bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermo-mechanical limits of a magnetically driven fast-ion loss detector in the ASDEX Upgrade tokamak
Authors: Hidalgo-Salaverri J. , Gonzalez-Martin J. , Ayllon-Guerola J. , Garcia-Munoz M. , Sieglin B. , Galdon-Quiroga J. , Silvagni D. , Viezzer E. , Rueda-Rueda J. , Lunt T. , Herrmann A.
Published: February 2022

A real-time control system is being developed for a magnetically driven Fast-Ion Loss Detector (FILD) at the ASDEX Upgrade tokamak. The insertion of the diagnostic head will be adjusted in real-time to react to changes in the graphite head temperature, plasma position and appearance of MHD instabilities. The graphite probe head of the detector is exposed to an intense heat flux (located ∼3–5 cm from separatrix). The control algorithm performance is constrained by: the graphite head sublimation temperature, the ultimate stress limit, the reaction time of the controller and the retraction time. In this work, the temperature and thermal induced stress distribution on the probe head are assessed to determine what temperature-related magnitude is the limiting factor. The heat flux at the probe head has been estimated using the time-averaged parallel heat flux measured at the divertor target via infrared thermography. A field line tracing algorithm determines which regions of the probe head receives a weighted heat flux due to shadowing (self-induced or from other structures) and the incidence angle of the field lines. A finite element model is used to simulate the temporal evolution of the graphite head temperature and to obtain the induced thermal stress. The temperature spatial distribution at the probe head is validated against measurements of the probe head for different FILD systems showing a good agreement. These measurements have been obtained from visible cameras with an infrared filter. The model concludes that the maximum stress (∼100 MPa) does not overcome the graphite mechanical limit (170 MPa) and that the probe head is not affected by fatigue. Therefore, the graphite sublimation temperature (2000 °C) is set as the limiting factor of the new control system.
Scintillation characteristics of a NaI(Tl) crystal at low-temperature with silicon photomultiplier
Authors: Lee H.Y. , Jeon J.A. , Kim K.W. , Kim W.K. , Lee H.S. , Lee M.H.
Published: February 2022

The scintillation characteristics of a thallium-doped sodium
iodide (NaI(Tl)) crystal with dimensions of
0.6 cm× 0.6 cm× 2 cm were studied by
attaching a silicon photomultiplier (SiPM) directly to the crystal
over a temperature range of 93–300 K. The scintillation light
output and decay time were measured by irradiating 59.54 keV
γ-rays with a 241Am source. We observed an
approximately 20% increase in the light yield at 230 K compared
with that at room temperature. Under these conditions, NaI(Tl)
crystals with SiPM readout can be suitable for future dark matter
search detectors.
Intensification of fire regimes and forest loss in the Território Indígena do Xingu
Authors: Silvério Divino V , Oliveira Robson Santana , Flores Bernardo Monteiro , Brando Paulo M , Almada Hellen Kezia , Furtado Marco Túlio , Moreira Fabio Garcia , Heckenberger Michael , Ono Katia Yukari , Macedo Marcia N
Published: February 2022

The contemporary fire regime of southern Amazonian forests has been dominated by interactions between droughts and sources of fire ignition associated with deforestation and slash-and-burn agriculture. Until recently, wildfires have been concentrated mostly on private properties, with protected areas functioning as large-scale firebreaks along the Amazon’s agricultural frontier. However, as the climate changes, protected forests have become increasingly flammable. Here, we have quantified forest degradation in the Território Indígena do Xingu (TIX), an iconic area of 2.8 million hectares where over 6000 people from 16 different ethnic Indigenous groups live across 100 villages. Our main hypothesis was that forest degradation, defined here as areas with lower canopy cover, inside the TIX is increasing due to pervasive sources of fire ignition, more frequent extreme drought events, and changing slash-and-burn agricultural practices. Between 2001 and 2020, nearly 189 000 hectares (∼7%) of the TIX became degraded by recurrent drought and fire events that were the main factors driving forest degradation, particularly in seasonally flooded forests. After three fire events, the probability of forest loss was higher in seasonally flooded areas (63%) compared to upland areas (41%). Given the same fire frequency, areas that have not suffered with extreme droughts showed a 24% lower probability of forest loss compared to areas that experienced three drought events. Distance from villages and human density also had a marked effect on forest cover loss, which was generally higher in areas close to the largest villages. In one of the most culturally diverse Indigenous lands of the Amazon, in a landscape highly threatened by deforestation, our findings demonstrate that climate change may have already exceeded the conditions to which the system has adapted.
New possibilities of using vegetable raw materials in the technology of fermented milk products: review
Authors: Khrundin D , Ponomarev V , Yunusov E
Published: February 2022

