bluuebunny/crossref_metadata_2025 huggingface dataset:
Using deep learning to predict the East Asian summer monsoon
Authors: Tang Yuheng , Duan Anmin
Published: October 2021

Accurate prediction of the East Asian summer monsoon (EASM) is beneficial to billions of people’s production and lives. Here, a convolutional neural network (CNN) and transfer learning are used to predict the EASM. The results of the constructed CNN regression model show that the prediction of the CNN regression model is highly consistent with the reanalysis dataset, with a correlation coefficient of 0.78, which is higher than that of each of the current state-of-the-art dynamic models. The heat map method indicates that the robust precursor signals in the CNN regression model agree well with previous theoretical studies and can provide the quantitative contribution of different signals for EASM prediction. The CNN regression model can predict the EASM one year ahead with a confidence level above 95%. The above method can not only improve the prediction of the EASM but also help to identify the involved physical predictors.
Inorganic fertilizers efficiency with using the liquid organic fertilizer to increase the cabbage yield (Brassica oleracea var. capitata L.)
Authors: Marpaung A E , Karo B , Barus S
Published: October 2021

Using organic materials as fertilizer has contributed a lot to protecting the environment and the future of human life through sustainable agriculture. Local resources are used in such a way that synthetic nutrients can be reduced as low as possible. This study aims to determine the effect of liquid organic fertilizer (LOF) on cabbage yield with inorganic fertilizers' efficiency. The research was conducted in Berastagi experimental farm, Karo regency, with the soil type and altitude of 1,340 m asl, which began from July - September 2018. The design used was a randomized block design consisting of 16 treatments with three replication. The treatments tested were: A. Without inorganic fertilizer + LOF 1, B. 25% inorganic fertilizer + LOF 1, C. 50% inorganic fertilizer + LOF 1, D. 75% inorganic fertilizer + LOF 1, E. 100% inorganic fertilizer + LOF 1, F. Without inorganic fertilizer + LOF 2, G. 25% inorganic fertilizer + LOF 2, H. 50% inorganic fertilizer + LOF 2, I. 75% inorganic fertilizer + LOF 2, J. 100% Inorganic Fertilizer + LOF 2, K. Without inorganic fertilizers + LOF 3, L. 25% inorganic Fertilizer + LOF 3, M. 50% inorganic Fertilizer + LOF 3, N. 75% inorganic Fertilizer + LOF 3, O. 100% Inorganic Fertilizer + LOF 3, P. 100% Inorganic Fertilizer + without LOF (Control). The results showed that, in general, the application of liquid organic fertilizer for rabbit urine, fish fertilizer, and fish teillation could stimulate the growth and yield of cabbage better than inorganic fertilizers. Applicationthe liquid organic fertilizer can increase theheight growth of cabbage was 0.67 - 0.88%, plant diameter was 0.33 - 2.56%, crop weight per plant was 5.14 - 5.84%, production per plot was 2.96 – 9.78%, and the crop ratio of 3.36 - 10.84% compared to the use of inorganic fertilizers.
Green economic based on low-carbon development on small islands
Authors: Kastanya A , Suhendy C C V , Pattimahu D V , Iskar
Published: October 2021

Global warming and climate change are having an impact on human and the planet. This occurs worldwide due to an exploitative economy, which does not consider the degradation of natural resources and the environment. Damage to terrestrial ecosystems in small island areas has a direct impact on the destruction of marine ecosystems, such as coral reefs, seagrasses, and another biodiversity. The most current devastating impact is the emergence of the “Covid-19 Pandemic”, which shows that so far humans have adopted an individualistic way of life that ignores their environment. This analysis is carried out through a literature review of the research results and scientific discussions that have developed so far. The results of the study show that if the economy continues to run as it is now, the Earth will continue to be in crises such as floods, extreme weather, rising sea levels, food shortage, and outbreaks of more viruses. Changes in paradigm and human behaviour are needed, not only from the government as the main actor of development but also support from the entire community. Science and innovation that are currently developing a change in development towards the ecological-economy, environmental economics, which is currently known as the “Green Economy Model” is already covered by controlling global warming and climate change. The transformation from an Exploitative Economy to a Green Economy has developed in the concept of Low Carbon Development and Build Back Better as part of the Sustainable Development Goals (SDGs), which needs to be formed in an integrated manner as a concept for Sustainable Small Islands Development and bring welfare for the community.
Isolation and identification of fenobucarb degrading bacteria from Pangalengan farm land
Authors: Akhdiya A , Sanjaya R A , Wartono
Published: October 2021

