bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Different Combinations of NPK Fertilizer and Seed Quantities on The Yields of Green and Dry Fodder for Egyptian Clover (Meskawi)
Authors: alzlzly Mohammad hachim nassir , Al-Tahir Faisal Mihbass Madlol
Published: November 2021

A field experiment was carried out at Abu Al-Fadl Forest Nursery affiliated to Al-Diwaniyah Agriculture Directorate (2 km away from the city center), during the winter season (2020-2021). In order to determine the best combination of NPK fertilizer under influence of different seeding rates to shorten the life of cutting the first To increase cutting number during the growing season and to improvment the quantity and quality of green and dry fodder and seed yield, The experiment includes six combinations of NPK fertilizer are (0-0-0), (20-15-10), (40-30-20), (60-45-30), (80-60-40) and (100-75-50) kg ha−1, and four of seeding rates are (20, 40, 60, 80) kg ha−1, The experiment was applied according to the arrangement of the split plots and using R.C.B. Design with three replications. The combination of NPK fertilizer were placed in the main-plot and the quantities of seeds in the sub-plot. The results showed that NPK5 fertilizer level excelled the yields of green and dry forage for the fourth cutting (20.98, 2.28) ton ha−1 respectively, and The total green and dry fodder yields (60.87, 6.48) ton ha−1 respectively, While the fertilizer level NPK4 exceeded The ratio of leaves to stems for the fourth cutting (37.61%). As for the of seeding rates, the results showed that (80 kg h−1) excelled for the ratio of leaves to stems for third cutting (34.67%) yields of green and dry fodder for the first cutting (9.92, 1.03) ton ha−1 respectively, and the total green fodder yield (59.40 t.h-1), While the 60 kg h−1 excelled the yields of green fodder for the second, third and fourth cutting (13.04, 19.50 and 17.64) ton ha−1, dry forage yield of the second, third and fourth cutting (1.47, 1.94, and 1.90) ton ha−1sequentially. and the total dry fodder yield (6.25) ton ha−1.
Response of Safflower to (N.P.K) Fertilizer Combinations and Plants Distribution
Authors: Jaffar Razaq Abd-Alrab , Al-Refai Shaimaa Ibraheem
Published: November 2021

To find out the effect of fertilizer levels and of plants distribution on safflower yield, an experiment was conducted in Iraq - Al-Diwaniyah Governorate in the growing season 2020/2021, The experiment included three replicates with 60 experimental units, and it included combinations levels of fertilization(F1F2, F3 and F4) which represented the following fertilizer levels(N0, P0, K0) (N140, P80, K40) (N160, P100, K60) (N180, P120, K80)Kg.h−1, in addition to five planting distribution (D1, D2, D3, D4 and D5) follows (30 × 30, 40 × 40, 50 × 50, 60 × 60 and 70 × 70 cm). The results showed that the fertilization level(N180, P120, K80) it gave the highest mean of seed weight and head diameter, which amounted to(23.12 g and 2.88cm) respectively. As for the plant distribution D5, Gave the highest of weight of the yield of petals, Head diameter and plant heads number reached to (2.23 g, 2.93 cm, 83.14 head. plant−1) respectively. While the superiority of the treatment D4 was in In seeds number per head 44.88 seed. head−1. Therefore, plants distribution between plants can be reduced with increased fertilization from NPK in the area.
Effect of Humic Acid on Growth and Yield Several Genotypes of Rice (Oryza Sativa L.)
Authors: Al-bourky Ragheb hadi , Manshood Mustafa A. , Mahmoud Mohammed Radwan , Al-mousawy Salama Tahseen
Published: November 2021

A field experiment in the province of Muthanna during the summer season 2014-2015 to study the effect of three levels of humic acid on the growth and yield five genotypes of rice, the experiment carried out using a design Split Plot Design with three replications as occupied the main panels three levels of Humic acid (0, 2 and 4) ml liter−1 while genotypes occupied (IR-60819 and PR-2235 and Mchkab-1 and Jasmine and Amber-33) secondary panels. The results showed that there were significant differences between the humic acid leves, treatment 4 ml liter −1 overtook in a period of flowering (109.88 days), plant height, (99.33 cm) area of flag leaf, (38.11 cm2) number of panicle 373.33 panicle/m2 the number of grains 129.83 grains/panicle and yield grains 4.66 ton/h and there was no significant difference in grain weight, as well as the presence of significant differences between genotypes for all growth traits, as observed superiority of class dormitory -33 moral in the period of flowering, (110.88 days), Mchkab−1 in plant height, (111.34 cm) Yasmin in the flag leaf area, which amounted to 45.00 cm 2, as it gave the class Mchkab-1 highest number of Panicles totaled 400.00 Panicles/m2, and the superiority of product was Jasmine and averaged 145.11 grain/Panicle, and the superiority of genotype RP -2235 average grain weight of 20 mg were given a The interaction (4 × Mchkab−1) higher average plant height was 118.27 cm whereas given the The interaction (0× IR-60819) less than an average of 77.44 cm, either on the flag leaf area has given The interaction (4 × Yasmin) averaged 45.45 cm 2, while given the The interaction (0 × RP-2235) below average for this trait was 30.02 cm 2, and for yield and its components given The interaction (2 × Mchkab−1) the highest average number of Panicles 450.00 Panicle/m 2, while the number of grains in the deltoid has The interaction gave (2 × Yasmin) the highest average number of grains/Panicle totaled 150.00 grain/Panicle while given The interaction (4 × IR-60819) less than an average of 98.66 grain/Panicle, also was given The interaction (2 × Mchkab −1) yield the highest average grain amounted to 5.82 tons/h, while the The interaction gave (0 × IR-60819) less than the average stood at 3.05 tons/ha.
The Effect of Efficacy Local Isolates of Paenibacillus Bacteria on Available Soil Phosphorus and Growth of Cultivars Wheat (Triticum Aestivum L.)
Authors: Noni Ghanim Bahlol , Ayat Hassan Abd
Published: November 2021

