bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation of Emulsions of some Vegetable Oils and Evaluation of Their Effectiveness in Inhibiting Pathogenic Fungus Didymella bryoniae
Authors: Hassan Abdullah Abdulkareem , Mazion Maryam Sarhan
Published: September 2023

Five pathogenic fungi were isolated from the infected melon/Cucumis melo, Cucumber/Cucumis sativus, Watermelon/Citrullus lanatus and Squash/Cucurbita pepo with gum stem blight disease. The fungi identified to the species level by the nucleotide sequence analysis method for the ITS region within the 5.8SrRNA gene as Stagonosporopsis cucurbitacearum strain Has. AA-16, S. cucurbitacearum strain Has. AA-17, S. cucurbitacearum strain Has. AA-18, S. cucurbitacearum strain Has. AA-19 and S. cucurbitacearum strain Has. AA-19 and S. cucurbitacearum strain Has. AA-20 then registered in the World Genetic Bank at the NCBI website under the accession numbers OP247683.1, OP247685.1, OP247686.1, OP247709.1 and OP247707.1, respectively. The physical and antagonistic properties of five types of emulsions produced from lavender, thyme, cinnamon and cloves oils with surfactants Inex A and Spam 80 were studied. The results showed a decrease in the surface tension of all emulsions produced from these oils with both surfactants. Increasing the temperature to 40°C led to a more decrease in the surface tension compared to 20°C. The lowest surface tension values for emulsions produced from clove, thyme and cinnamon oils with the Index A (1:6;oil:Inex A) at 40°C, the surface tension reached to 11.98, 13.22 and 14.17 Dyne/cm, respectively. The stability of all emulsions resulting from the studied oils increased with an increase in the ratios of the Inex A and Span 80, the highest stability was reached by decreasing the separation layer when emulsions of thyme and lavender oils with Inex A at a ratio of 1:6 at 20°C, which reached 0.61 and 0.66 cm, respectively. All emulsions consisting of oils and surfactants inhibited the growth of pathogenic fungus D. bryoniae, the highest inhibition zones were 1.9, 1.8, 1.7 and 1.6 cm for emulsions resulting from clove, cinnamon, thyme and lavender oils with Inex A at a ratio of 1:4 at a 20°C, respectively.
Efficiency of some Jasmonic Acid Concentrations on Mortality of Two-Spotted Spider Mite Tetranychus urticae Koch on Eggplant
Authors: Talib Yusra Jamal , Abass Mohammed Hamza , Thamer Nadia Kadhim
Published: September 2023

The efficiency of Jasmonic acid concentrations 0, 5, 50 and 100μM was examined mortality of adult female and nymphs of the two-spotted spider mite Tetranychus urticae fed on leaves of over four time intervals of 12, 24, 36 and 48 hours. The results showed the significant effect of the treatments on the corrected mortality ratios for both stages, as well as for the interaction of the treatments of variety, concentration and time. In general, the results indicated the increase of mortality with the increase of the time period. It was observed that the concentration of 100μM during the time periods and all varieties and the concentration of 50μM after the time periods 24, 36 and 48 hours on the Barcelona variety and the concentration of 5μM during the last two time periods on the Bowie variety had the highest corrected mortality ratio, which was 100%, while the lowest mortality ratio was 0% at the concentration 5μM with 12 hours after treatment on adult females fed on the leaves of Jawaher variety. Regarding the effect of treatment on nymphal stage, In general, the results of the triple interaction between treatments indicated that the concentration of 5 μM had a synergistic effect along with Bowie variety and at all time periods in obtaining of the highest mortality ratio of individuals of nymphal stage (100%) and with significant differences from the other treatment while the same concentration after 12 hours of treatment achieved lowest mortality ratio of the nymph fed on the leaves of the variety Jawaher which amounted 0%.
Response of Sorghum bicolor L. Cultivars to Added Levels of Salicylic Acid
Authors: Atwi Mustafa Raddad Drig , Hashem Mohamed Alwan
Published: September 2023

To determine the impact of sorghum variety and salicylic acid concentration on growth characteristics and yield of sorghum crop, a field experiment was applied in the spring of 2022 at the second agricultural research and experiment station of the College of Agriculture at Al-Muthanna University in the Al Bandar area (about 3 km from the city center). The experiment used split plots arranged in a completely random sector and randomized design. Items were plotted in the main plots, while salicylic acid concentrations were plotted in the sub plots. The most important results were the following, there was a significant effect of the salvaged cultivar on plant height (119.15 cm), number of leaves 9.60 (leaf), number of grains per panicle 1617 (grain panicle−1) and grain yield (3.36) tons ha−1, while the variety outperformed Good in the trait of the area of the flag leaf and the diameter of the stem (303.9 cm and 20.35 mm) respectively, as well as a significant effect of the concentration 120 ppm in the trait (number of days from planting until 75% of flowering, number of leaves per plant, number of grains per panicle, weight of 1000 grains, Grain yield, biological yield, harvest index (it amounted to 93.78) days, 9.45 tons of leaf−1 1494 grain panicle−1, 32.96 g, 3.46 tons H−1, 12.59 tons H−1, 29.76%) respectively. With respect to the characteristic of the number of grains per panicle, a significant difference was obtained for the interaction between the factors, as the combination (variety rescued x concentration 120 ppm) recorded a significant superiority, yielding the highest average amount, 2017 grain panicle−1.
Effect of Potassium Humate and Spraying With Boron on the Yield and Its Components of Sesame Crop
Authors: Madghash Majid Rasheed , Ali Omar Nazhan
Published: September 2023