The long term excessive use of pesticides can lead to their residues accumulation in the soils. Soil microbes were considered to convert the residues into harmless compounds, however the indigenous soil microbes having those beneficial properties are limited. Therefore this study aimed to isolate, select and identify the fenobucarb insecticide-degrading bacteria from agricultural soils. The soil samples were collected from the vegetable fields in Pangalengan, West Java, Indonesia. Isolation of the bacteria was conducted using Nitrate Mineral Salt Agar suplemented by 100 ppm of a fenobucarb. The bacteria isolates were selected based on its hypersensitive response, haemolytic activity, and its ability to degrade fenobucarb. The selected isolates was identified base on sequences of 16S rRNA gene. Twenty nine bacteria were isolated from four soil samples and 23 of the isolates were not potentially phytopathogenic and non haemolytic. The best three isolates that could degrade 94.2%, 94.5% and 95.47% fenobucarb residue are B41, B54 and B83 isolates, respectively. The 16S rDNA Sequence analysis showed that B41 and B83 isolates have 100% similarity to Bacillus thuringiensis MYBT 18426B54, while B54 isolate has 99% similarity to Bacillus luciferensis LMG 18422. These isolates are potential to be developed as a bioremediation agent.
Effort to reduce ammonia gas in the broiler chicken excreta with the addition of probiotic as substitute for antibiotic growth promoter
Authors: Mahardhika B P , Mutia R , Ridla M
Published: October 2021

This study has been carried out to evaluate the use of drinking water-soluble probiotics as an alternative to Zinc bacitracin Antibiotic Growth Promoter (AGP) in an effort to reduce the concentration of ammonia excreta as a result of increased feed digestibility. The probiotic used contains 2.0 × 107 CFU mL−1 Lactobacillus sp, 1.6 × 107 CFU mL−1 Bacillus sp, and 7.4 × 109 CFU mL−1 Streptomyces sp. The excreta sample was obtained from 15 male Lohmann strain broiler chickens aged 35 days from a total population of 300 chickens that had previously been reared since Day Old Chick. The chickens were distributed into three treatments and five replications in a metabolic cage with a size of 50 cm × 30 cm × 56 cm for three days. This study used Completely Randomized Design (CRD) with Analysis of Variance (ANOVA). The addition of probiotic significantly reduced (P <0.01) water content and ammonia concentration of broiler chicken excreta. The addition of drinking water-soluble probiotics significantly increased (P <0.01) the feed intake and feed digestibility of broiler chicken. The use of probiotics was better than Zinc bacitracin in reducing excreta ammonia concentration and feed digestibility.
Soybean varieties tolerance to intercropping with maize
Authors: Permanasari I , Sulistyaningsih E , Kurniasih B , Indradewa D
Published: October 2021

There is no available information in determining soybean varieties that shows tolerant when intercropped with maize. The objective of this study was to determine soybean varieties suitable for intercropping, based on changes in plant growth and yield when intercropped. The field experiment was conducted from October 2019 to February 2020 based on RCBD with 2 factors. The first factor was soybean with 16 national varieties. The second was cropping systems i.e., monoculture and intercropping. Morphology and yield data were observed and subsequently analysed based on performance difference (D) of each parameter between intercropping and monoculture. Tolerance level to cropping systems with maize was grouped based on the yield-based and selection index calculations. The results showed that different cropping systems affected morphological and yield parameters on 16 tested soybean varieties. Seven varieties i.e., Derap 1, Devon 1, Devon 2, Demas 1, Dena 1, Dena 2, and Wilis were grouped as tolerant to intercropping with maize. Among these, Derap 1 was the most tolerant variety.
Analysis of macro nutrient content in biofouling waste organic fertilizer pearl oyster (Pinctada maxima L.)
Authors: Nendissa J I , Makaruku M H , Tanasale V L , Kilkoda A K , Taribuka J
Published: October 2021

Biofouling development is a major problem in bilvave aquaculture around the world. The purpose of this study was to obtain macro nutrient analysis data for organic fertilizer from pearl oyster (Pinctada maxima L) biofouling waste. Where is the manufacture of solid organic fertilizer products that have quality equivalent to other commercial organic fertilizers by utilizing pearl oyster (Pinctada maxima L.) biofouling waste so that high quality solid organic fertilizers are produced which are in accordance with the Quality Standards for solid organic fertilizers and the Indonesian National Standard. Organic fertilizer from pearl oyster biofouling waste is obtained by using pearl oyster biofouling waste which is taken from the results of cleaning microorganisms attached to the pearl oyster shell area. Another major concern regarding biofouling is the potential for food competition caused by the attachment of the filter-feeder. Besides, the waste of biofouling pearl oysters is extracted and soaked in fresh water for one week at a time. Afterward, the pearl oyster biofouling waste is dried in the sun to dry, odorless, blackish brown in color. Analysis of macro nutrient content using Atomic Absorption Spectrophotometer and UV-Vis Spectrophotometer. The results of the analysis of macro nutrient content were Water Content (5.76%), C (14.48%), Organic Matter (24%), N-total (0.92%), P-total (0, 25%), K-total (1.02%), C/N ratio (15.72).
Breed availability analysis of local beef cattle in Seram Utara Timur Seti District Maluku Tengah Regency
Authors: Salamena J F , Rajab  , Papilaya B J , Sarfan R
Published: October 2021