A field experiment was carried out to study the effect of bio-inoculation with three local isolates of P. polymyxa and three Varieties of wheat on the growth and yield of the wheat plant (Triticum aestivum L). In the second agricultural research station affiliated to the College of Agriculture - University of Al-Muthanna, a field experiment was conducted in Al-Muthanna Governorate for the year 2020 in silty clay Loam soil texture. The experiment was designed in a randomized complete block method (RCBD) and with three replications. The experiment included two factors, where the first factor represents the local isolates of four levels, symbolized by P0-P1-P2-P3, and the second factor represents the three wheat varieties, Buhouth class 22, Iraq class, and Ibaa 99, which symbolized C1-C2-C3 respectively. The results showed the following: First: The P3 bio-pollination treatment achieved a significant increase in soil phosphorus, potassium, and nitrogen in the available part at the flowering stage, as the highest average was recorded for them (11.39 mg kg −1 soil - 1.4300%-1.4,000%), and the P2 treatment was superior for both soil potassium and plant height. And the dry weight, the highest average for them was recorded (157.8 mg kg −1 - 92.6 cm - 10.61 g plant −1). Second: As for the cultivars, they differed in most of the characteristics of the study. The Iraq cultivar excelled in soil phosphorous concentration with an average of (11.06 mg kg −1 soil), while Buhouth cultivar 22 was superior in soil potassium with an average of (158.02) mg kg −1 soil. Ibaa 99 had been recorded concentration nitrogen and potassium in plants with averages of (1.4208,1.3474%). Third: When the isolates overlapped with the cultivars, a discrepancy was observed. It gave Samawa isolate with Bohouth class 22 by recording the highest average in soil potassium concentration and plant height amounting to (166.7 mg kg −1 soil, 99.8 cm) respectively, while Al-Khidr isolate with Ibaa 99 cultivar in nitrogen and potassium concentration plant, where it reached (1.4567-1.4400)%, while the isolate without addition outperformed with the cultivar Iba 99 for dry weight, as it reached its highest average (11.40 gm plant −1). The isolate of vegetables also outperformed Iraq cultivar for phosphorous concentration in soil, as it recorded the highest average of (12.30) mg kg −1 soil.
Effect of Source of Organic Matter Level and Phosphorous Level on Phosphorous Forms and Humic Acids Release in Gypsiferous Soil
Authors: Muhawish Noor AL-Dean Mohammed , Hilal Nashmi Ahmed
Published: November 2021

A laboratory experiment was conducted in the Department of Soil Sciences and Water Resources, College of Agriculture/Tikrit University for the year 2019 for the purpose of studying the effect of the source and level of organic matter and the level of added phosphorous on the level of phosphorous forms and humic acids in gypsum soil. A factorial experiment was conducted with three factors: The first factor: the type of organic matter (sheep manure and compost), the second factor: the level of organic matter as follows (0.5, 1.0, 1.5)% of the weight of the soil, and the third factor: it included phosphorous levels (0, 40, 80, 120) mg kg−1. The experiment was carried out in a complete randomization design (RCD) with three replications. To reach the field capacity to maintain the humidity of the experimental units, after the end of the incubation period (two months), the samples were air-dried, ground and passed through a sieve with holes (2) mm in diameter, then humic and fulvic acids, soluble, ready-made and organic acids were measured. With water and phosphorous prepared and organic by increasing the level of organic matter added, 1.5% was the best. It was also noted that the best level of phosphorous for the above indicators was the level (120) mg kg−1compared to the rest of the levels, and that sheep manure outperformed the organic fertilizer in all the studied traits. Interventional treatment of 1.5% of the residual organic matter at a level of (120) mg kg−1gave the highest significant effect, and the concentrations of humic and fulvic acid were (8.35 and 2.95) g kg−1respectively. The treatment gave 1.5% organic matter for sheep manure and (120) mg kg−1which is the highest value in the amount of water-soluble, ready-made and organic phosphorus with an average of (13.80, 71.35 and 167.44) mg kg−1respectively.
Epidemiological Study of Common Bacterial and Parasitic Infections in Some Areas of Salah Al-Din Governorate, Iraq
Authors: Sabry Nuha Nazar , Owaied Yassin Hussein , Mahmoud Ashraf Jamal
Published: November 2021