The impact of ground addition of potassium humate and boron spraying on sesame indicators, yield, and its components was investigated in a field experiment at the Research Station of the Field Crops Department of the College of Agriculture - Tikrit University 2021. The experiment was carried out using a randomized complete block design (RCBD) using a factorial experiment consisting of two components, the first of which was the addition of potassium humate and the second of which was the spraying of boron. During the first week of June 2021, seeds were planted in soil that had been amended with potassium humate at five different concentrations: 0, 3.6, 7.2, 10.8, and 14.4 g.l-1. A randomized full block design was used to statistically assess the data gathered from spraying three different amounts of boron (0, 100, and 200) g.l-1 prior to the onset of flowering. Here is a rundown of the findings: The number of capsules per plant treated with potassium humate (H3) was the highest (89.111 capsule.plant-1), and the total yield was also much higher (compared to other treatments) (3.427 kg.ha-1). Both the capsule length (2.573 cm) and the individual yield (15.673 g) were significantly higher in plants that were subjected to a boron (B3) spraying treatment. For the features of the number of seeds per capsule (71,333 seeds.capsule-1) and the weight of one thousand seeds, the interaction combination (H5B3) yielded the greatest significant value (4.491 g).
Effect of Sowing Rates and Potassium Foliar Feeding on some Growth and Yield of Millet Panicum miliaceum L.
Authors: Al-Hassoun Osama Saleh Mahdi , Mohsen Haider Abdul Hussein
Published: September 2023

This study was conducted to determine the seeding rate reducing and potassium spraying on the growth and yield of local millet, at Abu Chwilana region (8 km north of the governorate), during the summer season 2022 was carry out by factorial experiment with Randomized Complete Block Design (R.C.B.D), the first factor include three seeding rates were 8, 10 and 12 kg ha−1, the second factor was four potassium spray treatment levels, were 0, 3000, 6000 and 9000 K PPM. the seeds were sown on 04/22/2022. The potassium spraying process was conducted in two stages, the first at the beginning of the branches and the second at the beginning of flowering. The results show that the seed rates affected the studied traits of the vegetative growth of the crop, as the seed treatment (10 kg ha−1) was superior in plant height, leaf area, tiller number, and most of the yield and its components, as the grains number, individual plant yield. Plant height, leaf area, and tiller count were all considerably increased by the 9000 ppm potassium spray treatment, while grain yield per dahlia and total plant yield were also increased by a statistically significant margin. The interaction treatment of 10 kg ha-1 × 900 ppm was significantly superior in majority of the obtained characteristics.
Effect of Alcohol Extract, Volatile Oil and Alkaloid Isolated from Capsicum frutescens L. Fruits on Candida albicans
Authors: Al-Ghazali Linda H , Al-Masoody Itlal Hakim , Ismael Maha Hameed , Al-Ibrahemi Nibras
Published: September 2023

This study involved extracting the of alcohol extract, volatile oil and alkaloid isolated from Capsicum frutescens L. fruits on Candida albican,. It also involved test a phytochemical screen and determine the percentage yield of the alcohol extract, volatile oil and alkaloid, Capsicum annuum L. was collected from the Karbala City, that approximately 24 hours to extract using Soxhlet apparatus with 400 ml of Methanol Alcohol Solvent in a 1000 ml Flask, and evaporation by rotary evaporation 40C° for drying, and storage at 4C° until use, indicate results that Percentage yield of Alcohol and volatile oils extracted was (3.8% and 4.1%), showing alcohol extract that high positive reaction with used reagent, Alkaloid, Phenol, Glycoside, and Flavonoid, Saponin and tannin. While volatile oil extract revealed positive results for Alkaloid, Glycoside, Flavonoid, tannin and Phenol while and Saponin indicate negative results. The antifungal effects of alcohol extract, volatile oil and alkaloid depended on different concentration, The alcohol extract’s inhibition zone measured 11.12 mm and had a 20 mg/ml concentration, while concentration 40 mg/ml was inhibition zone 12.34mm while concentration 80 mg/ml was inhibition zone 13.65mm, while concentration 100 mg/ml was inhibition zone 15.76 mm, while The inhibition zone of volatile oil extract was 12.76 mm in concentration 0.5 mg/ml, while concentration 0.1 mg/ml was inhibition zone 14.75mm, while concentration 1 mg/ml was inhibition zone 15.76, while concentration 2 mg/ml was inhibition zone 18.65 mm, Alkaloid’s inhibition zone measured 12.34 mm at concentrations of 1 mg/ml and 14.13 mm in those of 5 mg/ml. while concentration 10 mg/ml was inhibition zone 15.98mm, while concentration 15 mg/ml was inhibition zone 20.12 mm. The aim from this study is to determine the best extract (alcohol extract, volatile oil and alkaloid ) isolated from Capsicum frutescens L. fruits on Candida albican.
Effect of Embryo Weight and Seed Priming on Seedling Characteristics of Different Maize Cultvars
Authors: Dawood A. A , Jaddoa Khudhair A.
Published: September 2023