The analysis, systematization and updating of information in the field of production of fermented milk products was carried out. The range of modern fermented milk products and their characteristics is given. The main trends in the development of the market of fermented milk products related to changes in consumer demand, the emergence of new directions in nutrition, the achievements of science and technology in the food industry are considered. The prospects of using “traditional” vegetable raw materials in the production of new food products have been studied.Processing of this raw material by biotechnology methods will increase the efficiency of its use. This will increase the degree of processing of raw materials, reduce waste and harmful emissions. This will contribute to improving the environmental situation.
Effect of foliar nutrients application to the growth and yield of Physalis peruviana and Physalis alkekengi
Authors: Sholehah Diana Nurus , Ermavitalini Dini , Khasanah Miratul , Utami Edy Setiti Wida , Purnobasuki Hery
Published: February 2022

Physalis Sp. is a potential medicinal plant and functional food. The use of appropriate nutrients can gain optimal plant growth and productivity. This study aimed to determine the macro and micronutrients that can provide optimal growth and yield of Physalis sp. This research was conducted at a greenhouse in Bangkalan Madura. A factorial randomized block design with four replications was used in this study. The first factor was the species of Physalis Sp., namely P. peruviana and P. alkekengi. The second factor is nutrition at four levels: a spray of water only as control; foliar application of macronutrients at a dose of 2 g/L; foliar application of micronutrients at a dose of 0,125 g/L; foliar Application of a combination of macronutrients 1 g/L and micronutrients 0,0625 g/L. The data obtained were analyzed using analysis of variance (ANOVA) followed by Least Significant Difference (LSD) at the 5 % level. Nutrition significantly affected growth (plant height, stem diameter, and number of leaves) and yield (number of fruit). The interaction between treatments occurred in the number of fruits. Micronutrients gave the highest number of fruit, both species of Physalis sp.
Farming Support Systems for Smallholders Rubber Production in Jambi, Indonesia
Authors: Yardha  , Izhar L , Salwati
Published: February 2022

Rubber is one of the important agricultural commodities in Jambi, Sumatra, Indonesia. However, in developing rubber, especially smallholder plantations, there are still many obstacles existence. One of the efforts to overcome these problems is through the adoption of location-specific technological innovations. This paper described the efforts to introduce and disseminate local-specific rubber technology innovations in Jambi. Activities were carried out in several farmers’ plantations for several years (from 2010 to 2018). Numerous activities were applied in farmer fields such as assisting disease (JAP) control fertilization technology, training (SL-JAP) in replanting program, reducing dirty product contain (KKK)<55%, directing farmers to produce wind sheets and clean rubber products, increasing the role of farmer groups to partner with the private sector. The results showed that through mentoring and the introduction of site-specific technology: the average rubber productivity at the farmer level ranged from 1-1.2 tonnes/ha/year, in terms of the potential production can be reached up to 1.5-2 tonnes/ha/year, replanting, seeding, and improvement of seed quality, balanced fertilization recommendation, tapping shoot pattern and maintenance, and handling of harvest and post-harvest rubber products. The dissemination technologies that have been carried out by the Jambi AIAT as above will be described further in this paper.
The study of household willingness to pay for solid waste management at Bekasi and Tangerang cities
Authors: Ismail Y , Juwono R , Hadikusuma N
Published: February 2022

Organic waste is the dominant and the biggest waste from household. Actually, organic waste is degradable waste, but in city not enough place could used to dump the organic waste. The aim of this paper are to know the willingness to pay of household for solid waste facilities at Bekasi and Tangerang cities, to compare household retribution rate and willingness to pay among household in residential at Bekasi, and Tangerang cities, and to analyse the effort to improve the solid waste management at Bekasi and Tangerang cities. The quantitative method used in this research, and collect data by run the survey used questionnaire. Sampling method used purposively with criteria which are housewife live at residential in Bekasi or Tangerang city and manage their household solid waste by themselves. Data analysis method used descriptive and statistical t test. The average of household willingness to pay for solid waste facilities in Bekasi is Rp 33,814,- and at Tangerang is Rp 34,117,. From t test find that there are significance difference between retribution rate and willingness to pay of household at that two cities. Comparing the household willingness to pay among the household in Bekasi, and Tangerang cities not in amount of money paid, but more about the facilities that household got. The more good facilities offer, more willingness to pay from the household.
Effect of Biofertilizer Formulation with Addition of Consortium of Microbes and Biosurfactant DEA Palm Olein to Growth of Cacao (Theobroma cacao) Seedling
Authors: Nurmayulis  , Eris F R , Maida H , Hastuti D , Denny Y R
Published: February 2022

This study was to examine the response of biofertilizer formulation with the addition of consortium of microbes and biosurfactant DEA palm olein to the growth of cacao seedling. This research used randomized block design in factorial with two factors. The first factor was a biofertilizer formulation with addition of consortium of microbes consisting of seven levels: control; 2.5x107; 5x107; 7.5x107; 10x107; 12.5x107; and 15x107 CFU/mL. The second factor was the addition of biosurfactant DEA palm olein consisting of two levels, which are with and without the biosurfactant DEA palm olein. The result showed that the biofertilizer formulation with the addition of consortium of microbes was significantly affected the cacao height on 4 WAT (week after treatment), the leaf number on 6 and 12 WAT, and also in its root fresh weight parameters. The best level of the first factor was 5x107 CFU/mL. The respond of cacao height on 12 WAT and cacao root dry weight was significant to the addition of biosurfactant DEA palm olein. The best level of the second factor was with the addition of biosurfactant DEA palm olein.
Genetic variability and Heritability of Agronomic Traits of Selected Green Super Rice (GSR) Lines in Indonesia
Authors: Susanto Untung , Gumelar Asep Ikhsan , Ali Jauhar
Published: February 2022