The study was conducted for the period from October 2020 to April 2021 and includes the collection of 450 feces samples from patients visiting Salah El-Din General Hospital. to investigate the spread of bacteria and intestinal parasites. The results showed that the percentage of bacterial infection among males was 19.50% and females 14.83%. As for the parasitic infection, males recorded 12.44% and females 8.71%, and the highest rate of infection with E. Coli bacteria was recorded for the category (1-10) years it reached 8.82%. As for salmonella, the group (21-30) years recorded the highest infection rate of 8.64%. With regard to infection with intestinal parasites, it reached The total infection rate with E. histolytica was 6.88%. The group (1-10) years recorded the highest infection rate of the parasite, which amounted to 13.23%. As for the Giardia parasite, the total infection rate was 2.88%. The group (21-30) years recorded the highest infection rate of 6.17%. As for the months of the study, the highest bacterial and parasitic infection rate was in February, amounting to 22.66% and 16%, respectively.
Effect of Different Harvest Dates on Yield and Quality of Wheat Cultivars Triticum Aestivum L
Authors: Al-husnawy Asmaa Sahib Abd Al-Abbas , Al-refai shaimaa Ibraheem
Published: November 2021

Afield experiment was conducted at the Research station of the college of Agriculture - University of Al-Muthanna, in the Northeast of Al-Muthanna Governorate (9 km from center of the city of Samawa), in the seasons (2018-2019) and (2019-2020), to study the effect of four harvest dates and four varieties of wheat on yield and quality characteristics, The experiment was applied according to split-plots design Using the R.C.B.D with three replications, The results of the analysis showed the Significant effect of harvest dates on all studied traits, as the date of the third harvest increased by giving the highest grain yield of 5.01 and 5.32 t h−1 for the two seasons respectively, while the fourth harvest date was superior by giving the highest percentage of dry gluten in the first season amounted to 11.66%. As for the effect of the cultivars, it was noticed that the Babel cultivar was superior in grain yield of 4.81 and 5.04 t ha−1, for the two seasons respectively, while the Bora cultivar gave the highest average weight of 1000 grains for the second season which amounted to 32.68 g, and the percentage of protein in the grains was 12.83% for the second season, and Ash was 1.90 and 1.85% for the two seasons sequentially, while the interaction of the fourth harvest date with Babel cultivar was superior by giving highest weight of 1000 grains in the first season amounted to 33.41 m, while the interaction of the first harvest date with Bora cultivar in the vital yield first season was 16.6 t h−1.
Study of Vegetative Growth Characteristics for Seven Genotypes of Durum Wheat (Triticum Durum L.) Newly Derived Under Three Seeding Ratesin The Conditions of Anbar Governorate
Authors: Al-Haiti M. J. H. , Alubaidi M. O. G.
Published: November 2021

A field experiment was carried out in the fields of a farmer in the area of (Zakhikha) with mixed sandy soil, loam sand, which is one of the rural areas of western Heet district (about 15 kg) affiliated to Anbar Governorate during the season 2020-2021, to study seven newly derived genotypes from durum wheat, including two cultivars. They are registered, accredited, and commonly cultivated in Iraq, under three different seeding Ratesto select the ones that are suitable for the conditions of Anbar Governorate. The experiment layer was according to the randomized complete block design (RCBD), in the order of split - plots and with three replications. It included seeding Rates(140, 160 and 180 kg.ha−1) main plots. As for the sub plots, they were occupied by the seven genotypes (Latifa, genotype Babel-30, genotype Babel-31, genotype Babel-32, genotype Babel-86, and the two approved cultivars Dor-29 and Dor-85): The genotype (Babylon-32) outperformed the means number of tillers (573.3 m2) and the biological yield (22.94 mcg ha−1). While the genotype (Babylon-86) was superior to the plant height (113.02 cm). As for the variety (Dor). -85) It was superior in Flag leaf area (58.12 cm2) and the number of days from planting to 50% of physiological maturity (164.67 days). The genotyped plants of wheat grown with different seeding Rates showed significant differences among themselves in the characteristics of vegetative growth, where the plants grown at a seeding rate of (180 kg ha−1) recorded the highest means in the trait of plant height (105.20 cm), number of tillers/m2(596.9 tillers) and biological yield (23.31 mega grams ha−1), while planting plants at seeding rates (140 kg.ha−1) resulted in recording the highest rate of Flag leaf area (53.85 cm2), while planting plants at seeding rates (160 kg.ha−1) recorded the highest Means number of days from planting to 50% and physiological maturity (167.38 days). There was a significant interaction between the genotypes and seeding Rates of the wheat included in the study.
Selection of Parameters (Heritability, Expected Genetic Advance, Correlations and Genetic Variances) For Introduced Hybrids of Maize Zea Mays L
Authors: Ahmed Shehab Ahmed Rabie , Mohammed Mohammed Ibrahim
Published: November 2021