An laboratory experiment was carried out during the year 2020 at the Seed Technology Laboratory of the Crop Department - College of Agricultural Engineering Sciences - University of Baghdad in order to know the effect of seed priming and size of their embryos of different cultivars of maize on the seedling characteristics. The experiment was carried out in a completely randomized design with four replicates. The first factor included three synthetic cultivars of maize (Al-Maha, Baghdad 3 and Al-Fajr) and Al-Nahrain hybrid. For the second factor, it included the priming of seeds with ASA, CK, GA3, KCL, H2O2, DW and DS, in addition to the dry seeds (without priming). The seeds were soaked with solutions of these substances for 24 hours and six characteristics related to the germination process were estimated, which were the weight of the seed after stimulation, the weight of the embryo, the time of germination, the length of the radicle and shoot, and its dry weight. The results showed that the seed priming with H2O2 was significantly superior, as it gave the highest average of seed weight, lowest average germination time, longest average radiclelength and highest seedling dry weight (0.336 g, 3.12 days, 15.08 cm and 0.215 g, respectively). The treatment of seeds with ascorbic was superior in giving the highest average weight of the embryo that reached 0.049 gm, the treatment of stimulating the seeds with gibberellin was superior in giving the highest mean of the coleoptile length of 10.79 cm. Al-Maha cultivar excelled in giving it the highest average seed weight, embryo weight, radiclelength and dry weight, as it reached 0.335 g, 0.050 g, 14.42 cm and 0.194 g, respectively. Whereas, the Fajr cultivar was significantly superior by giving the highest average coleoptile length of 9.37 cm. The interaction effect between the study factors was significant in most of the studied traits.
Studying the Effect of Hydrogel and its Relationship to some Vegetative Growth and Yield Characteristics of Bread Wheat Genotypes (Triticum aestivum L.)
Authors: Zangana Dlawar D. , Aljburi Jasim M.
Published: September 2023

This study was conducted in two separate experiments, the first under conditions of irrigation water shortage and the second when irrigation water was sufficient to evaluate and determine the effect of Hydrogel on fifteen different genotypes of bread wheat and to identify the most superior varieties in terms of vegetative growth and yield of this crop, The grains of the genotypes were planted at the Sayada site - Agricultural Research and Experiment Station of the College of Agriculture - University of Kirkuk (longitude 44.42 0 east and latitude 35.16 0 north). For the season (2021-2022) using a randomized complete block design (R.C.B.D) with a split plot system, the two experiments included three sectors, and each sector included two main plots with the addition of Hydrogel (A1) and without the addition of Hydrogel (A0), and each secondary plot contained (15) genotypes Different from soft bread wheat, the cultivars were planted in four lines with a length of (3) m, and the distance between one line and other was (0.25) m. The characteristics of the total number of tillers were studied. m−2, the height of the plant (cm), the area of the flag leaf (cm2), the number of days from sowing to 50% flowering (day), and the grain yield in a ton. and- The biological yield. A meta-analysis was carried out and the results were summarized by the superiority of irrigation water sufficiency over the lack of irrigation water, and all cultivars excelled when adding hydrogel over not adding hydrogel for all the studied characteristics. this explained that the effect of the hydrogel in storing and retaining water in a way that guarantees the actual need of the crop and achieves its sufficiency, as it was shown that the cultivar Bohuth 22 was superior in terms of the number of prunings tillers all cultivars, at a rate of (533.7 tiller. m−2), and the kalar 1 in the area of the flag leaf, at a rate of (70.8) cm2 and Aras cultivar recorded the lowest average number of days from sowing until 50% of flowering amounted to (145.8) days, and the Fayadh cultivar had the highest average plant height of (105.1) cm, and the Kalar 1 cultivar had the highest average grain yield of (3.86) tons. h−1. The cultivar Tammuz 2, had the highest biological yield of(14.26 tons. h−1).
Influence of Husking Machine Type, and its Clearance on the Factory Rice, Mashkhab (M-33) Cultivar
Authors: Ajmi Nafea M. , Kheiralipour Kamran , Alwan Alsharifi Salih K. , Alaamer Shathar A.
Published: September 2023

This study aims to know the impact of the peeling machine type and the clearances on some qualitative characteristics of the Mashkhab (M-33) cultivar rice production. It was observed from this study that the S-KB40 peeling machine was significantly superior to the Y-ST50 peeling machine in all the studied characteristics, while it achieved the highest results with a clearance of 0.9cm, except for the husking efficiency that achieved the highest results with the clearance 0.5 cm. The experiments were conducted in a factorial experiment under CRD with three replications. For S-KB40 the MP, PR, HE, BR and CR were 1.747t.hr−1, 15.180Kw, 75.94 %,7.251% and 5.807% respectively. For 0.9cm clearance the MP, PR, HE, BR and CR, were 1.885 t.hr−1, 14.625 Kw, 74.03%,6.754 and 5.173% respectively.
Evaluation of the Performance of a Locally Manufactured Palm Service Platform
Authors: Ghali Aliwi Amir , Abdul-Munaim Ali Mazin
Published: September 2023

