and fish emulsion on the multiplication of Cavendish banana shoots. This study employed one factor of a complete randomized design, with 13 levels of treatment: MS (Murashige and Skoog) + purple sweet potato extract, MS + purple sweet potato extract + fish emulsion 2 ppm, MS + purple sweet potato extract + fish emulsion 4 ppm, MS + purple sweet potato extract + fish emulsion 6 ppm, MS + banana peel extract, MS + banana peel extract + fish emulsion 2 ppm, MS + banana peel extract + fish emulsion 4 ppm, MS + banana peel extract + fish emulsion 6 ppm, MS + bean sprouts extract, MS + Bean sprouts extract + fish emulsion 2 ppm, MS + bean sprouts extract + fish emulsion 4 ppm, MS + bean sprouts extract + fish emulsion 6 ppm, and MS + BAP (benzyl amino purine) as controls. The results show that the combination of synthetic materials (BAP) still has significantly different results compared to organic matter and fish emulsion treatment.
Comparison of out-of-field normal tissue dose estimates for pencil beam scanning proton therapy: MCNP6, PHITS, and TOPAS
Authors: Griffin Keith T , Yeom Yeon Soo , Mille Matthew M , Lee Choonik , Jung Jae Won , Hertel Nolan E , Lee Choonsik
Published: December 2022

Monte Carlo (MC) methods are considered the gold-standard approach to dose estimation for normal tissues outside the treatment field (out-of-field) in proton therapy. However, the physics of secondary particle production from high-energy protons are uncertain, particularly for secondary neutrons, due to challenges in performing accurate measurements. Instead, various physics models have been developed over the years to reenact these high-energy interactions based on theory. It should thus be acknowledged that MC users must currently accept some unknown uncertainties in out-of-field dose estimates. In the present study, we compared three MC codes (MCNP6, PHITS, and TOPAS) and their available physics models to investigate the variation in out-of-field normal tissue dosimetry for pencil beam scanning proton therapy patients. Total yield and double-differential (energy and angle) production of two major secondary particles, neutrons and gammas, were determined through irradiation of a water phantom at six proton energies (80, 90, 100, 110, 150, and 200 MeV). Out-of-field normal tissue doses were estimated for intracranial irradiations of 1-, 5-, and 15-year-old patients using whole-body computational phantoms. Notably, the total dose estimates for each out-of-field organ varied by approximately 25% across the three codes, independent of its distance from the treatment volume. Dose discrepancies amongst the codes were linked to the utilized physics model, which impacts the characteristics of the secondary radiation field. Using developer-recommended physics, TOPAS produced both the highest neutron and gamma doses to all out-of-field organs from all examined conditions; this was linked to its highest yields of secondary particles and second hardest energy spectra. Subsequent results when using other physics models found reduced yields and energies, resulting in lower dose estimates. Neutron dose estimates were the most impacted by physics model choice, and thus the variation in out-of-field dose estimates may be even larger than 25% when considering biological effectiveness.
Review of pMUTs for medical imaging: towards high frequency arrays
Authors: S Atheeth , Krishnan Kajoli , Arora Manish
Published: December 2022

pMUT (piezoelectric Micromachined Ultrasound Transducer) devices are an alternative that can overcome the limitations associated with conventional ultrasound transducers. pMUT’s are reported for many applications such as range-finding, biometrics, and ultrasound imaging. However, pulse-echo measurements from fabricated pMUT devices/arrays are not commonly reported in literature, a reason being lack of desirable performance either in transmit or receive mode of operation. There is also limited information about the design, fabrication and characterization of 2D-pMUT-arrays operating at high frequencies (>15 MHz) in water medium. In this paper we review ‘state-of-the-art’ for pMUT-array based medical ultrasound imaging, with a focus on their pulse-echo imaging capability. Over the next 3–5 years, we expect further improvement in piezoelectric thin film deposition techniques, on-chip integration of pre-amplification circuits and further miniaturization of pMUT devices, thus paving the way for development of pMUT-array based high frequency medical imaging systems.
Codetta: predicting the genetic code from nucleotide sequence
Authors: Shulgina Yekaterina , Eddy Sean R
Published: December 2022

Codetta is a Python program for predicting the genetic code table of an organism from nucleotide sequences. Codetta can analyze an arbitrary nucleotide sequence and needs no sequence annotation or taxonomic placement. The most likely amino acid decoding for each of the 64 codons is inferred from alignments of profile hidden Markov models of conserved proteins to the input sequence.

