Miracle-dz/UniFAR-FTUs huggingface dataset:
Gypsum amendment as a means to reduce agricultural phosphorus loading: an economic appraisal

This study analyzes the economic feasibility of gypsum amendment as a means to reduce particulate and dissolved phosphorus loads from arable areas. To this end, an optimization model is developed that includes gypsum amendment as well as matching phosphorus fertilization to crop need and the level of soil phosphorus reserves as phosphorus load mitigation measures, with soil phosphorus reserves measured by soil test phosphorus (STP). The optimal extent of gypsum amendment is then determined simultaneously with optimal fertilization use as a function of field STP level. The results indicate that whether or not gypsum amendment is economically feasible depends on field erosion susceptibility and STP level. When accounting for the costs and benefits to the society on the whole, gypsum treatment suits best to mitigation of phosphorus losses from soils with excessively high phosphorus reserves; once a threshold STP level is reached, gypsum amendment is optimally given up. This threshold level depends on field slope and on society’s willingness to pay for water quality.
脉冲微分方程的block-by-block方法

针对脉冲微分方程初值问题,首先,将脉冲微分方程转化为等价积分方程,然后,对等价的积分方程利用block-by-block方法构造了一个高阶数值格式,并分析了该数值格式的收敛性和稳定性。 数值算例验证了理论分析的正确性。
ANTIOXIDANT DEFENSE SYSTEM OF BLACK RICE GROWN UNDER DROUGHT

A pot experiment was conducted to study the oxidative response of drought-stressed black rice to foliar application of pyridoxine (0.03mM) and nicotinic acid (1.5mM). Drought stress was imposed by withholding water for 10 days, until leaf rolling symptoms was observed. After ten days from imposition of drought stress, water deficit resulted in a significant increase in H2O2 content thereby increased lipid peroxidation product; malonaldhyde (MDH) accompanied by high rate of ion leakage (IE) and consequently reduced the relative water content (RWC) compared with their corresponding controls. Drought stress resulted in a considerable increase in the activities of phenol peroxidase (POX), ascorbate oxidase (ASO), and catalase (CAT) enzymes of both shoots and roots of black rice seedlings, while the activities of glutathione reductase (GR), polyphenol oxidase (PPO) and superoxide dismutase (SOD) significantly decreased. Foliar application of pyridoxine or nicotinic acid mitigated the injurious effects of drought stress through the significant reduction in ion leakage, reducing membrane peroxidation, high ratio of chlorophylls/carotenoids thus restoring the membrane integrity and enhancing the defense system in terms of ascorbic acid, glutathione and total phenol contents as well as stimulating the activities of some antioxidant enzymes (GR, SOD, and POX). It may be suggested that the enhancement of the antioxidants in black rice seedlings is one of the mechanisms of drought tolerance under stress condition.
Heterogeneity of interneuron circuit function in sensory processing and synaptic plasticity

ii ACKNOWLEDGEMENTS iv TABLE OF CONTENTS v LIST OF FIGURES vii CHAPTER I: INTRODUCTION 1 A. THE SENSORY SIGNALING PATHWAY FROM WHISKER TO CORTEX 1 B. INTERNEURON DIVERSITY 5 1. Morphology 5 2. Interneuorn firing patterns and biochemical markers 8 C. TWO DISTINCT INHIBITORY CIRCUITS: LTS AND FS CELLS 10 D. GABAA RECEPTORS 12 E. SYNAPTIC PLASTICITY 16 F. THE CHARACTERISTICS AND FUNCTIONS OF FS INTERNEURONS.20 G. HYPOTHESIS 22 H. GENERAL METHODS 23 CHAPTER II: LONG-TERM SENSORY DEPRIVATION SELECTIVELY REARRANGES FUNCTIONAL INHIBITORY CIRCUITS IN MOUSE BARREL CORTEX 25 A. BRIEF OVERVIEW 25 B. MATERIALS AND METHODS 27 C. RESULTS 30
Macrophomina phaseolina as causal agent for charcoal rot of sunflower.

crophomina phaseolina has a wide host range and is responsible for causing losses on more than 500 cultivated and wild plant species. So far in Pakistan it has been reported to cause disease on 67 economic hosts including field crops, pulses, flowers and vegetable have been reported. Infection on sunflower was first reported from Sri Lanka in 1927 and in 1982 it was reported from sunflower field in Pakistan. The fungus is reported to be soil, seed and stubble borne. The fungus can survive for more than 10 months under dry soil conditions. The severity of the disease is directly related to the population of viable sclerotia in the soil. The pathogen generally affects the fibrovascular system of the roots and basal internodes. The parasitic fitness of a facultative soilborne pathogen before invading the host is linked with its ability to compete for its survival, utilization of organic sources and colonization in the host root rhizosphere by competing other microorganism in the vicinity.
The Vestibular Contribution to Balance Control in Older Adults During Locomotion and Stair Negotiation