GSR have been designed to have high and stable yields either under optimum or less chemical and water input conditions which is much required to meet the challenge of maintaining food security in Indonesia. This research aimed to test heritability and genetic variability of agronomic traits of GSR lines selected in Indonesia. Eighteen promising GSR lines identified from the second and third batch of IRRI bred GSR lines were tested along with Ciherang and Inpari 13 as check. The trial was conducted under irrigated conditions during WS2013 at ICRR Experimental Station in Sukamandi by transplanting at 21 days old seedlings with 20 x 20 cm spacing in a 6 m2 plot size laid out in a randomized complete block design of 3 replications. Heritability analysis showed that all traits had high heritability unless seed set and yield. All Traits had wide genetic variability unless yield. The tested lines had comparable yield with both checks. Among the lines, HHZ5-DT1-DT1 had been released for rainfed lowland named Inpari 46 GSR TDH.
Allelopathic effect of parthenium weed (Parthenium hysterophorus L.) leaf litter on the seedling emergence and growth of wheat (Triticum aestivum L.)
Authors: Putri Widia Eka
Published: February 2022

Parthenium weed (Parthenium hysterophorus L) is a pantropical weed from Central America that has invaded more than 40 countries in the world. The invasiveness and competitive advantage of this weed are attributed to its ability to produce large number of seeds, tolerance to environmental stresses, climate change adaptability, and allelopathic properties. Phenolics and sesquiterpene lactones are two major classes of allelopathic compound produced by parthenium weed and these chemicals are known to have significant negative effect on germination, seedling emergence and growth of various plants species. The allelopathic properties of parthenium weed had been investigated in various past studies, however, most of the studies conducted the experiment under laboratory conditions with the allelopathic effect being tested by applying the aqueous extract of the weed directly on the test plants. This study aimed to examine the allelopathic effect of the leaf litter of parthenium weed under more natural conditions. Fresh leaves were oven dried and crushed to crude powder, hereafter referred to as leaf litter. The leaf litter were incorporated into the upper layer of the media of Greenfingers compost bark in pots. In to this were sown the seeds of the test plans then set to germinate. Another treatment without leaf litter was set up as a series of control. The treatments were arranged in simple randomized design in the glasshouse. After one week, any seedling produced were counted and thinned to five seedlings per pot. The plants produced from these seedlings were harvested after further 40 days of growth and the growth parameter including root length, shoot length, and dry weight were measured. The measurable growth reduction increased as the amount of parthenium weed leaf litter increased but variability between results existed. The uncontrollable factors and seasonal conditions may cause this variability, in addition to the seed quality. The chemicals contained within the parthenium weed leaf litter has been shown to affect crop growth presumably through allelopathic activity under natural field conditions.
Food waste management regulation in Indonesia to achieve sustainable development goals
Authors: Cahyani F A , Wulandari P , Putri N A
Published: February 2022

This article discussed various regulation of food waste management in Indonesia. The purpose of this study was to find out the regulations governing food waste management in Indonesia. By using a normative research method that makes laws and regulations the main study material in this article. Population growth and changes in consumption patterns result in an increase of the volume, type, and characteristics of waste in Indonesia. Food waste was the biggest contributor to the waste production in Indonesia. Food waste occupied the first position in the composition of waste in Indonesia amount 40.3%. Article 28 H paragraph (1) of the 1945 Constitution of the Republic of Indonesia had mentioned that a good and healthy environment was the right of every citizen. The right to a good and healthy environment was aligned with other human rights so that their position was equal. By implementing food waste management from production to after consumption through the right strategy, it will be able to reduce the environmental impact of food waste and contribute to sustainable development goals. The results found by the authors that there were no specific rules governing food waste management in Indonesia. There were regulations governing both organic and non-organic waste in the laws that owned by Indonesia, but none had specifically discussed about food waste.
Production technology of livestock and poultry products using environmentally safe feed additives
Authors: Volostnova A N , Yakimov A V , Yakimov O A , Sh Salyakhov A , Frolov G S
Published: February 2022

Due to the growing demand for environmentally friendly products, the use of natural growth stimulants in animal husbandry has become especially relevant. Studies were conducted in accordance with generally accepted methods of zootechnical accounting, the average daily milk productivity of cows, safety, average daily and absolute growth of turkeys were determined. To assess the quality of milk, we used physicochemical and microbiological methods of investigation. The meat productivity of turkeys was evaluated by pre-slaughter weight, gutted carcass weight and slaughter yield. The use of activated zeolite in milk production technology made it possible to increase the milk productivity of cows and improve the quality characteristics of milk. The use of bentonite, poly enzyme preparation “Universal” and enzyme-mineral complex in poultry meat production contributed to an increase in the safety of turkeys, their growth rate and meat productivity.
Study of salicylic acid concentration in suppressing the development of Ganoderma spp. causes of stem rot disease in vitro and its effect on oil palm seedling growth
Authors: Saputra R , Hamzah A , Puspita F , Irfandri  , Nasrul B , Naibaho T E
Published: February 2022