Availability and implementation

Codetta 2.0 is implemented as a Python 3 program for MacOS and Linux and is available from http://eddylab.org/software/codetta/codetta2.tar.gz and at http://github.com/kshulgina/codetta.

Supplementary information

Supplementary data are available at Bioinformatics online.
Non-Lactobacillus-Dominant and Polymicrobial Vaginal Microbiomes Are More Common in Younger South African Women and Predictive of Increased Risk of Human Immunodeficiency Virus Acquisition
Authors: Wang Yiran , Noël-Romas Laura , Perner Michelle , Knodel Samantha , Molatlhegi Refilwe , Hoger Sarah , Birse Kenzie , Zuend Christina Farr , McKinnon Lyle R , Burgener Adam D
Published: December 2022

Background

Adolescent girls and young women aged 15‒24 years in sub-Saharan Africa are at disproportionate risk of human immunodeficiency virus (HIV) infection. Given the known association between vaginal microbial dysbiosis and HIV susceptibility, we performed an age-stratified analysis of the vaginal microbiome in South African women and compared this to their risk of HIV acquisition.

Methods

Vaginal microbiome data were generated by mass spectrometry–based proteomic analysis of cervicovaginal lavages collected from participants (n = 688) in the Centre for the AIDS Programme of Research in South Africa (CAPRISA) 004 trial. Participants were grouped by age (18–19 years, n = 93; 20–24 years, n = 326; 25–41 years, n = 269).

Results

Four microbiome types were identified based on predominant taxa, including Lactobacillus crispatus (CST-LC, 12.2%), Lactobacillus iners (CST-LI, 43.6%), Gardnerella vaginalis (CST-GV, 26.6%), or polymicrobial (CST-PM, 15.1%). Women aged 18–19 and 20–24 years had increased CST-PM and a non-Lactobacillus-dominant microbiome compared to those 25–41 years (odds ratio [OR], 3.14 [95% confidence interval {CI}, 1.12–7.87], P = .017; OR, 2.81 [95% CI, 1.07–7.09], P = .038, respectively; and OR, 1.65 [95% CI, 1.02–2.65], P = .028; OR, 1.40 [95% CI, 1.01–1.95], P = .030, respectively). The HIV incidence rate of women with CST-PM microbiome was 7.19-fold higher compared to women with CST-LC (hazard ratio [HR], 7.19 [95% CI, 2.11–24.5], P = .00162), which was also consistent in women aged 20–24 years (HR, 4.90 [95% CI, 1.10–21.9], P = .0375).

Conclusions

Younger women were more likely to have a higher-risk polymicrobial microbiome suggesting that vaginal microbiota are contributing to increased HIV-1 susceptibility in this group.

Clinical Trials Registration

NCT00441298.
Epidemiology of Human Parainfluenza Virus Type 3 and Respiratory Syncytial Virus Infections in the Time of Coronavirus Disease 2019: Findings From a Household Cohort in Maryland
Authors: Hetrich Marissa K , Oliva Jennifer , Wanionek Kimberli , Knoll Maria Deloria , Lamore Matthew , Esteban Ignacio , Veguilla Vic , Dawood Fatimah S , Karron Ruth A ,   for the SARS-CoV-2 Epidemiology And Response in Children Study Team, Council-DiBitetto Christine , Gatto Milena , Quesada Maria Garcia , Ghasri Tina , Gormley Amanda , Herbert Kristi , Jordan Maria , Loehr Karen , Morsell Jason , Na Yu Bin , Mateo Jocelyn San , Schappell Elizabeth , Smith Khadija , Weadon Cathleen , Williams-Soro Paula , Woods Suzanne
Published: December 2022

Background

During the coronavirus disease 2019 (COVID-19) pandemic, human parainfluenza type 3 (HPIV-3) and respiratory syncytial virus (RSV) circulation increased as nonpharmaceutical interventions were relaxed. Using data from 175 households (n = 690 members) followed between November 2020 and October 2021, we characterized HPIV-3 and RSV epidemiology in children aged 0–4 years and their households.