This study aim were to analyze the potential availability of breeds for beef cattle development in Seram Utara Timur Seti District. The research method used was a desk study and survey method. Desk studies were conducted by utilizing relevant secondary data from various related agencies, as well as relevant research results. Meanwhile, surveys and direct observations in the field were carried out in the Animal Husbandry Production Center (KSP) areas, namely Wailoping, Kobisonta and Waitila Village. The variables observed included population structure and potential availability of beef cattle. The results showed that the proportion of the beef cattle population for the categories of calves, youth and adults was 23.18; 22.18 and 54.64% respectively. The sex ratio of male to female in all age categories is still below the normal ratio of 1 male to 5. Total breed growth (net increase) was 70 tails per year from the total population of beef cattle in Seram Utara Timur Seti District (13,032 tails). The total growth of beef cattle is still less than 1% (around 130 heads) of the total population, so it is necessary to pay attention for the development of the source area for beef cattle breeding in Seram Utara Timur Seti District.
Study of dryland cultivation farming technology to support sustainable food independence on small islands
Authors: Riry J , Mahulette A S , Tapotubun A M , Riry W A
Published: October 2021

The agricultural sector's strategic roles for economic growth, including, among others: providing food for the Indonesian population, earning the country's foreign exchange through exports, providing industrial raw materials, increasing employment and business opportunities, increasing regional revenues, and alleviating poverty. The Food and Agriculture Organization (FAO) stated that food self-sufficiency occurs when everyone in every moment can access food both physically and economically to meet their daily needs. Drylands have characteristics such as water shortage, erosion sensitivity, low land productivity, high variability in soil fertility, limited plant species, low adoption of advanced technology, minimal capital availability, and inadequate infrastructure. Small islands are islands ecologically separated from the mainland island, have clear physical boundaries, and are isolated from the parent island's habitats, so they are insular. Small islands usually have relatively small catchment areas, are vulnerable to global warming, sensitive to natural disasters, isolated and far from the main market, open to small-scale economic systems, have high population growth rates, have limited infrastructure and education, and limited skills of its inhabitants. Small islands have a high rate of land degradation that threatens the long-term sustainability of agriculture. Technologies that can be applied to dryland on small islands are conservation farming, LIESA system, Biointensive Gardening, Dusung, Agropasture, Sloping Agricultural Land Technology (SALT), Rounders type, No-tillage, and small island weed management. This paper is an ideal contribution to overcome the food problem in small islands that generally have drylands. It was presented at the National Seminar of the Indonesian Agronomy Association (PERAGI) in Bogor
Implementation study of Good Agricultural Practices (GAP) of Red Fruit (Pandanus conoideus Lamk.)
Authors: Makaruku M H , Wattimena A Y , Mahulette A S , Kembauw E
Published: October 2021

This study aims to determine and analyze the GAP components that have implemented by red fruit farmers. The method used in the study was a survey method of plant cultivation. The multistage random sampling method used to taking sampling sampling. The area selected for the study area uses the land ownership startification. Each village was randomly sampled as many as 10 farmers, the total number of which was 30 sampled farmers. The results showed that the farmers in the Taniwel District had not fully implemented the GAP guidelines in the cultivation of red fruit plants which included seeding methods, maintenance and post-harvest processing. This is due to the absence of outreach or counseling from the relevant Dinas regarding the GAP guidelines for red fruit plants.
Consumption pattern and hope food pattern in Salahutu District, Maluku Tengah Regency
Authors: Timisela N R , Girsang W , Tupamahu L
Published: October 2021

This study aims to analyze food consumption patterns, the hope food patterns, and the factors that influence household food consumption patterns. The research was located in Suli and Liang Villages, Central Maluku Regency. The location was determined purposively based on the 2017 Central Maluku Regency Food Security and Vulnerability Atlas (FSVA) results included in Priority 1 and 2 as Food Vulnerable Areas. The research sample was determined by simple random sampling using the Slovin formula with a total sample size of 87 households, 44 (Suli Village) and 43 (Liang Village). The research data were analyzed qualitatively and quantitatively. The results showed that the pattern of household food consumption in the two villages was lower than the ideal weight of food consumption, namely 870 g/capita/day, respectively 783.83 (Liang Village) and 709.81 (Suli Village). The score of the hope food pattern in Liang Village is 75, and Suli Village is 76.9. Analysis of the factors that influence household food consumption patterns in the two villages with a coefficient of determination of 51.56 (Liang Village) and 59.19 (Suli Village). The results of the t-test show that the factors that influence the pattern of household food consumption in Liang Village include income (X
1), the number of family members (X
2), and the education of housewife (X
4), while the factors that influence food consumption patterns Households in Suli Village include income (X
1), age of the housewife (X
3) and education of housewife (X
4).
Organic matter and mixed biofertilizer for plant growth and yield of shallot grown in fertile soil
Authors: Hindersah R , Kalay A M , Ngabalin I A , Jamlean M , Talahaturuson A
Published: October 2021

