10,256 research outputs found

    Most Asked Agronomic Questions

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    Fatherhood and sperm DNA damage in testicular cancer patients

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    Testicular cancer (TC) is one of the most treatable of all malignancies and the management of the quality of life of these patients is increasingly important, especially with regard to their sexuality and fertility. Survivors must overcome anxiety and fears about reduced fertility and possible pregnancy-related risks as well as health effects in offspring. There is thus a growing awareness of the need for reproductive counseling of cancer survivors. Studies found a high level of sperm DNA damage in TC patients in comparison with healthy, fertile controls, but no significant difference between these patients and infertile patients. Sperm DNA alterations due to cancer treatment persist from 2 to 5 years after the end of the treatment and may be influenced by both the type of therapy and the stage of the disease. Population studies reported a slightly reduced overall fertility of TC survivors and a more frequent use of ART than the general population, with a success rate of around 50%. Paternity after a diagnosis of cancer is an important issue and reproductive potential is becoming a major quality of life factor. Sperm chromatin instability associated with genome instability is the most important reproductive side effect related to the malignancy or its treatment. Studies investigating the magnitude of this damage could have a considerable translational importance in the management of cancer patients, as they could identify the time needed for the germ cell line to repair nuclear damage and thus produce gametes with a reduced risk for the offspring