A field experiment was carried out in one of the orchards of Al-Qassim district in Babel Governorate to find out the ability of a locally manufactured platform to serve palm trees by working in flat and uneven orchard land, palm tree heights of 4, 8, and 12 meters, and it performs pollination, pruning and harvesting services. The time of ascent and descent, the palm service, and the palm/hour productivity were measured. A randomized complete block design with three replications used a split split-plot arrangement. The nature of the land (flat or uneven) represented the main plots, the height of the palm trees (4, 8, 12) meters, the sub-plots, and the palm service operations (pollination, pruning, harvesting) of the sub-sub plots. The data were analyzed and compared according to the L.S.D test at the probability level of 0.05. The results indicated that there is a significant effect of the palm height factor and the type of service factor on the studied characteristics. The highest time for ascent and descent was 101.22 and 50.86 seconds, respectively, at the height of 12 meters, and the highest time for serving the palm tree was 95.40 seconds/palm for the pruning process, and the least productivity was 7.33 palm trees/hour for the pruning process. There was a significant interaction between the palm tree’s height and the land’s nature regarding productivity characteristics. There was a significant difference between the height of the palm tree and the type of service with both times of ascent, descent, and service of a palm tree. Based on the previous, it is possible to use the locally manufactured platform in palm groves to reduce the suffering of palm farmers from the difficulty of performing the necessary operations to serve palm trees, especially those of high altitudes.
Effect of Plant Metabolism and Fertilizer Type in the Production of Root Exudates Under the Influence of Root Mechanical Stress
Authors: Al-Deliamy Abdullah Oda Alwan , Ameer Maha Ali Abdul
Published: September 2023

The current study was carried out in order to know the effect of plant metabolism, fertilizer type and michanical stress (soil compaction) factors on the content of root exudates of mungbean plant Vigna radiate L. and maize plant Zea mays L. from primary and secondary metabolites. Root exudates were collected and their contents of metabolites such as total sugars, total proteins, total phenols, total flavonoids total terpenoids, Hormons (gibberellic, abscisic and jasmonic acid), and enzymes (ATPase, catalase and DNase) were estimated using spectrophotometric and HPLC technology, and the results showed the following: (1) Significant superiority in the content of root exudates of maize plants (C4) from all metabolites except for total sugars and gibberellin hormone where their concentration decreased significantly Compared to the root exudates of mungbean plants (C3). (2) Significant superiority in the content of root exudates of plants grown in compacted soils from all metabolites except for gibberellin hormone and DNase, where theirconcentration decreased significantly compared to noncompacted soils. (3) Significant decrease in the concentration of most of the Components of the root exudates of mungbean and maize plants affected by different types of studid fertilizers from metabolites compared to the root exudates of plants not affected by those fertilizers. The complete randomized block design (RCBD) was adopted with a factorial experiment with three factors, namely metabolism (C), fertilizer (F) and mechanical stress (S), and with three replications, and averages of the trasactions were compared using the least significant difference (RLSD) test at the probability level 0.05.
The Economic Return of the Application of the Technical Recommendations of the Integrated Date Palm Pest Management Program (Babylon Governorate as a Model)
Authors: Ali Mohammed J. , Kadhim Zuhal R.
Published: September 2023

The research aimed to identify the effectiveness of the integrated control system in resisting pests that affect palm trees from an economic perspective, by measuring the impact of its application on some economic variables represented in productivity per donum, total costs per donum, total revenue and net return per donum. The results showed the positive impact of the application of the integrated control program on Productivity, where the average productivity of the donum for the low application level was about 1548 kg/donum, while the average application level was about 2264.2 kg/donum, the high application was about 1710.8 kg/donum. For the total costs, it was found that the low application level was about 182957.3 dinars/donum, the average application level was about 127188 dinars/donum, and the high application was about 176440.7 dinars/donum and for the net donum return, it was found that the low application level was about 253580 dinars/donum. The average level of application amounted to about 354,570 dinars/donum, while the high application reached about 576,230 dinars/donum, and the study recommended the concerned authorities implement the integrated pest management program in the palm sector the need to increase material and guidance support for the program because of its positive impact on the economic and environmental aspect, coordination with the Directorate of Agriculture in Babylon Governorate, in which the program was implemented to work on follow-up in spreading technology and convincing farmers to adopt it through agricultural extension departments in This governorate and the need to find appropriate methods and mechanisms by the Ministry of Agriculture that encourage the private sector to provide supplies and alternatives to chemical pesticides to farmers instead of relying on the government sector.
Is it possible to 3D bioprint load-bearing bone implants? A critical review
Authors: Gupta Tanmay , Ghosh Subrata Bandhu , Bandyopadhyay-Ghosh Sanchita , Sain Mohini
Published: September 2023