Nowadays, shallot is important horticultural crops in Maluku include in Tual City, Maluku Province. For ensuring the macronutrients level in soil and yield during shallot cultivation, fertilization composed of chemical, organic and bio fertilizer is needed. The objective of field experiment was to evaluate the effect of mixed biofertilizer integrated with organic matter on total nitrogen and available phosphorous in soil as well as shallot yield grown in Vertisols of Tual. The experiment was setup in randomized block design with four treatments of compost and chicken manure amendment with and without biofertilizer containing N-fixing bacteria and P-solubilizing. At the vegetative stage, consortia biofertilizer combined with either compost or chicken manure increased plant height and soil reaction but decreased the available phosphate (P) and didn't change nitrogen (N) total in soil. Chicken manure amendment combined with biofertilizer inoculation increased dry weight of shoots and bulbs even though didn't significantly differ with other treatments. Nonetheles, that treatment resulted in high yield of shallot bulbs up to 14 t/ha.
The feasibility of environmentally friendly and conventional shallot farming in Bantul Regency
Authors: Kamardiani D R , Fauzan M , Riansyah K S
Published: October 2021

This study analyses the differences in costs, profit, and feasibility of environmentally friendly and conventional shallot farming in Bantul Regency. Data were collected from 128 farmers taken by cluster sampling and analyzed quantitatively using profit analysis and R/C ratio. The results showed that the total production cost of environmentally friendly shallot farming was 12.29% higher than conventional shallot farming, but conventional shallot farming had a higher profit of 41.94%. Both environmentally friendly and conventional farming is feasible, but the R/C ratio of conventional shallot farming is higher by 0.7.
The impact of climate change on the resin productivity of dammar tree (Agathis alba) in Inamosol subdistrict, West Seram district, Maluku-Indonesia
Authors: Matinahoru J M
Published: October 2021

This research was aimed to determine the impact of climate change on the resin productivity of dammar tree. This research will be useful as data and information for farmers and government to maintain the resin of dammar tree to be optimal and sustainable in production. This research was conducted in Inamosol Sub-district, West Seram District, Maluku Indonesia, during September-October 2020. Village and farmer samples were determined by purposive sampling technique. The selected villages were Honitetu, Hukuanakota and Rambatu. Furthermore, from each village, It was ten farmers to select for interviews and filling the questionnaire. The results showed that the average resin production of farmers in 2019 was 904.2 kg/farmer, while in 2020 was 523.7 kg/farmer. This means that it occurred a decline in resin production in 2020 about 42.08 % for each farmer—the leading cause of the decreased production as climate change factors, namely rainfall, temperature and humidity. Based on climate data of West Seram District in 2019 indicated that rainfall has occurred during six months with an average temperature of 27 °C and relative humidity of 82 %. Meanwhile, in 2020 the rainfall occurs for nine months with an average temperature of 26.5 °C, and relative humidity of 85 %.
In-situ kuskus conservation strategy in Wakasihu Village, West Leihitu District, Central Maluku District
Authors: Th Latupapua Y , Tetelay F F , Soselisa F , Pattinasarany C K , Latupapua L , Sanduan A
Published: October 2021

Kuskus, a marsupial species belonging to the Phalangeridae family that is vulnerable in the IUCN Redlist, is one of the endemic animals whose survival is currently very concerning due to habitat destruction and poaching, so conservation activities need to be carried out immediately. This study aims to identify the characteristics of the habitat, type of feed, and in situ conservation strategies in the Wakasiu forest, Leihitu Barat sub-district, Central Maluku district. This research was conducted in October 2020. Habitat characteristics were identified using vegetation analysis, forage types were identified using direct and indirect observations, and insitu conservation strategies using SWOT analysis. The highest index of importance at the tree level in the line of observation is the type of gayam (lnocarpus fagifer) (20.19%), at the level of weaning is the langsat species (70.32%) the level of the pole type of brown (69.27%). The diversity level of plant species is high and the level of evenness of plant species is even. There are 24 types of plants recorded as potential for special feed. The in-situ conservation strategy that is carried out is planting the type of feed preferred by the specialists, so as to provide a stable feed availability during the successive fruiting period. Apart from that, the restriction of hunting for specialties is through written regulations and the imposition of sanctions.
Investigations of the properties of filaments generated in gas mixtures pumped by femtosecond laser pulses
Authors: Jing Chenrui , Wang Zhaohui , Qi Xiexing
Published: October 2021

In this paper, we compare the properties of filaments generated in a Ne–N2 mixture, pure N2, a Kr–N2 mixture, and a Xe–N2 mixture pumped by femtosecond laser pulses systematically. Due to different nonlinear refractive indices and ionization potentials of these noble gases, the clamped intensity and plasma density can be tuned in a certain range when small amounts of different noble gases are injected into pure N2. In addition, we also demonstrate that a higher proportion of noble gas and shorter incident pulse duration can have the benefit of manipulating the plasma density on a relatively larger scale.
Wavefronts, light rays and caustic associated with the refraction of a plane wavefront by a conospherical lens
Authors: Galindo-Rodríguez José Israel , Silva-Ortigoza Gilberto
Published: October 2021