    Soil Fragmentation and Friability. Effects of Soil Water and Soil Management

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    Soil fragmentation is a primary aim in most tillage operations in order to create a soil environment favourable for crop establishment and growth. Soils vary around the world from those exhibiting a self-mulching nature to those of a hardsetting nature. These extremes have been reported for Australian and other tropical and subtropical soils. In humid temperate climates, soil tillage is generally needed in order to produce a favourable environment for crop establishment and growth. The ease of preparing a favourable arable layer depends on complex interactions between climate, soil and the tillage implement. Especially soil water affects soil strength and fragmentation properties and thereby the ease of preparing a suitable arable layer. Soil management affects soil fragmentation and friability indirectly through effects on soil structure formation and stabilization and directly through the influence of soil tillage and traffic. The overall purpose of this thesis is to contribute to the understanding of soil fragmentation and friability as affected by soil management and soil water regime. The reaction of the soil upon tillage was evaluated within the concept of soil tilth as defined by Soil Science Society of America (SSSA) "the physical condition of soil as related to its ease of tillage, fitness as a seedbed, and its impedance to seedling emergence and root penetration". The study involved soils from two case studies, the Askov long-term experiment on animal manure and mineral fertilizers, a field experiment with non-inversion tillage and a field experiment on compaction and intensive tillage. All the soils included in the study were humid sandy loams predominantly developed on Weichselian glacial moraine deposits. The soils were classified as Oxy aquic Agriudolls/Glossic Phaeozems according to Soil Taxonomy/WRB except for the Askov soil that was classified as Ultic Hapludalfs/Dystric Luvisols according to Soil Taxonomy/WRB. For all soils the clay content ranged from about 12 to 21 g per 100g-1 and soil organic matter ranged from 1.8 to 3.9 g 100g-1. The case studies included two long-term forage cropping system soils with a grass ley in the crop rotation (DFG(1) and DFG(2)), which were compared with a neighbouring counterpart. DFG(1) was compared with a forage cropping system soil without grass ley in the crop rotation (i.e., only annual crops), labelled DFA, whereas DFG(2) was compared with a continuously cash cropped soil with very low input of organic matter (no animal manure and straw removed), labelled CCC. An unfertilized (UNF), animal manured (AM) and a mineral fertilized (NPK) soil was included from the Askov long-term experiment on animal manure and mineral fertilizers established in 1894. The tillage experiment included a non-inversion tilled soil, labelled NINV, (non-inversion subsoil loosening to 35 cm depth and seedbed preparation with rotovator) and a conventionally tilled soil, labelled CONV, (mouldboard ploughing to 22 cm and secondary tine cultivation). The experiment on soil compaction and intensive tillage involved two "extreme" tillage and traffic treatments and a reference treatment (REF). The extreme treatments were soil compaction (PAC) and intensive tillage (INT) that were performed on wet soil just after spring ploughing and prior to seedbed preparation. The field experiments on non-inversion tillage, and soil compaction and intensive tillage were both conducted at the organically managed Rugballegård Research Station. Ease of tillage is commonly extrapolated from measurement of tensile strength in a compression test using air-dry or oven-dry aggregates. This procedure may lead to erroneous conclusion on soil behaviour of moist soil in the field. Therefore a multi-level analytical strategy was followed, i.e., soil fragmentation and friability were characterized using qualitative and quantitative in situ, on-field and laboratory methods. Soil fragmentation and friability were assessed in the field qualitatively by visual examination and quantitatively by employing a simple drop-shatter fragmentation test, denoted soil drop test. The energy input in the soil drop test was low in comparison with the energy input in typical seedbed cultivation. However, the soil drop test was sensitive enough to display significant differences between treatments in most cases. In the laboratory soil fragmentation and friability were evaluated by measuring tensile strength and specific rupture energy on field-sampled aggregates. In general, tensile strength was determined on air-dry aggregates and in some cases on aggregates adjusted to pressure potentials in the range -100 hPa to -166 MPa (air-dry). In addition, a direct tension test was developed to measure tensile strength of moist soil without making assumptions on the mode of failure. Undisturbed field-sampled soil cores were used in the test. The method was applicable at high matric potentials (-50 and -100 hPa) but not at -300 hPa. The direct tension test results corresponded well with the predicted values determined from the indirect measurements of aggregate tensile strength. In general, a fairly good agreement was found between the different methods in the hierarchy of methods applied. This indicates that sophisticated laboratory methods for assessing soil strength and fragmentation characteristics may well be used for evaluating soil behaviour under conditions prevailing in the field at the time of tillage. Nevertheless, it is recommended that laboratory methods are evaluated by using simple field methods at times and soil conditions appropriate for tillage. The friability index showed in general a low sensitivity to long- and short-term differences in soil management. However, a clear effect of soil water was found, i.e. maximum friability index values at -300 to -1000 hPa pressure potential. The effect of soil water on tensile strength and specific rupture energy of aggregates and on estimation of friability was investigated. As expected the study revealed the paramount influence of soil water. Interactions between soil water regime and treatment were found for cropping system soils (DFG(2) vs. CCC) and the fertilization treatments (UNF, NPK and AM) but not for the compaction treatments (PAC vs. REF). It was concluded that it might be hazardous to characterize soil fragmentation and friability properties of different treatments based on measurements at a single pressure potential and significant influence of pore characteristics was detected. Macroporosity was found to correlate to tensile strength and friability index. However, a clear correlation between tensile strength properties and pore geometry characteristics (e.g. tortuousity and continuity) was not shown. This may be due to large small-scale variations in these properties, i.e. the samples for tensile strength determination were taken next to the samples for pore characterization. Marked long-term effects of cropping systems and fertilization were found. For two neighbouring soils with a high input of organic matter, poorer soil mechanical characteristics were found for a soil with grass in the rotation (DFG(1)) than for a soil solely grown with annual crops (mainly cereals). This difference in strength and friability characteristics may be related to a higher amount of biological structural binding and bonding agents in the soil with grass included in the rotation. Two soils with high inputs of organic matter (DFG(2) and AM) displayed more desirable aggregate strength and soil fragmentation characteristics than their counterparts (CCC and UNF, respectively) receiving low inputs of organic matter. Evidence suggests that cementation of dispersed clay was a determining factor for the stronger increase in aggregate tensile strength with increased dryness (decreased pressure potential) found for the CCC and UNF soils receiving low inputs of organic matter compared with DFG(2) and AM. An early-stage effect of non-inversion tillage treatment (NINV) resulted in a poorer soil tilth in the topsoil layer (i.e., higher soil strength and lower ease of fragmentation and friability index) than for a conventionally mouldboard ploughed soil (CONV). Surprisingly, the effect of tillage on topsoil tilth was clearer by the end of the growing season in September than in May. This indicates that natural soil processes occurring during the growing season were not able eliminate the differences between the primary tillage treatments. Soil compaction (PAC) resulted in strongly increased aggregate tensile strength at all the investigated water regimes (i.e., pressure potentials: -100 hPa to -166 MPa) in comparison with a reference treatment (REF). Surprisingly, soil compaction did not significantly affect the specific rupture energy of the aggregates. This was related to a clear difference in the stress-strain relationship for the soils. Aggregates from the compacted soil failed at higher stress but at lower strain than aggregates from the reference soil (i.e., higher Young modulus, (Y/()). This was characteristic for all size-classes and at all pressure potentials. The results obtained in this study indicate that the prediction of soil fragmentation from tensile strength properties of soil elements may be very complex. We need more basic understanding of the fragmentation of "unconfined" soil at the different size-scales (aggregates to bulk soil) and the correlation between the different scales in order to be able to predict soil fragmentation in tillage (mainly superficial tillage) from a priori information. More specifically, the role of soil biology and soil water and pore characteristics needs to be studied in further detail. The development of new methods and the application of well-know methods to quantify soil fragmentation and friability of soil at conditions similar to soil conditions at tillage (including water content) has been a primary aim in this thesis. However, there is still a strong need to develop new methods and modify existing methods to quantify soil fragmentation and friability under controlled conditions. This study shows that soil compaction and intensive tillage significantly influence soil fragmentation and friability. Increasingly heavier machinery and - to some extent - more intensive seedbed preparation (PTO-driven implements) are being used in Danish agriculture. A thorough evaluation of this development on soil fragmentation and friability is needed. Furthermore, the accumulated knowledge of soil fragmentation and tensile failure in soil ought to be implemented in the design of new tillage implements