A factorial experiment was conducted in Kirkuk govemorate, in which six introduced hybrids (DK 6050, Gimbson, ZP707, ZP6263, Saganto, Glorya) were used, purchased from local markets, and four chemical herbicides (Turkish Nicosulfuron, Rimsulfuron, Atrazine 80%, Nicosulfuron Chinese), as well as a comparison treatment that was purchased from the different original to study growth traits and yield its compound, the effect of each cross, estimation of variances, coefficients of variation, heritability, expected genetic improvement, genetic, environmental and phenotypic correlations for the of herbicides. The results showed that there were significant differences between hybrids in all traits except for the number of grains per ear, index of harvest, and selling %. The highest hybrid ZP707 was in the traits of plant height, ear leaf area, number of ear per plant, ear length, number of grains per row, number of grains per row, number of grains per row, ear weight, biological yield, harvest index and grain yield per plants, as it reached 183.03, 412.00, 1.14, 19.18, 36.97, 568.86, 221.27, 368.39, 59.85 and 205.45, respectively. The genetic correlation of grain yield plant was significant with all traits except the number of leaves per plant, weight of 300 grains, selling %, protein %, and hectoliter, which amounted to -0.406, - 0.385, -1.231, -0.466, -0.546 and -0.807 respectively. The phenotypic correlation of grain yield per plant was significant with all traits except for the number of leaves per plant, the weight of 300 grains, selling %, protein %, and hectoliter, as it amounted to -0.401, -0.332, -0.652, -0.424, -0.514 and -0.652, some of them were not significant and other Negative significant. The environmental correlation of grain yield with the plant was significant with some characteristics such as ear leaf area, number of ears per plant, number of rows per ear, ear weight, and biological yield, which amounted to 0.746, 0.555, 0.542, 0.663, and 0.509, respectively. The highest genetic and phenotypic difference coefficient for a number of grains per ear was 13.80 and 14.37, and the heritability was high in all traits except harvest index and grain yield per plant, which was medium, amounting to 40.15 and 50.35, and selling % and protein % was low, which reached 14.60 and 35.46 respectively, and highest expected genetic improvement for a number of grains per ear was 27.31.
Effect of Magnetization of Nano Fertilization on The Growth and Yield of Wheat Triticum Aestivum L
Authors: Yasir Al-Saidan Khudhair Joudah
Published: November 2021

A field experiment was conducted in Al-Fadhiliya city, Dhi Qar province during the winter agricultural season 2019 - 2020 for the purpose of studying the effect of magnetization of nano Fertilization on the growth and yield of wheat. The experiment was carried out according to Split Plot Design and using the RCBD Design with three replications. The first factor included Magnetization levels of the Nano Fertilization (Gs) (0 Gs (Gs1),750 Gs (Gs2),1500 Gs (Gs3) for 15 minute (in main plot) while the second factor included the Nano Fertilization levels for (N, P) (F) 1 Kg.ha−1(F1), 1.5 Kg.ha−1(F2), 2 Kg.ha−1(F3)(according to the recommendation of the manufacturer (1 - 2 Kg.ha−1))(in sub plot). Mineral fertilizer add for (N, P) by 120 Kg N.ha−1, 100 Kg P ha−1. Mineral and nano fertilizer section for three growth stages (ZGs21, ZGs32, ZGs49). The results showed a positive response to the studied traits of variety Bohouth 22 (Plant height, number of tillers, number of grains and total grain yield) given the highest averages at the level of magnetism (Gs3) and fertilization level (F3)(109.33 cm, 426.2 tiller.m−2, 73.22 grain. spike−1, 1.859 t.d−1),(108.44 cm, 471.4 tiller.m−2, 77.78 grain. spike−1, 1.915 t.d-1) respectively, while the level of magnetism (Gs1) and fertilization level (F1) giving the lowest averages (95.11 cm, 341.3 tiller.m−2, 60.11 grain. spike−1, 1.437 t.d−1), (96.22 cm, 312.1 tiller.m−2, 54.00 grain. spike−1, 1.412 t.d−1) respectively. The level of magnetism (Gs1) and fertilization level (F1) gave the highest average in weight 1000 grain (43.188, 44.266)g respectively, while the magnetization level (Gs3) and fertilization level (F3) giving the lowest average (42.092,41.182)g respectively. Interaction treatment (Gs3F3) gave the highest average grain yield 2.1773 t.d−1 while the interaction treatment (Gs1F1) gave the lowest average attained 1.218 t.d−1.
Numerical Investigation of the Shallow Water Effect on the Total Resistance, Vertical Motion and Wave Profile of a Container Ship Model
Authors: Bekhit A , Popescu F
Published: November 2021