Rehabilitative capabilities of any tissue engineered scaffold rely primarily on the triad of (i) biomechanical properties such as mechanical properties and architecture, (ii) chemical behavior such as regulation of cytokine expression, and (iii) cellular response modulation (including their recruitment and differentiation). The closer the implant can mimic the native tissue, the better it can rehabilitate the damage therein. Among the available fabrication techniques, only 3D bioprinting (3DBP) can satisfactorily replicate the inherent heterogeneity of the host tissue. However, 3DBP scaffolds typically suffer from poor mechanical properties, thereby, driving the increased research interest in development of load-bearing 3DBP orthopedic scaffolds in recent years. Typically, these scaffolds involve multi-material 3D printing, comprising of at-least one bioink and a load-bearing ink; such that mechanical and biological requirements of the biomaterials are decoupled. Ensuring high cellular survivability and good mechanical properties are of key concerns in all these studies. 3DBP of such scaffolds is in early developmental stages, and research data from only a handful of preliminary animal studies are available, owing to limitations in print-capabilities and restrictive materials library. This article presents a topically focused review of the state-of-the-art, while highlighting aspects like available 3DBP techniques; biomaterials’ printability; mechanical and degradation behavior; and their overall bone-tissue rehabilitative efficacy. This collection amalgamates and critically analyses the research aimed at 3DBP of load-bearing scaffolds for fulfilling demands of personalized-medicine. We highlight the recent-advances in 3DBP techniques employing thermoplastics and phosphate-cements for load-bearing applications. Finally, we provide an outlook for possible future perspectives of 3DBP for load-bearing orthopedic applications. Overall, the article creates ample foundation for future research, as it gathers the latest and ongoing research that scientists could utilize.
Effect of lattice boundary on Anderson localization of nonclassical light in optical waveguide arrays
Authors: Majumder Shubradeep , Rai Amit , Vemuri Gautam
Published: September 2023

We study the effect that the boundary of a one-dimensional lattice has on the Anderson localization of nonclassical light in a finite optical waveguide array in which neighboring waveguides are evanescently coupled and controlled disorder is introduced. By investigating the quantum properties of the output when nonclassical light is injected into the waveguide, we show enhancements of localization and quantum features due to the boundary.
Effect of varying molarity and curing conditions on the mechanical and microstructural characteristics of alkali activated GGBS binder
Authors: A Tamilarasan , OM Suganya
Published: September 2023

Geopolymer binder offers a more sustainable choice for producing concrete in comparison to traditional ordinary Portland cement (OPC). The substitution of geopolymer binder for construction practices can decrease carbon dioxide emissions by decreasing OPC usage and repurposing industrial waste materials like ground granulated blast furnace slag (GGBS), fly ash, red mud, silica fume. In order to assess the suitability of GGBS as a binding material, it is essential to conduct conventional tests like consistency, setting times, and compressive strength, which are widely employed in cement testing. This study produced alkali activated paste (AAP) from GGBS and an alkaline activator comprising sodium hydroxide at various molarities from 1 M to 8 M. This investigation focused on the compressive strength of alkali-activated GGBS-based AAP under varying alkali activation molarities and curing conditions, including ambient, hot air oven, and humidity chamber curing. Additionally, the end reaction products of AAP showing higher compressive strength were examined for scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), x-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) analysis. The experimental outcomes indicated that GGBS reduced the final setting time of AAP while increasing its compressive strength. Additionally, increasing the quantity of NaOH in the AAP increased its compressive strength. Furthermore, the research findings indicated that the mechanical properties of the alkali-activated GGBS-based material were notably influenced by the chosen curing conditions. Specifically, ambient curing demonstrated superior compressive strength, measuring at 47.06 MPa after 28 days, surpassing the results obtained from hot air oven curing and humidity curing.
Mechanical properties of an improved grout for cementitious precast beam-column joints
Authors: Jiang Hao T , Zhang XR , Dong JN , Wei LU , Mei Jiangtao
Published: September 2023

This study proposed a new formulation for an improved grout with superior early strength and ultra-high cured strength; it was designed on the basis of the theory of closest packing. Orthogonal experiments were conducted to analyse the effects of four factors, silica powder content, water reducer content, steel fibre content, and water-cement ratio, on the flowability, compressive strength, and compactness of grout. The criteria for determining whether the grout met the requirements for Code included initial flowability greater than 300 mm, flowability more than 260 mm after 30 min, and compressive strength more than 60 MPa after 12 h of standard curing. The results showed that the performance of the grout satisfied specified requirements for Code with small internal voids and acceptable durability. After the ratio of raw materials was optimized, The grout sleeve test showed that the failure occurred in the steel bars outside the sleeve, and no grout pulling, slipping, splitting, or other behaviour occurred within the sleeve, which meant that the specimens met the design requirements. The development of this grout will greatly reduce construction time for Code and improve the quality of connections in prefabricated components. The results of this study will provide a reference for the design and development of new grouts in the future.
Improved passive optical network RoF system based vertical cavity-surface emitting laser (VCSEL) optical source external modulation
Authors: Jalal Sirwan Kareem , Al-Maqdici Raghad Zuhair Yousif
Published: September 2023