    Threats to soil quality in Denmark - A review of existing knowledge in the context of the EU Soil Thematic Strategy

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    The EU Commission is preparing a proposal for a Soil Framework Directive with the purpose of protecting the soil resources in Europe. The proposal identifies six major threats to the sustained quality of soils in Europe. This report addresses the threats that are considered most important under the prevailing soil and climatic conditions in Denmark: compaction, soil organic matter decline, and erosion by water and tillage. For each of these threats, the relevance and damage to soil functions as well as the geographic distribution in Denmark are outlined. We suggest a procedure for identifying areas at risk. This exercise involves an explicit identification of: i) the disturbing agent (climate / management) exerting the pressures on soil, and ii) the vulnerability of the soil to those stresses. Risk reduction targets, measures required to reach these targets, and the knowledge gaps and research needs to effectively cope with each threat are discussed. Our evaluation of the threats is based on soil resilience to the imposed stresses. Subsoil compaction is considered a severe threat to Danish soils due to frequent traffic with heavy machinery in modern agriculture and forestry. The soil content of organic matter is critically low for a range of Danish soils, which should be counteracted by appropriate management options. Soil erosion by tillage, and to a lesser degree by water, adversely affects soil quality on much of the farmland because degradation rates are much higher than generation of soil

    Manual on prototyping methodology and multifunctional crop rotation

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    This VEGINECO manual is one of a series of publications resulting from the VEGINECO project. VEGINECO specialises in producing tested and improved multi-objective farming methods for key farming practices – e.g. crop rotation, fertilisation and crop protection – to facilitate the integration of potentially conflicting objectives like economy and ecology. This report consists of two parts. The first part describes the prototyping methodology and how it was used in the VEGINECO project (Chapters 2 - 5). The second part describes the methodology for developing crop rotation strategies with examples of its application under different conditions in Europe (Chapter 6 - 11)

    Validation and Utilization of a Clinical Next-Generation Sequencing Panel for Selected Cardiovascular Disorders

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    The development of high-throughput technologies such as next-generation sequencing (NGS) has allowed for thousands of DNA loci to be interrogated simultaneously in a fast and economical method for the detection of clinically deleterious variants. Whenever a clinical diagnosis is known, a targeted NGS approach involving the use of disease-specific gene panels can be employed. This approach is often valuable as it allows for a more specific and clinically relevant interpretation of results. Here, we describe the customization, validation, and utilization of a commercially available targeted enrichment platform for the scalability of clinical diagnostic cardiovascular genetic tests, including the design of the gene panels, the technical parameters for the quality assurance and quality control, the customization of the bioinformatics pipeline, and the post-bioinformatics analysis procedures. Regions of poor base coverage were detected and targeted by Sanger sequencing as needed. All panels were successfully validated using genotype-known DNA samples either commercially available or from research subjects previously tested in outside clinical laboratories. In our experience, utilizing several of the sub-panels in a clinical setting with 33 real-life cardiovascular patients, we found that 20% of tests requested were reported to have at least one pathogenic or likely pathogenic variant that could explain the patient phenotype. For each of these patients, the positive results may aid the clinical team and the patients in best developing a disease management plan and in identifying relatives at risk