A ship sailing in shallow water is affected by the interaction between the moving hull and the seabed in different forms such as: significant increase in total resistance, increase in the sinkage and trim that may result in squatting effect, a change in wave pattern and increased wave amplitude, a change in the propeller wake field and an altered propeller and manoeuvring performance. In order to investigate the influence of shallow water on a container ship that is assumed to be subjected to work in different water depths, the KRISO container ship model is analysed in both deep and shallow water, with a special focus on the change in resistance, vertical motion and wave profile. A viscous flow simulation is performed first to predict the ship performance in deep water and the results are compared with the experimental data that are available in the public domain. Then, the critical shallow water condition is investigated and the obtained results are compared against those formerly obtained in deep water. The numerical simulations are performed using the viscous flow solver ISIS-CFD of the FINETM/Marine software provided by NUMECA. The solver is based on the finite volume method to build the spatial discretization of the transport equation in order to solve the Reynolds-Averaged Navier-Stokes (RANS) equations. Closure to turbulence is achieved using the Menter Shear Stress Transport (K-ω SST) model, while the free-surface is captured through an air-water interface based on the Volume of Fluid (VOF) method. The comparison between the numerically obtained results and the available EFD data showed a satisfactory congruence.
Electrodeposited WS2 monolayers on patterned graphene
Authors: Noori Y J , Thomas S , Ramadan S , Greenacre V K , Abdelazim N M , Han Y , Zhang J , Beanland R , Hector A L , Klein N , Reid G , Bartlett P N , de Groot C H
Published: November 2021

The development of scalable techniques to make two-dimensional (2D) material heterostructures is a major obstacle that needs to be overcome before these materials can be implemented in device technologies. Electrodeposition is an industrially compatible deposition technique that offers unique advantages in scaling 2D heterostructures. In this work, we demonstrate the electrodeposition of atomic layers of WS2 over graphene electrodes using a single source precursor. Using conventional microfabrication techniques, graphene was patterned to create micro-electrodes where WS2 was site-selectively deposited to form 2D heterostructures. We used various characterization techniques, including atomic force microscopy, transmission electron microscopy, Raman spectroscopy and x-ray photoelectron spectroscopy to show that our electrodeposited WS2 layers are highly uniform and can be grown over graphene at a controllable deposition rate. This technique to selectively deposit transition metal dichalcogenides over microfabricated graphene electrodes paves the way towards wafer-scale production of 2D material heterostructures for nanodevice applications.
Deeptime: a Python library for machine learning dynamical models from time series data
Authors: Hoffmann Moritz , Scherer Martin , Hempel Tim , Mardt Andreas , de Silva Brian , Husic Brooke E , Klus Stefan , Wu Hao , Kutz Nathan , Brunton Steven L , Noé Frank
Published: November 2021

Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics to fluid mechanics. In the physical sciences, structures such as metastable and coherent sets, slow relaxation processes, collective variables, dominant transition pathways or manifolds and channels of probability flow can be of great importance for understanding and characterizing the kinetic, thermodynamic and mechanistic properties of the system. Deeptime is a general purpose Python library offering various tools to estimate dynamical models based on time-series data including conventional linear learning methods, such as Markov state models (MSMs), Hidden Markov Models and Koopman models, as well as kernel and deep learning approaches such as VAMPnets and deep MSMs. The library is largely compatible with scikit-learn, having a range of Estimator classes for these different models, but in contrast to scikit-learn also provides deep Model classes, e.g. in the case of an MSM, which provide a multitude of analysis methods to compute interesting thermodynamic, kinetic and dynamical quantities, such as free energies, relaxation times and transition paths. The library is designed for ease of use but also easily maintainable and extensible code. In this paper we introduce the main features and structure of the deeptime software. Deeptime can be found under https://deeptime-ml.github.io/.
Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture
Authors: Strock Christopher F , Rangarajan Harini , Black Christopher K , Schäfer Ernst D , Lynch Jonathan P
Published: November 2021

Background and Aims

Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies.

Methods

We utilize the functional–structural plant model ‘OpenSimRoot’ to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with (1) uniform bulk density, (2) plow pans and (3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources.

Key Results

Soils with plow pans and bulk density gradients affected overall size, distribution and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of nitrogen and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these.

Conclusions

While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.
Genomic style: yet another deep-learning approach to characterize bacterial genome sequences
Authors: Yoshimura Yuka , Hamada Akifumi , Augey Yohann , Akiyama Manato , Sakakibara Yasubumi
Published: November 2021

Motivation

Biological sequence classification is the most fundamental task in bioinformatics analysis. For example, in metagenome analysis, binning is a typical type of DNA sequence classification. In order to classify sequences, it is necessary to define sequence features. The k-mer frequency, base composition and alignment-based metrics are commonly used. On the other hand, in the field of image recognition using machine learning, image classification is broadly divided into those based on shape and those based on style. A style matrix was introduced as a method of expressing the style of an image (e.g. color usage and texture).

Results

We propose a novel sequence feature, called genomic style, inspired by image classification approaches, for classifying and clustering DNA sequences. As with the style of images, the DNA sequence is considered to have a genomic style unique to the bacterial species, and the style matrix concept is applied to the DNA sequence. Our main aim is to introduce the genomics style as yet another basic sequence feature for metagenome binning problem in replace of the most commonly used sequence feature k-mer frequency. Performance evaluations showed that our method using a style matrix has the potential for accurate binning when compared with state-of-the-art binning tools based on k-mer frequency.