The aim of the present work is to introduce a lens whose faces are a conical surface and a spherical surface. We illuminate this lens by a plane wavefront and its associated refracted wavefronts, light rays and caustic are computed. We find that the caustic region has two branches and can be virtual, real or one part virtual and the other real, depending on the values of the parameters characterizing the lens. Furthermore, we present a particular example where one of the branches of the caustic region is constituted by two segments of a line, one part is real and the other one virtual. The second branch is a two-dimensional surface with a singularity of the cusp ridge type such that its Gaussian curvature is different from zero. It is important to remark that for this example, the two branches of the caustic are disconnected. Because of this property and the result obtained by Berry and Balazs on the relationship between the acceleration of an Airy beam and the curvature of its corresponding caustic, we believe that using this optical element one could generate a scalar optical accelerating beam in the region where the caustic is a two-dimensional surface of revolution, and at the same time a scalar optical beam with similar properties to the Bessel beam of zero order in the region were the real caustic is a segment of a line along the optical axis.
On the relation between visual quality and landscape characteristics: a case study application to the waterfront linear parks in Shenyang, China
Authors: Sun Dong , Li Qingyu , Gao Weijun , Huang Gonghu , Tang Ning , Lyu Mei , Yu Yiqing
Published: October 2021

In recent years, Chinese cities have begun to pay attention to their rivers, and a large number of waterfront linear parks have been built in the riverside areas, so that the public can easily enjoy their landscape and entertainment functions. In this study, the visual quality of the waterfront trails and the greenbelt trails in the Waterfront linear Park around the Hunhe river in Shenyang was evaluated the basis of the Scenic Beauty Estimation Method and Semantic Differential Method, and the principal components of the landscape characteristics were extracted and a regression model of the visual quality and the landscape characteristics was established. Results show that the natural feature and the formal feature have a positive influence on the visual quality in waterfront linear parks, and the man-made feature has a negative impact on the visual quality. The six landscape characteristics are Sense of seclusion, ecology, intactness, uniqueness, unity and vitality, which are the main factors which affect the visual quality. This study puts forward improvement measures for the waterfront trails and the greenbelt trails, and the results can be applied to the planning, construction, and management of waterfront linear parks.
Type 2 Diabetes–Prevention Diet and All-Cause and Cause-Specific Mortality: A Prospective Study
Authors: Wang Chun-Rui , Hu Tian-Yang , Hao Fa-Bao , Chen Nan , Peng Yang , Wu Jing-Jing , Yang Peng-Fei , Zhong Guo-Chao
Published: October 2021

We aimed to examine whether type 2 diabetes–prevention diet, a dietary pattern previously developed for reducing type 2 diabetes risk, was associated with mortality in a US population. A population-based cohort of 86,633 subjects was identified from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (1993–2015). Dietary information was collected with a food frequency questionnaire. A dietary diabetes risk-reduction score was calculated to reflect adherence to this dietary pattern, with higher scores representing better adherence. Hazard ratios (HRs) and absolute risk differences (ARDs) in mortality rates per 10,000 person-years were calculated. After a mean follow-up of 13.6 years, 17,532 all-cause deaths were observed. Participants with the highest versus the lowest quintiles of dietary diabetes risk-reduction score were observed to have decreased risks of death from all causes (HR = 0.76, 95% CI: 0.72, 0.80; ARD: −81.94, 95% CI: −93.76, −71.12), cardiovascular disease (HR = 0.73, 95% CI: 0.66, 0.81; ARD: −17.82, 95% CI: −24.81, −11.30), and cancer (HR = 0.85, 95% CI: 0.78, 0.94; ARD: −9.92, 95% CI: −15.86, −3.59), which were modified by sex, smoking status, or alcohol consumption in subgroup analyses (P for interaction < 0.05 for all). In conclusion, a type 2 diabetes–prevention diet confers reduced risks of death from all causes, cardiovascular disease, and cancer in this US population.
The Romance of Consequentiality
Authors: James David
Published: October 2021

Criticism has had a long-standing love affair with the prospect of its own real-world impact. An enchantment with the notion that literary-critical acts might not only change minds but also challenge political structures unites professional readers of all dispositions and allegiances, despite the climate of ideological friction and internecine dispute that has emerged from vociferous method debates in the past decade. Enduring, seductive, deeply consoling—this romance of consequentiality both supplies and reinforces criticism’s ongoing sense of self-importance, becoming a rich resource for sustaining our field’s dreams of social agency. This essay reflects on how that romance is at once instantiated and contested across this special issue, identifying its principal registers in critics’ defiance, longing, and self-conscious aggrandizement. Literary studies’ desire to leave some sort of material footprint has only been intensified by current pressures on the humanities to withstand institutional disinvestment and populist ridicule, on the one hand, while also interpreting and opposing systemically magnified forms of injustice, on the other. A certain baseline level of disciplinary faith is therefore impossible to ignore in these essays—including a faith in the possibility that criticism could still influence constituencies beyond those with whom, in solidarity, it already comfortably converses.
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools
Authors: Pockrandt Christopher , Steinegger Martin , Salzberg Steven L
Published: October 2021

PhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments (MSAs). It can score alignments or produce browser tracks for entire genomes in the wig file format. Additionally, PhyloCSF++ annotates coding sequences in GFF/GTF files using precomputed tracks or computes and scores MSAs on the fly with MMseqs2.