Ganoderma spp. is the main pathogen that is commonly found in oil palm plantations, which is known to cause stem rot and top stem rot disease. Many control techniques have been carried out, but there are still few that use salicylic acid suppression techniques on oil palm seedlings to inhibit the development of Ganoderma spp. This study aimed to examine the inhibitory ability of Ganoderma spp. using salicylic acid in vitro. This research was conducted descriptively with several concentrations of salicylic acid, namely 50 ppm (A1), 100 ppm (A2), 150 ppm (A3) and 200 ppm (A4) against Ganoderma sp. isolates LPTUNRI-Gan001 and LPTUNRI-Ga003. The aplication of 50 and 100 ppm salicylic acid was able to inhibit the growth of Ganoderma sp. isolate LPTUNRI-Gan001 by 100% and Ganoderma sp. isolate LPTUNRI-Gan003 by 100% after application of 50, 100 and 150 ppm. The application of 100-200 ppm salicylic acid can increase the height and number of leaves of oil palm seedlings. The application of 50-200 ppm salicylic acid can increase the total chlorophyll content.
Analysis of the diversity of local ginger (Zingiber officinale Rosc.) in Pandeglang Regency, Banten Province based on morphological characteristics
Authors: Prasetyo F D , Muztahidin N I , Fatmawaty A A , Laila A , Nurfadilah M
Published: February 2022

Ginger plant is a medicinal plant widely cultivated by farmers, especially in Pandeglang regency. This research was aimed to find out the relationship of local ginger based on morphological characteristics as well as to dig up information about e×isting varieties so that it can be a reference for plant breeding of local ginger in Pandeglang regency. The research was conducted in a way of e×ploration from October to November 2021 in Bojong, Menes, Cisata and Majasari sub-districts as the location of accession. 3 samples were taken from each accession so that the total of sample was 12 observation samples. The relationship of kinship was observed with the SPSS program of cluster analysis. The results showed that in Pandeglang were e×plored 2 types of ginger planted, namely red ginger and small white ginger (emprit), scattered in all accessions. Based on the morphological characteristics, the two types of ginger had similarities on the shape of stem, the color of stem, the shape of leaf, the tip of leaf, the base of leaf, and the shape of root. It was found that the closest kinship relationship was in the sample A1 with A2 with a coefficient value of 3.733 and the furthest kinship was found in the sample A1 with C3 with a coefficient value of 24.499. Thus it can be known that there is a close kinship relationship between ginger plants in Pandeglang Regency.
The Response of AB Mix Utilization on Growth and Yield of Several Melon Varieties (Cucumis melo L.) in Hydroponic Drip Irrigation System
Authors: Sugiartini E , Rusmana  , Hilal S , Feronica C I A , Wahyuni S E
Published: February 2022

Melon (Cucumis melo L.) is one of popular fruit commodities in Indonesia, because of its sweet and fresh taste, and very high of nutritional content. Appropriate dose of Ab Mix on growth and yield is essential in melon cultivation with a hydroponic system. The study was conducted to determine the best AB Mix dose levels for growth and yield of three melon varieties. A Split Plot Design was used which arranged using a randomized block design with 2 factors. The first factor as the main plot was 2 levels of AB Mix doses (N), and the second factor as the subplot was 3 varieties (V) of melon. The results showed that the effect of AB Mix doses on the growth and yield of three melon varieties were not significantly different between the two treatments (1600 ppm and 1800 ppm). The Golden Aroma variety gave different response at the age of two weeks after planting in term of plant height. Whereas the AB Mix dose level influenced the number of leaves only at the age of two weeks after planting. In conclusion, 1600 ppm of AB Mix dose was sufficiently meet the nutrition level required by the melon in hydroponic drip irrigation system.
Utilization of Ulva spp. in Biscuit Formulation: Feasibility Studies at the Household Scale
Authors: Kusumawati R , Sinurat E , Sihono  , Fransiska D , Subaryono  , Nurhayati  , Purnomo A H , Utomo B S B , Basmal J
Published: February 2022

Green seaweed Ulva spp. contains dietary fiber and bioactive compounds and can be used as raw material for biscuit products. People from toddlers widely consume biscuits to the elderly. The technique of making biscuits is easy and does not require significant capital. The addition of 1% Ulva flour in biscuit formulations reported could control blood sugar levels. This study aimed to calculate the feasibility of Ulva biscuits production on a household scale with variations in 1 and 2 kg production capacity in 3 replications. The results showed that the yields were 74.94 to 77.02% and were not significantly different. The nutritional contents were also not significantly different, i.e., 2.89 to 3.53% of water content, 2.84 to 3.14% of protein content, 42.61 to 45.03% of fat content, 46.80 to 49.59% of total carbohydrates, and 41.71 to 45.57% of reducing sugar. Based on the calculation of business feasibility with a financial approach, the break-even point (BEP) value will be achieved if a minimum production of 2 batch processes per day is carried out with a production capacity of 15 kg of flour per batch and a working period of 25 days per month. The net present value (NPV) will be reached 85.9 million rupiahs, and the payback period (PP) will be achieved in 14 months.
Attitude of young farmers to on-farm business sustainability based on the behavior and success of seeking digital information related to agriculture (case of Lebak Regency, Banten Province-Indonesia)
Authors: Khaerunnisa  , Nurmayulis  , Salampessy Y L A
Published: February 2022