Methods

Households with ≥1 child aged 0–4 years were enrolled; members collected weekly nasal swabs (NS) and additional NS with respiratory illnesses (RI). We tested NS from RI episodes in children aged 0–4 years for HPIV-3, RSV, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse-transcriptase polymerase chain reaction (RT-PCR). Among children with HPIV-3 or RSV infection, we tested contemporaneous NS from household members. We compared incidence rates (IRs) of RI with each virus during epidemic periods and identified household primary cases (the earliest detected household infection), and associated community exposures.

Results

41 of 175 (23.4%) households had individuals with HPIV-3 (n = 45) or RSV (n = 46) infections. Among children aged 0–4 years, RI IRs /1000 person-weeks were 8.7 [6.0, 12.2] for HPIV-3, 7.6 [4.8, 11.4] for RSV, and 1.9 [1.0, 3.5] for SARS-CoV-2. Children aged 0-4 years accounted for 35 of 36 primary HPIV-3 or RSV cases. Children attending childcare or preschool had higher odds of primary infection (odds ratio, 10.81; 95% confidence interval, 3.14–37.23).

Conclusions

Among children aged 0–4 years, RI IRs for HPIV-3 and RSV infection were 4-fold higher than for SARS-CoV-2 during epidemic periods. HPIV-3 and RSV were almost exclusively introduced into households by young children.
Estimating reproductive costs in marine mammal bioenergetic models: a review of current knowledge and data availability
Authors: McHuron Elizabeth A , Adamczak Stephanie , Costa Daniel P , Booth Cormac
Published: December 2022

Reproductive costs represent a significant proportion of a mammalian female's energy budget. Estimates of reproductive costs are needed for understanding how alterations to energy budgets, such as those from environmental variation or human activities, impact maternal body condition, vital rates and population dynamics. Such questions are increasingly important for marine mammals, as many populations are faced with rapidly changing and increasingly disturbed environments. Here we review the different energetic costs that marine mammals incur during gestation and lactation and how those costs are typically estimated in bioenergetic models. We compiled data availability on key model parameters for each species across all six marine mammal taxonomic groups (mysticetes, odontocetes, pinnipeds, sirenians, mustelids and ursids). Pinnipeds were the best-represented group regarding data availability, including estimates of milk intake, milk composition, lactation duration, birth mass, body composition at birth and growth. There were still considerable data gaps, particularly for polar species, and good data were only available across all parameters in 45% of pinniped species. Cetaceans and sirenians were comparatively data-poor, with some species having little or no data for any parameters, particularly beaked whales. Even for species with moderate data coverage, many parameter estimates were tentative or based on indirect approaches, necessitating reevaluation of these estimates. We discuss mechanisms and factors that affect maternal energy investment or prey requirements during reproduction, such as prey supplementation by offspring, metabolic compensation, environmental conditions and maternal characteristics. Filling the existing data gaps highlighted in this review, particularly for parameters that are influential on bioenergetic model outputs, will help refine reproductive costs estimated from bioenergetic models and better address how and when energy imbalances are likely to affect marine mammal populations.
Seismic source mapping by surface wave time reversal: application to the great 2004 Sumatra earthquake
Authors: Sharma Dhakal Apsara , Molinari Irene , Boschi Lapo
Published: December 2022

Different approaches to map seismic rupture in space and time often lead to incoherent results for the same event. Building on earlier work by our team, we ‘time-reverse’ and ‘backpropagate’ seismic surface wave recordings to study the focusing of the time-reversed field at the seismic source. Currently used source-imaging methods relying on seismic recordings neglect the information carried by surface waves, and mostly focus on the P-wave arrival alone. Our new method combines seismic time reversal approach with a surface wave ray-tracing algorithm based on a generalized spherical-harmonic parametrization of surface wave phase velocity, accounting for azimuthal anisotropy. It is applied to surface wave signal filtered within narrow-frequency bands, so that the inherently 3-D problem of simulating surface wave propagation is separated into a suite of 2-D problems, each of relatively limited computational cost. We validate our method through a number of synthetic tests, then apply it to the great 2004 Sumatra–Andaman earthquake, characterized by the extremely large extent of the ruptured fault. Many studies have estimated its rupture characteristics from seismological data (e.g. Lomax, Ni et al., Guilbert et al., Ishii et al., Krüger & Ohrnberger, Jaffe et al.) and geodetic data (e.g. Banerjee et al., Catherine et al., Vigny et al., Hashimoto et al., Bletery et al.). Applying our technique to recordings from only 89 stations of the Global Seismographic Network (GSN) and bandpass filtering the corresponding surface wave signal around 80-to-120, 50-to-110 and 40-to-90 s, we reproduce the findings of earlier studies, including in particular the northward direction of rupture propagation, its approximate spatial extent and duration, and the locations of the areas where most energy appears to be released.
Holographic realization of the prime number quantum potential
Authors: Cassettari Donatella , Mussardo Giuseppe , Trombettoni Andrea
Published: December 2022