Availability and implementation

PhyloCSF++ is released under the AGPLv3 license. Binaries and source code are available at https://github.com/cpockrandt/PhyloCSFpp. The software can be installed through bioconda. A variety of tracks can be accessed through ftp://ftp.ccb.jhu.edu/pub/software/phylocsfpp/.
Deepfakes and Digitally Altered Imagery Abuse: A Cross-Country Exploration of an Emerging form of Image-Based Sexual Abuse
Authors: Flynn Asher , Powell Anastasia , Scott Adrian J , Cama Elena
Published: October 2021

Deepfake and digitally altered nude and sexual imagery is a serious and harmful emerging form of image-based sexual abuse (IBSA). This article reports on a multi-methods and cross-country study of IBSA across the United Kingdom, New Zealand and Australia, with a specific focus on the creation, distribution and threat to distribute deepfake and digitally altered imagery. Our findings suggest this abuse involves poly-victimization and poly-perpetration, and is disproportionately experienced and engaged in by those with mobility and/or communication assistance needs, members of the LGB+ community, males, young people and racial minorities (perpetration only). In this article, we discuss the pervasiveness and harms of deepfake and digitally altered imagery abuse, as well as challenges in legal responses, policing and prevention.
Minimising carbon and financial costs of steam sterilisation and packaging of reusable surgical instruments
Authors: Rizan Chantelle , Lillywhite Rob , Reed Malcolm , Bhutta Mahmood F
Published: October 2021

Background

The aim of this study was to estimate the carbon footprint and financial cost of decontaminating (steam sterilization) and packaging reusable surgical instruments, indicating how that burden might be reduced, enabling surgeons to drive action towards net-zero-carbon surgery.

Methods

Carbon footprints were estimated using activity data and prospective machine-loading audit data at a typical UK in-hospital sterilization unit, with instruments wrapped individually in flexible pouches, or prepared as sets housed in single-use tray wraps or reusable rigid containers. Modelling was used to determine the impact of alternative machine loading, opening instruments during the operation, streamlining sets, use of alternative energy sources for decontamination, and alternative waste streams.

Results

The carbon footprint of decontaminating and packaging instruments was lowest when instruments were part of sets (66–77 g CO2e per instrument), with a two- to three-fold increase when instruments were wrapped individually (189 g CO2e per instrument). Where 10 or fewer instruments were required for the operation, obtaining individually wrapped items was preferable to opening another set. The carbon footprint was determined significantly by machine loading and the number of instruments per machine slot. Carbon and financial costs increased with streamlining sets. High-temperature incineration of waste increased the carbon footprint of single-use packaging by 33–55 per cent, whereas recycling reduced this by 6–10 per cent. The absolute carbon footprint was dependent on the energy source used, but this did not alter the optimal processes to minimize that footprint.

Conclusion

Carbon and financial savings can be made by preparing instruments as part of sets, integrating individually wrapped instruments into sets rather than streamlining them, efficient machine loading, and using low-carbon energy sources alongside recycling.
Leveraging machine learning predictive biomarkers to augment the statistical power of clinical trials with baseline magnetic resonance imaging
Authors: Lou Carolyn , Habes Mohamad , Illenberger Nicholas A , Ezzati Ali , Lipton Richard B , Shaw Pamela A , Stephens-Shields Alisa J , Akbari Hamed , Doshi Jimit , Davatzikos Christos , Shinohara Russell T
Published: October 2021

A key factor in designing randomized clinical trials is the sample size required to achieve a particular level of power to detect the benefit of a treatment. Sample size calculations depend upon the expected benefits of a treatment (effect size), the accuracy of measurement of the primary outcome, and the level of power specified by the investigators. In this study, we show that radiomic models, which leverage complex brain MRI patterns and machine learning, can be utilized in clinical trials with protocols that incorporate baseline MR imaging to significantly increase statistical power to detect treatment effects. Akin to the historical control paradigm, we propose to utilize a radiomic prediction model to generate a pseudo-control sample for each individual in the trial of interest. Because the variability of expected outcome across patients can mask our ability to detect treatment effects, we can increase the power to detect a treatment effect in a clinical trial by reducing that variability through using radiomic predictors as surrogates. We illustrate this method with simulations based on data from two cohorts in different neurologic diseases, Alzheimer’s disease and glioblastoma multiforme. We present sample size requirements across a range of effect sizes using conventional analysis and models that include a radiomic predictor. For our Alzheimer’s disease cohort, at an effect size of 0.35, total sample size requirements for 80% power declined from 246 to 212 for the endpoint cognitive decline. For our glioblastoma multiforme cohort, at an effect size of 1.65 with the endpoint survival time, total sample size requirements declined from 128 to 74. This methodology can decrease the required sample sizes by as much as 50%, depending on the strength of the radiomic predictor. The power of this method grows with increased accuracy of radiomic prediction, and furthermore, this method is most helpful when treatment effect sizes are small. Neuroimaging biomarkers are a powerful and increasingly common suite of tools that are, in many cases, highly predictive of disease outcomes. Here, we explore the possibility of using MRI-based radiomic biomarkers for the purpose of improving statistical power in clinical trials in the contexts of brain cancer and prodromal Alzheimer’s disease. These methods can be applied to a broad range of neurologic diseases using a broad range of predictors of outcome to make clinical trials more efficient.
The molecular makeup of peripheral and central baroreceptors: stretching a role for Transient Receptor Potential (TRP), Epithelial Sodium Channel (ENaC), Acid Sensing Ion Channel (ASIC), and Piezo channels
Authors: Yang Hannah , Tenorio Lopes Luana , Barioni Nicole O , Roeske Jamie , Incognito Anthony V , Baker Jacquie , Raj Satish R , Wilson Richard J A
Published: October 2021