Information and communication technology (ICT) utilization in the agricultural sector is crucial to increase productivity, farming efficiency, and agricultural information seeking. Therefore, increasing the number of young farmers who mastered employing ict is essential. The study was conducted to analyze the attitudes of young farmers in the Lebak Regency towards the sustainability of on-farm business based on the carrying capacity of ICT. The survey engaged 66 young farmers in Lebak Regency, which were drawn by proportional simple random sampling. Path analysis was applied to analyze the data. The result showed young farmers’ behaviour of seeking digital agriculture information directly affects the success of the seeking activities. The success of seeking digital agriculture information affects the attitude of on-farm activity sustainability. The behaviour of seeking digital agriculture information affects the attitudes of young farmers towards the sustainability of on-farm work through the success of seeking digital agriculture information.
Nori solar dryer performance: in relation to the colour of the product
Authors: Utomo Bagus S B , Sinurat Ellya
Published: February 2022

One of the critical steps in nori processing is drying. Nori, a special product from seaweed, requires a special design of a dryer to facilitate an efficient drying room and condition. Ordinary mechanical dryers are not suitable for drying nori and are considerably expensive as well, so that a simple model of the solar dryer was required. This dryer uses renewable energy resource in the form of solar energy which is abundantly available and sound environmentally. The study aimed to test the drying performance of the designed dryer correlated with the quality of the nori produced, especially it’s colour. Performance test was conducted in two days from 8.30 to 16.00 WIT each day with main drying parameters temperature and humidity. The observation was conducted every 30 mins. The quality parameters for nori produced were emphasized on colour and sensory evaluation. It was concluded that the drying conditions performed by the dryer were suitable for drying nori producing nori with acceptable colour and texture.
The effect of variation concentration white oyster mushroom flour for quality yogurt mushroom taro synbiotic during storage
Authors: Setiarto R H B , Widhyastuti N , Risty A R
Published: February 2022

Yoghurt was probiotic drink fermented by Lactobacillus bulgaricus, Streptococcus thermophiles, and Lactobacillus acidophilus. The source of prebiotics was 0.5% taro flour from a previous studied. This studied aims to investigate the effect of variations concentration of white oyster mushroom flour on the quality of synbiotic mushroom taro yogurt during a storage period of 4 weeks. The mushroom flour was added with a concentration of 0%; 0.10%; 0.20%; 0.30%; and 0.40%. The results for the concentration factor of white oyster mushroom flour and storage time had significantly different (p<0.05), namely the viscosity test, total lactic acid titrated, pH, viability lactic acid bacteria, and organoleptic tests. The results for the best mushroom taro yogurt, namely 0.01% white oyster mushroom flour, produced a valued that was not significant with previous studied. The results of the antioxidant test for the mushroom taro yogurt was very weak (ES50 807.50 ppm). There was an increase in dietary fibre content (0.11%), a decrease in total fat content (0.04%), an increase in protein content (0.24%), decrease in moisture content (0.5%), and increased levels of total carbohydrates (0.30%) from mushroom taro yogurt. The results of the quality test of mushroom taro yogurt was in accordance with Indonesian National Standard.
Biotechnological transformation of raw materials with reduced technological properties by proteolytic preparations of various origins
Authors: Ponomarev V , Yunusov E , Ezhkova G
Published: February 2022

The paper expands the information about the effect of proteolytic enzyme preparations on the main properties of collagen-containing meat raw materials. The effect of enzyme proteolytic preparations on the main protein fractions of meat raw materials and native collagen obtained from collagen-containing meat raw materials was studied. The effect of Megaterin and collagenase enzymes on collagen-containing raw materials was studied. In the process of treatment, a decrease in protein content and accumulation of low-molecular-weight hydrolysis products in the samples under study were found. Protein hydrolysates were obtained from fermented collagen-containing raw materials by chemical processing. The effect of the obtained hydrolysates on the functional-technological properties of meat raw materials with reduced functional-technological properties was evaluated. The results showed that the use of protein hydrolysates from fermented collagen-containing raw materials can improve the functional and technological properties of low-grade meat raw materials and opens up broad prospects for their use in the meat industry.The scientific principles of designing recipes and technologies for the production of meat products from fermented meat raw materials are proposed.
Antioxidant activity of young leaves extracts of Lygodium microphyllum on boiling variation
Authors: Widiyantoro Ari , Wahdaningsih Sri , Luliana Sri
Published: February 2022