Availability and implementation

The source code for the implementation of this genomic style method, along with the dataset for the performance evaluation, is available from https://github.com/friendflower94/binning-style.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Geodispersal of the Typical Neotropical cenocron from South America to the Mexican Transition Zone: a cladistic biogeographical test
Authors: López-García Margarita M , Morrone Juan J
Published: November 2021

Analysis of the biotic assembly of the Mexican Transition Zone (MTZ) is challenging because of the convergence of taxa with different origins and biogeographical histories. The typical Neotropical cenocron corresponds to genera widespread in South America that might have dispersed to the MTZ in the Pliocene–Holocene. It has been exemplified with distributional patterns of several plant and animal taxa; however, their historical congruence has not been tested. We examined the historical relationships among the areas of endemism where Typical Neotropical taxa are found through a cladistic biogeographical analysis to determine whether they have dispersed simultaneously, showing a geodispersal pattern. We searched for Neotropical clades that dispersed to the MTZ from the Pliocene to the present. The distribution of nine animal clades in seven areas of endemism was analysed by cladistic biogeography. Redundant areas and widespread taxa were treated with paralogy-free and transparent methods. Patterns of area relationships were searched using a parsimony analysis of paralogy-free subtrees. The parsimony analysis found a single resolved tree showing a general pattern of area relationships: (Chacoan ((South Brazilian (Boreal Brazilian + Lesser Antilles)), (South American Pacific (Mesoamerican-Central America + Western Mexico)))). Distributional and phylogenetic information on the groups analysed contrast with a previous cladistic biogeographical analysis that has shown different area relationships, thus supporting the general hypothesis of a geodispersal event of the Typical Neotropical cenocron in the MTZ. Additionally, the analysis provided evidence of vicariant events related to the lifting of the Northern Andes and climatic changes during the Pleistocene.
Phylogeny is a stronger predictor of activity than allometry in an African mammal community
Authors: Kasozi Herbert , Moll Remington J , Kityo Robert M , Montgomery Robert A
Published: November 2021

In promoting coexistence, sympatric species often partition shared resources along spatio-temporal domains. Similarly sized and phylogenetically close species, for instance, partition the times of day in which they are active to limit interference competition. Given that variation in species body mass has evolutionary underpinnings, species activity levels (time spent active in a 24-h daily cycle) within animal communities might be structured by phylogeny. However, few studies have tested this hypothesis across animal communities, and none among medium-sized to large mammals. We quantified the relative contributions of phylogeny and body mass in predicting activity levels in a community of 22 sympatric mammal species in Murchison Falls National Park, Uganda. We show that phylogeny is a stronger predictor of species activity levels than body mass. Our findings provide empirical evidence for the phylogenetic structuring of mammal activity in diverse communities. More broadly, our results suggest that evolutionary relationships mask allometry in predicting species traits in diverse animal communities.
Paediatric Ulcerative Colitis Is a Fibrotic Disease and Is Linked with Chronicity of Inflammation
Authors: Gordon Ilyssa O , Abushamma Suha , Kurowski Jacob A , Holubar Stefan D , Kou Lei , Lyu Ruishen , Rieder Florian
Published: November 2021

Background and Aims

Intestinal fibrosis has recently been characterised in adult ulcerative colitis and may affect motility, diarrhoea, and the symptom of urgency. We aimed to charactersze the presence of fibrosis in paediatric patients with ulcerative colitis, and its link to severity and chronicity of mucosal inflammation, as well as clinical factors of severity.

Methods

We performed a single-centre cross-sectional study in children ages 1–18 years with ulcerative colitis, undergoing colectomy or proctocolectomy. Tissue cross-sections were derived from proximal, mid, and distal colon and rectum, and inflammation and fibrosis were graded based on previously developed scores. Clinical data were collected prospectively.

Results

From 62 patients, 205 intestinal sections were evaluated. Median age at diagnosis was 13 years, 100% had extensive colitis, and all resections were done for refractory disease. The presence, chronicity, and degree of inflammation were linked with the presence of fibrosis. Thickness of the muscularis mucosa was also linked with presence and chronicity of inflammation. The overall submucosal fibrosis burden was associated with prior anti-tumour necrosis factor use.

Conclusions

Paediatric patients with ulcerative colitis exhibit colorectal submucosal fibrosis and muscularis mucosa thickening, which correlate with the presence, chronicity, and degree of mucosal inflammation. Fibrosis should be recognised as a complication of paediatric ulcerative colitis, and ulcerative colitis should be considered a progressive disease.
STAT3 as a target for sensitizing prostate cancer cells to irradiation
Authors: Zhang Qu , Zhou Xiao-Mei , Wei Shao-Zhong , Cui Dian-Sheng , Deng Kang-Li , Liang Gai , Luo Yan , Luo Bo , Liang Xin-Jun
Published: November 2021

Radioresistance of prostate cancer (PCa) is a major factor leading to local failure of radiotherapy. STAT3 is an oncogenic protein that was recently found to be activated in PCa tumors. This study aimed to investigate the radiosensitization effect of targeting STAT3 in PCa tumors. Here, the radiosensitization effect of STAT3 blockade was investigated by clonogenic assay, flow cytometry and western blot analysis in human PCa cells in vitro and in vivo. We demonstrated that STAT3 blockade with a STAT3 inhibitor or siRNA increased the radiosensitivity of PCa cells and that radiation together with STAT3 blockade induced more apoptosis and double-strand breaks (DSBs) than radiation alone in LNCaP cells. In addition, radiation induced STAT3 activation and survivin expression in PCa cells, which was inhibited by STAT3 blockade. Transfection with survivin cDNA attenuated the radiosensitization effect of STAT3 blockade. These effects were further confirmed by in vivo studies, which showed that the STAT3 inhibitor enhanced the treatment efficacy of radiation on LNCaP xenografts with decreased STAT3 activation and survivin expression.