We report the experimental realization of the prime number quantum potential VN(x), defined as the potential entering the single-particle Schrödinger Hamiltonian with eigenvalues given by the first N prime numbers. Using computer-generated holography, we create light intensity profiles suitable to optically trap ultracold atoms in these potentials for different N values. As a further application, we also implement a potential whose spectrum is given by the lucky numbers, a sequence of integers generated by a different sieve than the familiar Eratosthenes’s sieve used for the primes. Our results pave the way toward the realization of quantum potentials with arbitrary sequences of integers as energy levels and show, in perspective, the possibility to set up quantum systems for arithmetic manipulations or mathematical tests involving prime numbers.
Regulatory T cells and systemic vasculitis
Authors: Mirouse Adrien , Cacoub Patrice , Saadoun David
Published: December 2022

Purpose of the review

Emerging data suggest that regulatory T-cells (Treg) alterations play a major role in systemic vasculitis pathophysiology. We performed a systematic review of recent advances in the role of Treg and interleukin (IL)-10 in the pathogenesis and treatment of systemic vasculitis, including giant cell arteritis (GCA), Takayasu arteritis, Behçet's disease, antineutrophil cytoplasm antibodies (ANCA) associated vasculitis (AAV), and cryoglobulinemia associated vasculitis.

Recent findings

Emerging data suggest that Treg deficiencies are disease-specific, affecting distinct pathways in distinct vasculitides. Decreased peripheral blood frequencies of Treg are described in all vasculitis when compared to healthy donors. Altered Treg functions are reported in GCA, Takayasu arteritis, AAV, and Behçet's disease with different mechanisms proposed. Treatment with biologics, and sometimes other immunosuppressants, may restore Treg frequencies and/or immune activity with significant differences in active disease or disease in remission in several systemic vasculitis. IL-10 is elevated in GCA, AAV, cryoglobulinemia associated vasculitis. In Behçet's disease, IL-10 is decreased in peripheral blood and elevated in saliva. In Takayasu arteritis, IL-10 levels were essentially elevated in patients’ vessel wall. Several new therapeutic approaches targeting Treg and Il-10 (low dose IL-2, CAR Treg…) are developed to treat patients with systemic vasculitis.

Treg and IL-10 play a central role in the regulation of inflammation in vasculitis and new targeting approaches are emerging.
A Russian carol: impact and dependence on global equity markets during the Ukraine invasion
Authors: Ferrández-Serrano Victoria , Angosto-Fernández Pedro L.
Published: December 2022

Purpose

The authors present a study of the short-term impact of the Russian–Ukrainian war on global equity returns. The study aims to show that the conflict was priced into markets and whether the intensity of the impact depends on economic factors, such as dependence on gas, or/and political factors, such as belonging to the former Soviet power circle.

Design/methodology/approach

Using the event study and a sample of 77 capital markets, accounting for over 99% of global capitalisation, the authors apply a system of seemingly unrelated regressions to the daily returns of the indices, isolating the short-term effect on the markets and finally apply cross-sectional methods to help determine the size and variability of the impact.

Findings

The authors show that the impact is concentrated around day zero but is relevant in the days before and after. In addition, the authors show that being in the Soviet orbit and NATO simultaneously, as well as having high gas consumption and importing gas from Russia were key factors for investors.