The autonomic nervous system maintains homeostasis of cardiovascular, respiratory, gastrointestinal, urinary, immune, and thermoregulatory function. Homeostasis involves a variety of feedback mechanisms involving peripheral afferents, many of which contain molecular receptors sensitive to mechanical deformation, termed mechanosensors. Here, we focus on the molecular identity of mechanosensors involved in the baroreflex control of the cardiovascular system. Located within the walls of the aortic arch and carotid sinuses, and/or astrocytes in the brain, these mechanosensors are essential for the rapid moment-to-moment feedback regulation of blood pressure (BP). Growing evidence suggests that these mechanosensors form a co-existing system of peripheral and central baroreflexes. Despite the importance of these molecules in cardiovascular disease and decades of research, their precise molecular identity remains elusive. The uncertainty surrounding the identity of these mechanosensors presents a major challenge in understanding basic baroreceptor function and has hindered the development of novel therapeutic targets for conditions with known arterial baroreflex impairments. Therefore, the purpose of this review is to (i) provide a brief overview of arterial and central baroreflex control of BP, (ii) review classes of ion channels currently proposed as the baroreflex mechanosensor, namely Transient Receptor Potential (TRP), Epithelial Sodium Channel (ENaC), Acid Sensing Ion Channel (ASIC), and Piezo, along with additional molecular candidates that serve mechanotransduction in other organ systems, and (iii) summarize the potential clinical implications of impaired baroreceptor function in the pathophysiology of cardiovascular disease.
Cryoballoon vs. radiofrequency catheter ablation: insights from NOrwegian randomized study of PERSistent Atrial Fibrillation (NO-PERSAF study)
Authors: Shi Li-Bin , Rossvoll Ole , Tande Pål , Schuster Peter , Solheim Eivind , Chen Jian
Published: October 2021

Aims

Pulmonary vein isolation (PVI) is still regarded as a cornerstone for treatment of persistent atrial fibrillation (AF). This study evaluated the effectiveness of PVI performed with cryoballoon ablation (CBA) in comparison with radiofrequency ablation (RFA) in patients with persistent AF.

Methods and results 

A total of 101 patients with symptomatic persistent AF were enrolled and randomized (1:1) to CBA or RFA groups and followed up for 12 months. The primary endpoint was any documented recurrent atrial tachyarrhythmia (ATA) lasting longer than 30 s following a 3-month blanking period. Secondary endpoints were procedure-related complications, procedure and ablation duration, and fluoroscopy time. The ATA-free survival curves were estimated by Kaplan–Meier method and analysed by the log-rank test. According to intention-to-treat analysis, freedom from ATA was achieved in 36 out of 52 patients in the CBA group and 30 out of 49 patients in the RFA group (69.2% vs. 61.2%, P = 0.393). No difference in AF recurrence was found between the two groups (27.5% in CBA vs. 38.0% in RFA, P = 0.258), and less atrial flutter recurrence was documented in the CBA group compared with the RFA group (3.9% vs. 18.0%, P = 0.020). The procedure and ablation duration were significantly shorter in the CBA group (160 ± 31 vs. 197 ± 38 min, P < 0.0001; 36.7 ± 9.5 vs. 55.3 ± 16.7 min, P < 0.0001). There was no difference regarding fluoroscopy time (21.5 ± 7.8 vs. 23.4 ± 11.2 min, P > 0.05).

Conclusion 

Compared with RFA, PVI performed by CBA led to shorter procedure and ablation duration, with less atrial flutter recurrence and similar freedom from ATA at 12-month follow-up.
1588, the first ministerial revolution in France or the King in check
Authors: Fontvieille Damien
Published: October 2021

In 1588, Henri III dismissed his secrétaires d’État, chancelier, surintendant des finances and intendants. This first ministerial revolution provoked much surprise in France as the men who occupied these offices had been in power for a long time, were very experienced and seemed, to many, to have the king’s favour. This fall from grace raised many questions, the event being seen, for example, as an expression of the king’s desire to retake control of his kingdom or as the result of political differences between the monarch and his ministers. This article reconsiders the causes of this loss of favour from the point of view of the secrétaires d’État in order to show how this event revealed the new position they had acquired within the monarchical government. As the secrétaires foiled the king’s projects, examining their new role is, indeed, a way to put the impact of this fall from grace into perspective.
Bacterial adaptation by a transposition burst of an invading IS element
Authors: Miller Scott R , Abresch Heidi E , Ulrich Nikea J , Sano Emiko B , Demaree Andrew H , Oman Andrew R , Garber Arkadiy I
Published: October 2021