These findings suggest that STAT3 blockade radiosensitizes PCa cells through regulation of survivin. Thus, our study has revealed STAT3 as a potential sensitizer for irradiation in PCa cells. Its clinical application as an adjuvant in radiotherapy of PCa should be explored in the future.
Hybrid simulations of the ring-beam instabilities driven by the pickup ions in the outer heliosheath
Authors: Mousavi Ameneh , Liu Kaijun , Sadeghzadeh Sina
Published: November 2021

One-dimensional hybrid simulations are performed to investigate the plasma instabilities driven by the pickup ions in the outer heliosheath, which are believed to have a ring-beam velocity distribution in general. The modes propagating parallel and antiparallel to the background magnetic field are studied for pickup ion ring-beam distributions of different pickup angles, following the linear kinetic instability analysis presented in our previous work. The simulation results first confirm the unstable modes predicted by the linear analysis and further reveal how the pickup ions are scattered by the excited waves. While the maximum growth rate of the low-frequency, left-helicity waves occurs at the pickup angle of 82° (consistent with the linear analysis results), the saturation level of the fluctuating magnetic field is the highest around 45° pickup angle. For the pickup ion parameters examined, the pitch-angle spread of the pickup ions at the end of the simulations decreases with increasing pickup angle. Our study goes beyond previous studies of the pickup-ion-driven instabilities in the outer heliosheath which mainly focused on ring-like distributions of around 90° pickup angle. With the caveats that the pickup ion parameters are in the Alfvén cyclotron stability gap and that the one-dimensional simulations only include parallel and antiparallel-propagating modes, our results show that the scattering of pickup ions at small pickup angles is limited to one hemisphere so they can drift away from the ribbon direction as required by the spatial retention scenario of the energetic neutral atom ribbon observed by the Interstellar Boundary EXplorer.
Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches
Authors: Castells-Garcia Alvaro , Ed-daoui Ilyas , González-Almela Esther , Vicario Chiara , Ottestrom Jason , Lakadamyali Melike , Neguembor Maria Victoria , Cosma Maria Pia
Published: November 2021

Transcription and genome architecture are interdependent, but it is still unclear how nucleosomes in the chromatin fiber interact with nascent RNA, and which is the relative nuclear distribution of these RNAs and elongating RNA polymerase II (RNAP II). Using super-resolution (SR) microscopy, we visualized the nascent transcriptome, in both nucleoplasm and nucleolus, with nanoscale resolution. We found that nascent RNAs organize in structures we termed RNA nanodomains, whose characteristics are independent of the number of transcripts produced over time. Dual-color SR imaging of nascent RNAs, together with elongating RNAP II and H2B, shows the physical relation between nucleosome clutches, RNAP II, and RNA nanodomains. The distance between nucleosome clutches and RNA nanodomains is larger than the distance measured between elongating RNAP II and RNA nanodomains. Elongating RNAP II stands between nascent RNAs and the small, transcriptionally active, nucleosome clutches. Moreover, RNA factories are small and largely formed by few RNAP II. Finally, we describe a novel approach to quantify the transcriptional activity at an individual gene locus. By measuring local nascent RNA accumulation upon transcriptional activation at single alleles, we confirm the measurements made at the global nuclear level.
An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element
Authors: Ramsay Joshua P , Bastholm Tahlia R , Verdonk Callum J , Tambalo Dinah D , Sullivan John T , Harold Liam K , Panganiban Beatrice A , Colombi Elena , Perry Benjamin J , Jowsey William , Morris Calum , Hynes Michael F , Bond Charles S , Cameron Andrew D S , Yost Christopher K , Ronson Clive W
Published: November 2021

Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore, QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.
Tubular phosphate handling: references from child to adulthood in the era of standardized serum creatinine
Authors: Derain Dubourg Laurence , Aurelle Manon , Chardon Laurence , Flammier Sacha , Lemoine Sandrine , Bacchetta Justine
Published: November 2021

Background

The assessment of phosphate homeostasis in clinical practice relies not only on circulating phosphate levels but also on phosphate tubular reabsorption, ideally assessed using the tubular maximum phosphate reabsorption per glomerular filtration rate (TmP/GFR). TmP/GFR reference values were established before the onset of isotope-dilution mass spectrometry-standardized (IDMS) creatinine assays and thus need to be updated. Our objective is to provide reference values for TmP/GFR from childhood to adulthood, using the gold-standard of GFR assessment and IDMS-standardized creatinine values.