Passive Optical Network (PON) is a promising 5 G optical fiber network technology, that can enhance reliability data rate, and bandwidth saving. This simulation-based study investigates the feasibility of implementing a vertical cavity-surface emitting laser (VCSEL) optical source along with wavelength-division multiplexing (WDM) for designing a PON radio over fiber (RoF) system that can authorize multi-subscribers, users, to simultaneously use the same optical fiber for Front long-haul data transmission. Three scenarios are proposed: First, a VCSEL, and a Mach–Zehnder Modulator with a distinctive frequency are made accessible to every user in the PON system. Whereas, in the second scenario, a continuous wave (CW) laser is used to replace the VCSEL in the same PON. 16 users are multiplexed by a WDM and transmitted over a link length of 200 km. The system performance is, thus measured in terms of Q-factor, and it is revealed that the VCSEL-based system outperforms the system utilized CW laser to a distance of 150 km, with a maximum gain in the Q-factor of about 4.5. Both postulated systems are able to achieve a maximum transmission distance of 180 km with a minimum Q-factor of 6. Moreover, to minimize, the input current of around 1 mA and the system complexity, a third scenario is presented in which one VCSEL with 193.1 THz is shared among multiple users. The Q-factor performance is then simulated for up to 72 users, revealing that the minimum level of acceptable Q-factor has been maintained up to a link length of 180 km.
Distribution of bacterial community structures on human scalp hair shaft in relation to scalp sites
Authors: Watanabe Kota , Yamada Azusa , Nakayama Shunichi , Kadokura Toshimori , Sakai Kenji , Tashiro Yukihiro
Published: September 2023

Bacterial community structure on the human skin is specific to each individual and varies among different body sites. In this study, we investigated differences in bacterial community structure among 5 hair sampling sites and among 12 individuals. Significant differences were found between individuals in terms of alpha diversity and relative abundance of major bacterial phyla and genera, whereas no differences were found between hair sampling sites. The principal coordinate analysis plots of within-individual group tended to converge individually, whereas those of within-hair sampling site group did not cluster. In addition, weighted UniFrac analysis showed that the individual-based category was a statistically significant category but not the scalp hair sampling site-based category. These results suggest that the distribution of bacterial community structures on scalp hair shafts within individuals was relatively steady, even when the scalp hair sampling site was different.
Sequence Alignment/Map format: a comprehensive review of approaches and applications
Authors: Liu Yuansheng , Shen Xiangzhen , Gong Yongshun , Liu Yiping , Song Bosheng , Zeng Xiangxiang
Published: September 2023

The Sequence Alignment/Map (SAM) format file is the text file used to record alignment information. Alignment is the core of sequencing analysis, and downstream tasks accept mapping results for further processing. Given the rapid development of the sequencing industry today, a comprehensive understanding of the SAM format and related tools is necessary to meet the challenges of data processing and analysis. This paper is devoted to retrieving knowledge in the broad field of SAM. First, the format of SAM is introduced to understand the overall process of the sequencing analysis. Then, existing work is systematically classified in accordance with generation, compression and application, and the involved SAM tools are specifically mined. Lastly, a summary and some thoughts on future directions are provided.
Relationship of quantitative reverse transcription polymerase chain reaction (RT-PCR) to RNA Sequencing (RNAseq) transcriptome identifies mouse preimplantation embryo reference genes
Authors: Tscherner Allison K , McClatchie Taylor , Macaulay Angus D , Baltz Jay M
Published: September 2023

Numerous reference genes for use with quantitative reverse transcription polymerase chain reaction (RT-qPCR) have been used for oocytes, eggs, and preimplantation embryos. However, none are actually suitable because of their large variations in expression between developmental stages. To address this, we produced a standardized and merged RNA sequencing (RNAseq) data set by combining multiple publicly available RNAseq data sets that spanned mouse GV oocytes, MII eggs, and 1-cell, 2-cell, 4-cell, 8-cell, morula, and blastocyst stage embryos to identify transcripts with essentially constant expression across all stages. Their expression was then measured using RT-qPCR, with which they did not exhibit constant expression but instead revealed a fixed quantitative relationship between measurements by the two techniques. From this, the relative amounts of total messenger RNA at each stage from the GV oocyte through blastocyst stages were calculated. The quantitative relationship between measurements by RNAseq and RT-qPCR was then used to find genes predicted to have constant expression across stages in RT-qPCR. Candidates were assessed by RT-qPCR to confirm constant expression, identifying Hmgb3 and Rb1cc1 or the geometric mean of those plus either Taf1d or Cd320 as suitable reference genes. This work not only identified transcripts with constant expression from mouse GV oocytes to blastocysts, but also determined a general quantitative relationship between expression measured by RNAseq and RT-qPCR across stages that revealed the relative levels of total mRNA at each stage. The standardized and merged RNA data set should also prove useful in determining transcript expression in mouse oocytes, eggs, and embryos.
Order-based structure learning without score equivalence
Authors: Chang Hyunwoong , Cai James J , Zhou Quan
Published: September 2023