Lygodium microphyllum is one of the ferns that is often used as raw material for food and traditional medicine. L. microphyllum as food ingredients are usually used in the young leaves. This study aims to determine the antioxidant activity of the young leaves extracts of L. microphyllum by boiling variations.The research method is a pure experiment by extracting the young leaves of L. microphyllum by boiling with variations in temperature (30, 40, and 50°C) and boiling time (10, 15, and 20 minutes).The results showed that boiling at a temperature of 50°C and a boiling time of 20 minutes had the highest antioxidant activity with IC50 99±1.23 µg/mL.
Stylus tip radius and wear estimation using the Rsk or the Rp and Rv parameter of a sine wave (Type C1) standard
Authors: Haitjema Han , Thanki Aditi
Published: February 2022

Determination of the stylus tip radius and its wear or damage is a classical problem in tactile surface topography measurements. The determination of the stylus geometry may be tedious and inconvenient, therefore we looked for an easily applicable method. This study shows that the Rsk parameter and the difference between the Rv and Rp parameter may indicate the stylus tip radius as well as wear when using a sine-wave profile material measure, which is commonly supplied with a roughness tester for calibrating and/or adjusting the vertical amplification coefficient. This effect is derived from theoretical calculations on real and simulated styli and specimens and verified experimentally using two commonly used specimens and stylus tips with radii of nominally 1, 2, 5, and 10 µm. When using a standardized stylus with a nominal 2 µm tip radius and 60° cone angle on a typical C1 reference specimen with nominal parameters Ra = 3 µm and RSm = 100 µm, the Rsk value should be approximately −0.01. Any stylus wear will decrease the measured Rsk value. When the Rsk value decreases to a value of −0.06 or lower it may be time for closer inspection and/or replacement of the stylus.
Ductile-brittle transition at edge cracks (001)[110] in BCC iron under different loading rates in mode I: a 3D atomistic study
Authors: Uhnáková Alena , Machová Anna , Červ Jan , Hora Petr , Joch Jaroslav
Published: February 2022

3D atomistic simulations via molecular dynamics (MD) at temperature of 0 K and 295 K (22 °C) with a high quasi-static loading rate dP/dt of 2.92 kN s−1 show that cleavage fracture is supported by surface emission of oblique dislocations

11

1
¯

011

and by their subsequent cross slip to {112} planes, which increases separation of the (001) cleavage planes inside the crystal. Under the slower loading rate by a factor 5, the crack growth is hindered by twin generation on oblique planes {112} and the fracture is ductile. The MD results explain the contribution of the crack itself to the ductile-brittle transition observed in our fracture experiments on Fe-3wt%Si single crystals of the same orientation and geometry, loaded at the same rates dP/dt as in MD. The loading rates are equivalent to the cross head speed of 5 mm min−1 and 1 mm min−1 used in the experiment. The MD results also agree with the stress analysis performed by the anisotropic LFM and comply with experimental observations.
Screen-printed bismuth telluride nanostructured composites for flexible thermoelectric applications
Authors: Amin A , Huang R , Newbrook D , Sethi V , Yong S , Beeby S , Nandhakumar I
Published: February 2022

We herein report the results of a facile two-step surfactant assisted reflux synthesis of bismuth telluride (Bi2Te3) nanowires (NWs). The as-synthesised NWs had diameters ranging from 70 to 110 nm with a length varying between 0.4 and 3 µm and a preferential lattice orientation of (0 1 5) as determined by grazing incidence x-ray diffraction. We demonstrate for the first time that a solvent/binder paste formulation of N-methyl-2-pyrrolidone/polyvinylidene fluoride (PVDF) is suitable for screen-printing the Bi2Te3 NWs with the potential for the fabrication of flexible thermoelectric (TE) materials. The wt% of PVDF in the composite films was varied from 10% to 20% to identify the optimal composition with a view to achieving maximum film flexibility whilst retaining the best TE performance. The films were screen-printed onto Kapton substrates and subjected to a post-printing annealing process to improve TE performance. The annealed and screen printed Bi2Te3/PVDF NW composites yielded a maximum Seebeck coefficient −192 µV K−1 with a power factor of 34 µW m−1K−2 at 225 K. The flexible screen printed composite films were flexible and found to be intact even after 2000 bending cycles.
localpdb—a Python package to manage protein structures and their annotations
Authors: Ludwiczak Jan , Winski Aleksander , Dunin-Horkawicz Stanislaw
Published: February 2022

Motivation

The wealth of protein structures collected in the Protein Data Bank enabled large-scale studies of their function and evolution. Such studies, however, require the generation of customized datasets combining the structural data with miscellaneous accessory resources providing functional, taxonomic and other annotations. Unfortunately, the functionality of currently available tools for the creation of such datasets is limited and their usage frequently requires laborious surveying of various data sources and resolving inconsistencies between their versions.

Results

To address this problem, we developed localpdb, a versatile Python library for the management of protein structures and their annotations. The library features a flexible plugin system enabling seamless unification of the structural data with diverse auxiliary resources, full version control and powerful functionality of creating highly customized datasets. The localpdb can be used in a wide range of bioinformatic tasks, in particular those involving large-scale protein structural analyses and machine learning.