    Genetic Normalization of Differentiating Aneuploid Human Embryos

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    Early embryogenesis involves a series of dynamic processes, many of which are currently not well described or understood. Aneuploidy and aneuploid mosaicism, a mixture of aneuploid and euploid cells within one embryo, in early embryonic development are principal causes of developmental failure.^1,2^ Here we show that human embryos demonstrate a significant rate of genetic correction of aneuploidy, or "genetic normalization" when cultured from the cleavage stage on day 3 (Cleavage) to the blastocyst stage on day 5 (Blastocyst) using routine in vitro fertilization (IVF) laboratory conditions. One hundred and twenty-six human Cleavage stage embryos were evaluated for clinically indicated preimplantation genetic screening (PGS). Sixty-four of these embryos were found to be aneuploid following Cleavage stage embryo biopsy and single nucleotide polymorphism (SNP) 23 chromosome molecular karyotype (microarray). Of these, 25 survived to the Blastocyst stage of development and repeat microarray evaluation was performed. The inner cell mass (ICM), containing cells destined to form the fetus, and the trophectoderm (TE), containing cells destined to form the placenta were evaluated. Sixteen of 25 embryos (64%) [95% CI: 44-80%] possessed diploid karyotypes in both the ICM and TE cell populations. An additional three Blastocyst stage embryos showed genetic correction of the TE but not the ICM and one Blastocyst stage embryo showed the reverse. Mosaicism (exceeding 5%), was not detected in any of the ICM and TE samples analyzed. Recognizing that genetic normalization may occur in developing human embryos has important implications for stem cell biology, preimplantation and developmental genetics, embryology, and reproductive medicine. 

1)Hassold, T. et al. A cytogenetic study of 1000 spontaneous abortions. Ann Hum Genet. 44, 151-78 (1980).
2)Menasha, J., Levy, B., Hirschhorn, K., & Kardon, N.B. Incidence and spectrum of chromosome abnormalities in spontaneous abortions: new insights from a 12-year study. Genet Med. 7, 251-63 (2005)

    Improved Stroke Detection at Early Stages Using Haar Wavelets and Laplacian Pyramid

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    Stroke merupakan pembunuh nomor tiga di dunia, namun hanya sedikit metode tentang deteksi dini. Oleh karena itu dibutuhkan metode untuk mendeteksi hal tersebut. Penelitian ini mengusulkan sebuah metode gabungan untuk mendeteksi dua jenis stroke secara simultan. Haar wavelets untuk mendeteksi stroke hemoragik dan Laplacian pyramid untuk mendeteksi stroke iskemik. Tahapan dalam penelitian ini terdiri dari pra proses tahap 1 dan 2, Haar wavelets, Laplacian pyramid, dan perbaikan kualitas citra. Pra proses adalah menghilangkan bagian tulang tengkorak, reduksi derau, perbaikan kontras, dan menghilangkan bagian selain citra otak. Kemudian dilakukan perbaikan citra. Selanjutnya Haar wavelet digunakan untuk ekstraksi daerah hemoragik sedangkan Laplacian pyramid untuk ekstraksi daerah iskemik. Tahapan terakhir adalah menghitung fitur Grey Level Cooccurrence Matrix (GLCM) sebagai fitur untuk proses klasifikasi. Hasil visualisasi diproses lanjut untuk ekstrasi fitur menggunakan GLCM dengan 12 fitur dan kemudian GLCM dengan 4 fitur. Untuk proses klasifikasi digunakan SVM dan KNN, sedangkan pengukuran performa menggunakan akurasi. Jumlah data hemoragik dan iskemik adalah 45 citra yang dibagi menjadi 2 bagian, 28 citra untuk pengujian dan 17 citra untuk pelatihan. Hasil akhir menunjukkan akurasi tertinggi yang dicapai menggunakan SVM adalah 82% dan KNN adalah 88%
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