We propose an empirical Bayes formulation of the structure learning problem, where the prior specification assumes that all node variables have the same error variance, an assumption known to ensure the identifiability of the underlying causal directed acyclic graph. To facilitate efficient posterior computation, we approximate the posterior probability of each ordering by that of a best directed acyclic graph model, which naturally leads to an order-based Markov chain Monte Carlo algorithm. Strong selection consistency for our model in high-dimensional settings is proved under a condition that allows heterogeneous error variances, and the mixing behaviour of our sampler is theoretically investigated. Furthermore, we propose a new iterative top-down algorithm, which quickly yields an approximate solution to the structure learning problem and can be used to initialize the Markov chain Monte Carlo sampler. We demonstrate that our method outperforms other state-of-the-art algorithms under various simulation settings, and conclude the paper with a single-cell real-data study illustrating practical advantages of the proposed method.
The Incidence and Prevalence of Inflammatory Bowel Disease Continues to Increase in the Faroe Islands – A Cohort Study from 1960 to 2020
Authors: Nielsen Kári Rubek , Midjord Jóngerð , Nymand Lophaven Søren , Langholz Ebbe , Hammer Turid , Burisch Johan
Published: September 2023

Background and Aims

The highest reported incidence rate of inflammatory bowel disease [IBD], and especially of ulcerative colitis [UC], is found in the Faroe Islands. This study aimed to assess the incidence rate and temporal trends in prevalence over six decades.

Methods

All incident and prevalent patients diagnosed with IBD between 1960 and 2020 from the nationwide and population-based Faroese IBD cohort were included in this study. All patients fulfilled the Copenhagen Diagnostic Criteria.

Results

Overall, 873 individuals were diagnosed with IBD during the study period, 559 [64%] with UC, 151 [17%] with Crohn’s disease, and 163 [19%] with IBD unclassified. A total of 59 patients had paediatric-onset IBD. The incidence of IBD continued to increase throughout the study period, as the age-standardized incidence rate started at 8 per 100 000 person-years [py] [European Standard Population, ESP] in 1960–79 and reached 70 by 2010–20. In 2021, the age-standardized period prevalence was 1414 per 100 000 persons. The IBD incidence was unevenly distributed among the islands with Sandoy having the highest rate of 106 per 100 000 py in 2010–2020.

Conclusions

The incidence of IBD continues to increase in the Faroe Islands, mainly driven by UC. The incidence shows an uneven geographical distribution, which suggests an adverse interaction between unknown environmental factors and genetic traits. The prevalence in 2021 corresponded to 1.3% of the Faroese population. Environmental risk factors are suspected to impact this homogeneous high-risk population; however, the reason for this is unclear.
Parental care shapes the evolution of molecular genetic variation
Authors: Mashoodh Rahia , Trowsdale Angela T , Manica Andrea , Kilner Rebecca M
Published: September 2023

Cooperative social behaviors, such as parental care, have long been hypothesized to relax selection leading to the accumulation of genetic variation in populations. Although the idea has been discussed for decades, there has been relatively little experimental work to investigate how social behavior contributes to genetic variation in populations. Here, we investigate how parental care can shape molecular genetic variation in the subsocial insect, Nicrophorus vespilloides. Using whole-genome sequencing of populations that had evolved in the presence or absence of parental care for 30 generations, we show that parental care maintains levels of standing genetic variation. In contrast, under a harsh environment without care, strong directional selection caused a reduction in genetic variation. Furthermore, we show that adaptation to the loss of care is associated with genetic divergence between populations at loci related to stress, morphological development, and transcriptional regulation. These data reveal how social behavior is linked to the genetic processes that shape and maintain genetic diversity within populations, and provides rare empirical evidence for an old hypothesis.
Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research
Authors: Baker Jonathon L
Published: September 2023

The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.
Tree Mastication and Helimulching: Two Alternatives for Mitigating Soil Erosion and Carbon Loss After Wildfire
Authors: Fernández Cristina
Published: September 2023

The use of masticated tree debris to protect burned soil from post-fire erosion is not common and very little is known about its effectiveness in reducing the risk of erosion after fire. The main objective of this research was to assess the effects of agricultural straw helimulching and tree mastication on soil and carbon losses and recovery of vegetation during 2 years after fire in two wildfire-affected areas in northwestern Spain. Eighteen plots were established in each experimental site for monitoring the following treatments: helimulching, mastication, and control (untreated burned soils). Salvage logging was carried out in the first spring after fire in one of the experimental areas, thus enabling study of whether the application of mulch after fire also protects the soil during logging. Mean soil cover in helimulched areas was more than 90% in both experimental sites, whereas masticated slash from juvenile pine trees covered around 60% of the burned soil. In both study sites, soil and carbon losses were significantly higher in the untreated soils than in the helimulched and masticated soils. Mulching was effective in reducing soil and carbon losses even after salvage logging.