The general importance of transposable elements (TEs) for adaptive evolution remains unclear. This in part reflects a poor understanding of the role of TEs for adaptation in non-model systems. Here, we investigated whether insertion sequence (IS) elements are a major source of beneficial mutations during 400 generations of laboratory evolution of the cyanobacterium Acaryochloris marina strain CCMEE 5410, which has experienced a recent or on-going IS element expansion and has among the highest transposase gene contents for a bacterial genome. Most mutations detected in the eight independent experimental populations were IS transposition events. Surprisingly, however, the majority of these involved the copy-and-paste activity of only a single copy of an unclassified element (ISAm1) that has recently invaded the strain CCMEE 5410 genome. ISAm1 transposition was largely responsible for the highly repeatable evolutionary dynamics observed among populations. Notably, this included mutations in multiple targets involved in the acquisition of inorganic carbon for photosynthesis that were exclusively due to ISAm1 activity. These mutations were associated with an increase in linear growth rate under conditions of reduced carbon availability but did not appear to impact fitness when carbon was readily available. Our study reveals that the activity of a single transposase can fuel adaptation for at least several hundred generations but may also potentially limit the rate of adaptation through clonal interference.
Azimuthal anisotropy from eikonal tomography: example from ambient-noise measurements in the AlpArray network
Authors: Kästle E D , Molinari I , Boschi L , Kissling E ,   and the AlpArray Working Group
Published: October 2021

Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150 000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wave fronts that affect the phase traveltime measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the traveltime field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at mid-crustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E–W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
A large animal model of RDH5-associated retinopathy recapitulates important features of the human phenotype
Authors: Occelli Laurence M , Daruwalla Anahita , De Silva Samantha R , Winkler Paige A , Sun Kelian , Pasmanter Nathaniel , Minella Andrea , Querubin Janice , Lyons Leslie A ,   99 Lives Consortium, Robson Anthony G , Heon Elise , Michaelides Michel , Webster Andrew R , Palczewski Krzysztof , Vincent Ajoy , Mahroo Omar A , Kiser Philip D , Petersen-Jones Simon M
Published: October 2021

Pathogenic variants in retinol dehydrogenase 5 (RDH5) attenuate supply of 11-cis-retinal to photoreceptors leading to a range of clinical phenotypes including night blindness because of markedly slowed rod dark adaptation and in some patients, macular atrophy. Current animal models (such as Rdh5−/− mice) fail to recapitulate the functional or degenerative phenotype. Addressing this need for a relevant animal model we present a new domestic cat model with a loss-of-function missense mutation in RDH5 (c.542G > T; p.Gly181Val). As with patients, affected cats have a marked delay in recovery of dark adaptation. In addition, the cats develop a degeneration of the area centralis (equivalent to the human macula). This recapitulates the development of macular atrophy that is reported in a subset of patients with RDH5 mutations and is shown in this paper in seven patients with biallelic RDH5 mutations. There is notable variability in the age at onset of the area centralis changes in the cat, with most developing changes as juveniles but some not showing changes over the first few years of age. There is similar variability in development of macular atrophy in patients and while age is a risk factor, it is hypothesized that genetic modifying loci influence disease severity, and we suspect the same is true in the cat model. This novel cat model provides opportunities to improve molecular understanding of macular atrophy and test therapeutic interventions for RDH5-associated retinopathies.
Cwc27, associated with retinal degeneration, functions as a splicing factorin vivo
Authors: Bertrand Renae Elaine , Wang Jun , Li Yumei , Cheng Xuesen , Wang Keqing , Stoilov Peter , Chen Rui
Published: October 2021

Previous in vitro studies indicate that CWC27 functions as a splicing factor in the Bact spliceosome complex, interacting with CWC22 to form a landing platform for eIF4A3, a core component of the exon junction complex. However, the function of CWC27 as a splicing factor has not been validated in any in vivo systems. CWC27 variants have been shown to cause autosomal recessive retinal degeneration, in both syndromic and non-syndromic forms. The Cwc27K338fs/K338fs mouse model was shown to have significant retinal dysfunction and degeneration by 6 months of age. In this report, we have taken advantage of the Cwc27K338fs/K338fs mouse model to show that Cwc27 is involved in splicing in vivo in the context of the retina. Bulk RNA and single cell RNA-sequencing of the mouse retina showed that there were gene expression and splicing pattern changes, including alternative splice site usage and intron retention. Positive staining for CHOP suggests that ER stress may be activated in response to the splicing pattern changes and is a likely contributor to the disease mechanism. Our results provide the first evidence that CWC27 functions as a splicing factor in an in vivo context. The splicing defects and gene expression changes observed in the Cwc27K338fs/K338fs mouse retina provide insight to the potential disease mechanisms, paving the way for targeted therapeutic development.