Availability and implementation

localpdb is freely available at https://github.com/labstructbioinf/localpdb. Documentation along with the usage examples can be accessed at https://labstructbioinf.github.io/localpdb/.
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data
Authors: Li Xingyi , Li Min , Xiang Ju , Zhao Zhelin , Shang Xuequn
Published: February 2022

Motivation

Biomarkers with prognostic ability and biological interpretability can be used to support decision-making in the survival analysis. Genes usually form functional modules to play synergistic roles, such as pathways. Predicting significant features from the functional level can effectively reduce the adverse effects of heterogeneity and obtain more reproducible and interpretable biomarkers. Personalized pathway activation inference can quantify the dysregulation of essential pathways involved in the initiation and progression of cancers, and can contribute to the development of personalized medical treatments.

Results

In this study, we propose a novel method to evaluate personalized pathway activation based on signaling entropy for survival analysis (SEPA), which is a new attempt to introduce the information-theoretic entropy in generating pathway representation for each patient. SEPA effectively integrates pathway-level information into gene expression data, converting the high-dimensional gene expression data into the low-dimensional biological pathway activation scores. SEPA shows its classification power on the prognostic pan-cancer genomic data, and the potential pathway markers identified based on SEPA have statistical significance in the discrimination of high- and low-risk cohorts and are likely to be associated with the initiation and progress of cancers. The results show that SEPA scores can be used as an indicator to precisely distinguish cancer patients with different clinical outcomes, and identify important pathway features with strong discriminative power and biological interpretability.

Availability and implementation

The MATLAB-package for SEPA is freely available from https://github.com/xingyili/SEPA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins
Authors: Dong Chuan , Wang Xin , Ma Cong , Zeng Zhi , Pu Dong-Kai , Liu Shuo , Wu Candy-S , Chen Shixin , Deng Zixin , Guo Feng-Biao
Published: February 2022

We previously released the Anti-CRISPRdb database hosting anti-CRISPR proteins (Acrs) and associated information. Since then, the number of known Acr families, types, structures and inhibitory activities has accumulated over time, and Acr neighbors can be used as a candidate pool for screening Acrs in further studies. Therefore, we here updated the database to include the new available information. Our newly updated database shows several improvements: (i) it comprises more entries and families because it includes both Acrs reported in the most recent literatures and Acrs obtained via performing homologous alignment; (ii) the prediction of Acr neighbors is integrated into Anti-CRISPRdb v2.2, and users can identify novel Acrs from these candidates; and (iii) this version includes experimental information on the inhibitory strength and stage for Acr-Cas/Acr-CRISPR pairs, motivating the development of tools for predicting specific inhibitory abilities. Additionally, a parameter, the rank of codon usage bias (CUBRank), was proposed and provided in the new version, which showed a positive relationship with predicted result from AcRanker; hence, it can be used as an indicator for proteins to be Acrs. CUBRank can be used to estimate the possibility of genes occurring within genome island―a hotspot hosting potential genes encoding Acrs. Based on CUBRank and Anti-CRISPRdb, we also gave the first glimpse for the emergence of Acr genes (acrs).

Database URL

http://guolab.whu.edu.cn/anti-CRISPRdb
CEFR and the ELT practitioner: empowerment or enforcement?
Authors: Savski Kristof
Published: February 2022

Over the last two decades, the Common European Framework of Reference for Languages (CEFR) has become ubiquitous in ELT. In this article, I consider how differences in the way in which the framework is being interpreted by different powerful actors, including governments and for-profit organizations, affect its usability for ELT practitioners, a key segment of its intended audience and thus, at least in theory, key beneficiaries of its spread. I highlight three key paradoxes faced by ELT practitioners working with the framework, relating to whether CEFR is to be seen as a flexible point of reference or a set standard, whether the communicative competence described by CEFR is to be seen in a conventional, universal sense or from a more dynamic contemporary perspective, and whether CEFR is to be seen as associated with prepackaged methods (textbooks) or as a vehicle for the development of local pedagogies. I conclude by calling for deeper awareness of these paradoxes among ELT practitioners to support the productive implementation of CEFR.
Psychosocial workplace factors and alcohol-related morbidity: a prospective study of 3 million Swedish workers
Authors: Almroth Melody , Hemmingsson Tomas , Sörberg Wallin Alma , Kjellberg Katarina , Falkstedt Daniel
Published: February 2022

Background

Psychosocial workplace factors may be associated with alcohol-related morbidity, but previous studies have had limited opportunities to take non-occupational explanatory factors into account. The aim of this study is to investigate associations between job control, job demands and their combination (job strain) and diagnosed alcohol-related morbidity while accounting for several potentially confounding factors measured across the life-course, including education.

Methods

Job control, job demands and job strain were measured using the Swedish job exposure matrix measuring psychosocial workload on the occupational level linked to over 3 million individuals based on their occupational titles in 2005 and followed up until 2016. Cox regression models were built to estimate associations with alcohol-related diagnoses recorded in patient registers.

Results

Low job control was associated with an increased risk of alcohol-related morbidity, while high job demands tended to be associated with a decreased risk. Passive and high-strain jobs among men and passive jobs among women were also associated with an increased risk of alcohol diagnoses. However, all associations were found to be weakened in models adjusted for other factors measured prospectively over the life-course, especially in models that included level of education.