Study Implications: The use of mulches to protect burned soil from post-fire erosion is becoming common in fire-prone areas. Agricultural straw is the most common material, whereas other alternatives such as the use of masticated tree debris to reduce soil erosion risk after fire is not as common. The results obtained in this study show that mastication of noncommercial trees is a feasible technique to reduce post-fire soil erosion, although cover of more than 60% must be achieved to reduce soil erosion and carbon loss to sustainable values. Application of straw mulch is effective to protect burned soil during salvage logging.
Missing persons patterns from Mexico: evidence of a forensic emergency crisis
Authors: Quinto-Sanchez Mirsha , Huerta-Pacheco N Sofia
Published: September 2023

The relatives of missing persons in Mexico have denounced the slowness with which a court prosecution file is created by the justice administration system. Theoretically, the search is immediate, but many cases must wait 72 h to build an investigation folder as a legal criterion. This standard has been copied from the UK and Australian police reports without adapting to the Mexican context. The analysis of disappearance reports between 2006 and 2018 shows that this timing criterion in Mexico is not supported. The analyzed database (the National Center for Planning, Analysis, and Information to Combat Crime, CENAPI) showed that in the 72-h range, only 34.53% of the people had been found alive or dead; figure far from 50% to 80% of Europe or Australia. This fact shows that those searching officers or the judicial bureaucracy can act as a factor that limits the search for missing persons. Additionally, there is a random pattern in the geospatial distribution of disappearance, with non-homogeneous frequencies per year. Results highlight the participation of families, the adoption of an evidence-based model, and the generation of geospatial forensic intelligence analysis to generate evidence-based public policies. The social demand of families to the government for not considering them takes relevance in forensic practice in Mexico, and the disappearance data support this assertion.
Improving the quality of high-frequency surface waves retrieved from ultrashort traffic-induced noise based on eigenvalue selection
Authors: Ning Ling , Xia Jianghai , Dai Tianyu , Zhang Hao , Liu Ya , Hong Yu
Published: September 2023

Stacking cross-correlations of time windows from continuous long-duration noise data is an effective solution to improve the quality of retrieved high-frequency (>1 Hz) surface waves and the accuracy of dispersion energy. The observation duration, however, is usually limited due to traffic control, making it difficult for ambient noise sources to fulfill the requirement of uniform distribution. Additionally, strong human-related noise sources exist near survey lines deployed along urban roads, which often act as interfering sources, such as local noise sources located in the non-stationary-phase zones. Local noise sources cause spurious arrivals in cross-correlations, degrade signal-to-noise ratio (SNR) of retrieved surface waves and distort their dispersion energy. To attenuate these adverse effects and improve the quality of surface waves retrieved from ultrashort noise data, we perform the eigendecomposition technique on the cross-spectral density matrix (CSDM) and apply a Wiener filter on the decomposed eigenvectors. The correct eigenvalues and the corresponding filtered eigenvectors are selected to reconstruct the CSDM related to stationary-phase sources based on the matched-field processing outputs. This procedure significantly suppresses the backpropagated signals and efficiently recovers surface waves by improving the contribution of the stationary-phase sources. We validate our scheme on a synthetic test and two practical applications and show that we obtain higher-SNR virtual shot gathers and higher-quality surface-wave dispersion images compared to seismic interferometry. Our scheme can be a new alternative technique to conduct passive seismic surveys in densely populated urban environments without being affected by local noise sources.
Short incubation of disc diffusion for Streptococcus pneumoniae and Haemophilus influenzae to reduce time to susceptibility report
Authors: Åkerlund Anna , Serrander Lena , Sundqvist Martin
Published: September 2023

Background

Rapidly instituted antimicrobial therapy is important in severe infections, and reduced time to the antimicrobial susceptibility testing (AST) report is thus of importance. Disc diffusion (DD) is a cheap, rapidly adaptable, flexible and comprehensive method for phenotypic AST. Previous studies have shown that early reading of inhibition zones for non-fastidious species is possible.

Objectives

To evaluate zone reading after short incubation of DD in Haemophilus influenzae (n = 73) and Streptococcus pneumoniae (n = 112).

Methods

The readability was evaluated and susceptibility interpretation (SIR) was performed, using the EUCAST 18 ± 2 h incubation breakpoint table (version 12.0), after 6 and 8 h of incubation. Categorical agreement (CA) and error rates were calculated using standard DD and broth microdilution as reference.

Results

The proportion of readable zones in H. influenzae was 19% (6 h) and 89% (8 h). The CA was 98% after 8 h. The corresponding readability in S. pneumoniae was 63%/98% and CA was 95%/97% after 6 and 8 h, respectively. Early reading of the screening discs (benzylpenicillin 1 unit in H. influenzae and oxacillin 1 µg in S. pneumoniae) correctly identified 18/22 of the H. influenzae isolates and all the readable S. pneumoniae isolates with reduced β-lactam susceptibility. For non-β-lactam agents, very major errors were most common for quinolones in S. pneumoniae. Introduction of areas of technical uncertainty (ATUs) reduced the error rate to ≤1.1%.

Conclusions

We conclude that shortened incubation is feasible for H. influenzae and S. pneumoniae. To reduce the risk of false categorization a buffer zone (i.e. ATU) near the breakpoints must be used.