Methods

We retrospectively analysed all the inulin and iohexol clearances [measured glomerular filtration rate (mGFR)] performed in children and in adults screened for a living-donation in our unit since the beginning of IDMS-creatinine assays. TmP/GFR was calculated on a fasting sample, using the conventional formula without correction for tubular reabsorption of phosphate (TRP) in subjects below 19 years of age.

Results

A total of 2051 subjects (1711 children, 340 adults), aged from 1.9 to 73.4 years with normal GFR, normal phosphate and normal calcium levels, were included for TmP/GFR analysis. As expected, there was a progressive decrease along puberty in both genders of plasma phosphate and TmP/GFR, the decrease occurring earlier in girls. After the age of 19 years, there was a stabilization of plasma phosphate and TmP/GFR levels until the age of 55 years, phosphate levels and TmP/GFR being slightly lower in men than in women.

Conclusion

We present the largest cohort describing TmP/GFR reference values in the era of IDMS-standardized creatinine assays. We believe that these data will help physicians to better diagnose and manage patients with abnormal phosphate metabolism in daily clinical routine.
COVID-19 vaccination uptake amongst ethnic minority communities in England: a linked study exploring the drivers of differential vaccination rates
Authors: Gaughan Charlotte Hannah , Razieh Cameron , Khunti Kamlesh , Banerjee Amitava , Chudasama Yogini V , Davies Melanie J , Dolby Ted , Gillies Clare L , Lawson Claire , Mirkes Evgeny M , Morgan Jasper , Tingay Karen , Zaccardi Francesco , Yates Thomas , Nafilyan Vahe
Published: November 2021

Background

Despite generally high coronavirus disease 2019 (COVID-19) vaccination rates in the UK, vaccination hesitancy and lower take-up rates have been reported in certain ethnic minority communities.

Methods

We used vaccination data from the National Immunisation Management System (NIMS) linked to the 2011 Census and individual health records for subjects aged ≥40 years (n = 24 094 186). We estimated age-standardized vaccination rates, stratified by ethnic group and key sociodemographic characteristics, such as religious affiliation, deprivation, educational attainment, geography, living conditions, country of birth, language skills and health status. To understand the association of ethnicity with lower vaccination rates, we conducted a logistic regression model adjusting for differences in geographic, sociodemographic and health characteristics. Results

All ethnic groups had lower age-standardized rates of vaccination compared with the white British population, whose vaccination rate of at least one dose was 94% (95% CI: 94%–94%). Black communities had the lowest rates, with 75% (74–75%) of black African and 66% (66–67%) of black Caribbean individuals having received at least one dose. The drivers of these lower rates were partly explained by accounting for sociodemographic differences. However, modelled estimates showed significant differences remained for all minority ethnic groups, compared with white British individuals.

Conclusions

Lower COVID-19 vaccination rates are consistently observed amongst all ethnic minorities.
Predictors of interest in predictive testing for rheumatoid arthritis among first degree relatives of rheumatoid arthritis patients
Authors: Wells Imogen , Zemedikun Dawit T , Simons Gwenda , Stack Rebecca J , Mallen Christian D , Raza Karim , Falahee Marie
Published: November 2021

Objectives

There is increasing interest in prediction and prevention of RA. It is important to understand the views of those at risk to inform the development of effective approaches. First-degree relatives (FDRs) of RA patients are at increased risk of RA. This study assessed predictors of their interest in predictive testing for RA.

Methods

Questionnaires were completed by RA patients (provided with their questionnaire by a healthcare professional) and their FDRs (provided with their questionnaire by their RA proband). FDR surveys assessed interest in taking a predictive test, demographic variables, perceived RA risk, attitudes about predictive testing, autonomy preferences, illness perceptions, avoidance coping and health anxiety. Patient surveys included demographic variables, disease impact, RA duration and treatment. Ordinal logistic regression examined the association between FDRs’ characteristics and their interest in predictive testing. Generalized estimating equations assessed associations between patient characteristics and FDRs’ interest in predictive testing.

Results

Three hundred and ninety-six FDRs responded. Paired data from the RA proband were available for 292. The proportion of FDRs interested in predictive testing was 91.3%. Information-seeking preferences, beliefs that predictive testing can increase empowerment over health and positive attitudes about risk knowledge were associated with increased interest. Beliefs that predictive testing could cause psychological harm predicted lower interest. Patient characteristics of the proband were not associated with FDRs’ interest.

Conclusions

FDRs’ interest in predictive testing for RA was high, and factors associated with interest were identified. These findings will inform the development of predictive strategies and informational resources for those at risk.
Reimagining Physician Development and Lifelong Learning: An Ecological Framework
Authors: Mazmanian Paul E. , Cervero Ronald M. , Durning Steven J.
Published: November 2021

Learners and leaders in medical education recognize the remarkable growth in clinically relevant information, persistent changes in the organization of health care, and the need to develop physicians able to adapt successfully to changes in their lives and practices. The success of those physicians and of those who facilitate their learning depends on a careful understanding of the psychological, social, and biological factors that influence physician development and lifelong learning. To improve research and policy, development and learning must be explored for finer understandings of physicians in relation to other beings and to the physical and social surroundings most conducive to better learning and outcomes.