Conclusion

The associations between low job control and high job demands, and the risk of alcohol-related morbidity reflect underlying socioeconomic differences to some extent. Lower job control, however, remained associated with a higher risk of alcohol-related morbidity.
Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments
Authors: Thompson Andrew W , Wojtas Harrison , Davoll Myles , Braasch Ingo
Published: February 2022

The Rio Pearlfish, Nematolebias whitei, is a bi-annual killifish species inhabiting seasonal pools in the Rio de Janeiro region of Brazil that dry twice per year. Embryos enter dormant diapause stages in the soil, waiting for the inundation of the habitat which triggers hatching and commencement of a new life cycle. Rio Pearlfish represents a convergent, independent origin of annualism from other emerging killifish model species. While some transcriptomic datasets are available for Rio Pearlfish, thus far, a sequenced genome has been unavailable. Here, we present a high quality, 1.2 Gb chromosome-level genome assembly, genome annotations, and a comparative genomic investigation of the Rio Pearlfish as representative of a vertebrate clade that evolved environmentally cued hatching. We show conservation of 3D genome structure across teleost fish evolution, developmental stages, tissues, and cell types. Our analysis of mobile DNA shows that Rio Pearlfish, like other annual killifishes, possesses an expanded transposable element profile with implications for rapid aging and adaptation to harsh conditions. We use the Rio Pearlfish genome to identify its hatching enzyme gene repertoire and the location of the hatching gland, a key first step in understanding the developmental genetic control of hatching. The Rio Pearlfish genome expands the comparative genomic toolkit available to study convergent origins of seasonal life histories, diapause, and rapid aging phenotypes. We present the first set of genomic resources for this emerging model organism, critical for future functional genetic, and multiomic explorations of “Eco-Evo-Devo” phenotypes of resilience and adaptation to extreme environments.
Constructing nuclear responsibility in US–India relations
Authors: Hamidi Sidra
Published: February 2022

In 2005, the United States recognized India as a ‘responsible state with advanced nuclear technology’. How did India go from pariah to a legitimate nuclear state? This article historicizes the concept of nuclear responsibility to explain India's shifting place in the nuclear regime. Existing perspectives view responsibility as a function of discrete state behaviors to the detriment of understanding the relationship between power and responsibility as a discourse. This article tracks the evolving discourse of early proliferators, such as the US, UK and France, who legitimated their possession of nuclear weapons by linking responsibility with deterrence. In its early nuclear history, India challenged these hegemonic perspectives but more recently adopted the deterrence model of responsibility to be granted recognition and legitimacy in the global nuclear regime. The article concludes that nuclear states’ success in linking deterrence with responsibility complicates the place of disarmament as an alternative nuclear responsibility discourse. Tying deterrence to responsibility reshaped the global order around the continual presence of nuclear weapons, narrowing moral agency and limiting a nuclear weapon-free future. Reclaiming responsibility will require moving beyond the typical state-centric politics of blame towards institutional and structural approaches to moral agency.
Early Pouchitis Is Associated With Crohn’s Disease–like Pouch Inflammation in Patients With Ulcerative Colitis
Authors: Kayal Maia , Kohler David , Plietz Michael , Khaitov Sergey , Sylla Patricia , Greenstein Alexander , Dubinsky Marla C
Published: February 2022

Background

Despite the initial diagnosis of ulcerative colitis (UC), approximately 10% to 20% of patients develop Crohn’s disease–like pouch inflammation (CDLPI) after restorative proctocolectomy (RPC) with ileal pouch anal anastomosis (IPAA). The aim of this study was to evaluate whether early pouchitis, defined as pouchitis within the first year after IPAA, is a predictor of CDLPI.

Methods

This was a retrospective cohort analysis of patients with UC or IBD unclassified (IBDU) who underwent RPC with IPAA at Mount Sinai Hospital between January 2008 and December 2017. The primary outcome was development of CDLPI. Predictors of CDLPI were analyzed via univariable and multivariable Cox regression models.

Results

The analytic cohort comprised 412 patients who underwent at least 1 pouchoscopy procedure between 2009 and 2018. Crohn’s disease–like pouch inflammation developed in 57 (13.8%) patients a median interval of 2.1 (interquartile range, 1.1-4.3) years after surgery. On univariable analysis, older age at colectomy (hazard ratio [HR], 0.97; 95% CI, 0.95-0.99) was associated with a reduced risk of CDLPI; although early pouchitis (HR, 2.43; 95% CI, 1.32-4.45) and a greater number of pouchitis episodes (HR, 1.38; 95% CI, 1.17-1.63) were associated with an increased risk. On multivariable analysis, early pouchitis (HR, 2.35; 95% CI, 1.27-4.34) was significantly associated with CDLPI. Time to CDLPI was significantly less in patients who developed early pouchitis compared with those who did not (P = .003).

Conclusion

Early pouchitis is significantly associated with subsequent CDLPI development and may be the first indication of enhanced mucosal immune activation in the pouch.