Originality/value

This study is the first to try to discern whether the impact on stock markets caused by the war in Ukraine is due to purely economic factors, especially energy, or whether there is also a geopolitical component. Specifically, whether the countries closest to Russia are being more threatened by the fact that they are closer to Russia.
Indirect effects of personality on high‐intensity drinking: The role of drinking motives
Authors: Bachrach Rachel L. , Zhou Agnes , Kumar Lakshmi , Lyons Greta , Skrzynski Carillon J. , Creswell Kasey G.
Published: December 2022

Background

Researchers have long been interested in identifying risk factors for binge drinking behavior (4+/5+ drinks/occasion for females/males), but many studies have demonstrated that a substantial proportion of young adults are drinking at levels far beyond (often 2 to 3 times) the standard binge threshold. The consumption of such large quantities of alcohol, typically referred to as high‐intensity drinking (HID), can cause severe alcohol‐related problems, such as blackouts, unintended sexual experiences, and death. This study is the first to investigate whether personality is indirectly associated with the likelihood of HID via drinking motives in a large (N = 999) sample of underage young adult drinkers. We hypothesized that trait neuroticism would be indirectly associated with the likelihood of HID via coping motives and that extraversion would be indirectly associated with the likelihood of HID via social and enhancement motives.

Methods

To investigate these hypotheses, we used two archival data sets that recruited current underage (18‐ to 20‐year‐old) adult drinkers residing in the United States from online panel services. Participants completed self‐report survey items assessing constructs of interest. To investigate the role of drinking motives in the association between personality and HID, both the direct and indirect effects were calculated via three path analyses.

Results

Findings revealed that neuroticism was partially indirectly associated with the likelihood of HID via coping motives (b = 0.02, SE = 0.004, p < 0.01). In addition, extraversion was indirectly associated with the likelihood of HID via social (b = 0.031, SE = 0.002, p < 0.01) and enhancement motives (b = 0.01, SE = 0.002, p = 0.01).

Conclusions

These findings are an initial step in examining the interplay among personality traits, drinking motives, and HID in underage drinkers and point to the need for longitudinal studies assessing these associations.
Annual Research Review: Stability of psychopathology: lessons learned from longitudinal population surveys
Authors: Oldehinkel Albertine J. , Ormel Johan
Published: December 2022

Background

Psychopathology has been long recognized as a fluctuating process with various expressions over time, which can only be properly understood if we follow individuals and their social context from childhood up until adulthood. Longitudinal population‐based studies have yielded powerful data to analyze this process. However, the resulting publications have not been reflected upon with regard to (a) the homotypic and heterotypic stability of internalizing and externalizing problems and (b) how transactions between psychopathology and environmental factors shape its development.

Methods

In this narrative review, we primarily focused on population‐based studies that followed cohorts repeatedly from an early age (<18 years) onwards, across multiple stages of development, using statistical methods that permit inferences about within‐person bidirectional associations between internalizing and externalizing problems or psychopathology–environment transactions.

Results

There is robust evidence that mental health problems in childhood or adolescence predict psychiatric problems later in development. In terms of the broadband domains internalizing and externalizing problems, homotypic stability greatly exceeds heterotypic stability and transitions from purely internalizing to purely externalizing problems or vice versa are rare. Homotypic rank‐order stabilities seem to increase over time. Findings regarding transactions with environmental factors are less robust, due to widely varying research topics and designs, and a scarcity of studies that separated between‐person differences from within‐person changes. In general, however, the literature shows little consistent evidence for substantial mutual prospective influences between psychopathology and environmental factors.

Conclusions

Longitudinal surveys have strongly augmented insight into homotypic and heterotypic stability and change. Attempts to unravel the myriad of risk and protective factors that place individuals on particular pathways or deflect them from these pathways are still in a pioneering phase and have not yet generated robust findings. As a way forward, we propose to join forces and develop a common risk factor taxonomy.
Inhibition of the largemouth bass virus replication by piperine demonstrates potential application in aquaculture
Authors: Wang Mengmeng , Yang Bin , Ren Zongyi , Liu Jietao , Lu Chenwang , Jiang Haifeng , Ling Fei , Wang Gaoxue , Liu Tianqiang
Published: December 2022

Largemouth bass virus (LMBV) is a systemic viral pathogen that can cause high mortality rates in cultivated largemouth bass. However, no treatment is currently approved. Therapeutic strategies against LMBV infection are urgently needed. In this study, we investigated the antiviral activity of piperine against LMBV in vitro and in vivo. In vitro antiviral activity assay showed that 210.28 μM piperine significantly decreased LMBV major capsid protein (MCP) gene expression in epithelioma papulosum cyprinid (EPC) cells by a maximum inhibitory rate of >95%. Piperine treatment inhibited LMBV replication in a dose‐dependent manner, with the half‐maximal activity (IC50) of 34.61 μM. Moreover, piperine significantly decreased the viral titers and cytopathic effects (CPE), contributing to the protection of infected cells. With regard to the steps of piperine affecting the life cycle of viruses, piperine had a direct inactivating effect on LMBV. During the virus adsorption phase, piperine prevented the adsorption of LMBV to EPC cells. Furthermore, piperine played an antiviral role mainly in the later stages of viral infection (4–8 h). To further evaluate the antiviral activity of piperine against LMBV in vivo, largemouth bass as a model organism was carried out in relevant experiments. Intraperitoneal injection of piperine (25 mg/kg) effectively improved the survival rate of LMBV‐infected largemouth bass by 20%. In addition, RT‐qPCR results of viral replication in liver, spleen, kidney, gill and swim bladder tissues showed that piperine significantly inhibited LMBV replication in vivo, thus protecting largemouth bass from LMBV‐induced death. Together, our results suggested that piperine is a therapeutic and preventative agent against LMBV infection.
Systematic review and meta‐analysis on the association between chronic low back pain and cognitive function
Authors: Pereira Nery Ellen C. H. , Rocha Nelson P. , Cruz Vitor T. , Silva Anabela G.
Published: December 2022

This study aimed to identify and assess the evidence on the association between idiopathic chronic low back pain (LBP) and cognitive function in individuals with LBP. A secondary aim was to explore whether changes in cognitive function are associated with pain characteristics and psychological factors (eg, catastrophizing and fear of movement). Eleven studies were included in this systematic review, and four meta‐analyses were conducted. Low to very low‐quality evidence suggests impaired cognitive function in individuals with LBP compared to asymptomatic controls for problem solving (k = 5; d = 0.33; CI = 0.16–0.50; z = 3.85 p = 0.0001), speed of information processing (k = 5; d = 0.44; CI = 0.22–0.65; z = 4.02 p < 0.0001), working memory (k = 6; d = 0.50; CI = 0.34–0.66; z = 6.09 p < 0.0001), and delayed memory (k = 3; d = 0.34; CI = 0.07–0.6, z = 2.49 p = 0.02). The association between LBP intensity and psychological factors and cognitive function was inconclusive. More studies are needed to explore these associations and improve evidence in this field. The results of this study suggest that cognitive aspects should be considered during the rehabilitation process of patients with LBP and raise further questions, including whether individuals with LBP are at a greater risk of developing dementia or whether targeting cognitive function will increase the probability of success of LBP treatment. These questions should, also, be considered in future studies.
Horizontally acquired fungal killer protein genes affect cell development in mosses
Authors: Guan Yanlong , Ma Lan , Wang Qia , Zhao Jinjie , Wang Shuanghua , Wu Jinsong , Liu Yang , Sun Hang , Huang Jinling
Published: December 2022

The moss Physcomitrium patens is crucial for studying plant development and evolution. Although the P. patens genome includes genes acquired from bacteria, fungi and viruses, the functions and evolutionary significance of these acquired genes remain largely unclear. Killer protein 4 (KP4) is a toxin secreted by the phytopathogenic fungus Ustilago maydis that inhibits the growth of sensitive target strains by blocking their calcium uptake. Here, we show that KP4 genes in mosses were acquired from fungi through at least three independent events of horizontal gene transfer. Two paralogous copies of KP4 (PpKP4‐1 and PpKP4‐2) exist in P. patens. Knockout mutants ppkp4‐1 and ppkp4‐2 showed cell death at the protonemal stage, and ppkp4‐2 also exhibited defects in tip growth. We provide experimental evidence indicating that PpKP4‐1/2 affects P. patens protonemal cell development by mediating cytoplasmic calcium and that KP4 genes are functionally conserved between P. patens and fungi. The present study provides additional insights into the role of horizontal gene transfer in land plant development and evolution.