Background: Stability is known to decrease as we age, but currently we know very little about how the body's balance system, the vestibular system, contributes to balance control in older adults, particularly while walking and climbing stairs. The purpose ofthis study was to take the first step in understanding vestibular contribution to balance control during locomotion and stair negotiation, and how this changes with age. Methods: Ten young adults and six older adults ascended and descended a nine-step staircase 78 times and walked on a treadmill for 10 minutes to complete a total of 300 complete steps in each condition. During each trial, a small amplitude, random electric current was applied behind the subject's ears to stimulate the nearby vestibular nerve, and surface electromyography was recorded from eight leg muscles. We used time-dependent correlations (coherence) to determine how the vestibular stimulus influences muscle behavior, how this influence is modulated by the phase of the step cycle. Results: The vestibular stimulus influenced select muscles in a phase-dependent manner over the step cycle in both age groups. In general, in muscles where vestibular influence over the muscle's behavior was apparent in both the older and younger groups, the influence was stronger and longer-lasting in the older adults. Additionally, prominent vestibular influence over a muscle was observed in more muscles in the older group than the younger group. Conclusions: This offers a first look at the functional contribution of the vestibular system to maintaining balance during locomotion and stair negotiation in older adults. These results suggest that as we age, we may rely more on vestibular signals in order to maintain balance during locomotion and stair negotiation.
Processus post-transcriptionnels inédits dans la mitochondrie des diplonémides

iii Table des matières . v Liste des tableaux . xi Liste des figures . xii Liste des abréviations . xiv Dédicace . xviii Remerciements . xix Chapitre
Co-transferring of AtDREB2A gene and bar gene into wheat through microprojectile bombardment.

To improve the salt and drought tolerance in wheat,the DREB2A gene of Arabidopsis thaliana (AtDREB2A) driven by rice Actin promoter was integrated into a high-efficient constitutive vector.This construct and bar gene were introduced into wheat varieties Alondra and Yangmai 12 by co-transformation through microprojectile bombardment. The averages of transformation frequency were 2.4%(bar),0.4%(AtDREB2A) and 0.2%(bar+AtDREB2A), respectively.The RT-PCR showed that AtDREB2A gene and bar gene were expressed stably in the transgenic plants.The transgenic plants were potential for developing the salt and drought tolerant wheat germplasm after removing the bar selection gene.
Bone regeneration and repair : biology and clinical applications

Bone Dynamics: Morphogenesis, Growth Modeling, and Remodeling Jeffrey O. Hollinger Fracture Repair Charles Sfeir, Lawrence Ho, Bruce A. Doll, Kodi Azari, and Jeffrey O. Hollinger Common Molecular Mechanisms Regulating Fetal Bone Formation and Adult Fracture Repair Theodore Miclau, Richard A. Schneider, B. Frank Eames, and Jill A. Helms Biology of Bone Grafts Victor M. Goldberg and Sam Akhavan Cell-Based Strategies for Bone Regeneration: From Developmental Biology to Clinical Therapy Scott P. Bruder and Tony Scaduto Biology of the Vascularized Fibular Graft Elizabeth Joneschild and James R. Urbaniak Growth Factor Regulation of Osteogenesis Stephen B. Trippel Grafts and Bone Graft Substitutes Doug Sutherland and Mathias Bostrom Gene Transfer Approaches to Enhancing Bone Healing Oliver Betz, Mark Vrahas, Axel Baltzer, Jay R. Lieberman, Paul D. Robbins, and Christopher H. Evans Bone Morphogenic Proteins and Other Growth Factors to Enhance Fracture Healing and Treatment of Nonunions Calin S. Moucha and Thomas A. Einhorn The Ilizarov Technique for Bone Regeneration and Repair James Aronson Biology of Spinal Fusion: Biology and Clinical Applications K. Craig Boatright and Scott D. Boden Bone Allograft Transplantation: Theory and Practice Henry J. Mankin, Francis J. Hornicek, Mark C. Gebhardt, and William W. Tomford Bone Grafting for Total Joint Arthroplasty: Biology and Clinical Applications Moussa Hamadouche, Daniel A. Oakes, and Daniel J. Berry Biophysical Stimulation Using Electrical, Electromagnetic, and Ultrasonic Fields: Effects on Fracture Healing and Spinal Fusion James T. Ryaby Vascularized Fibula Grafts: Clinical Applications Richard S. Gilbert and Scott W. Wolfe Craniofacial Repair Bruce A. Doll, Charles Sfeir, Kodi Azari, Sarah Holland, and Jeffrey O. Hollinger Bone Regeneration Techniques in the Orofacial Region Samuel E. Lynch Index
Identification of Proteins Involved in Chloroplast DNA Replication

IDENTIFICATION OF PROTEINS INVOLVED IN CHLOROPLAST DNA REPLICATION Matthew Gordon Lassen Department of Microbiology & Molecular Biology Master of Science Chapter 1 Chloroplast nucleoids (ct-nucleoids) are DNA/protein complexes involved in compacting the chloroplast genome, and may play a role in regulating DNA replication. Ct-nucleoids were isolated from young soybean plants and separated by 2-D gel electrophoresis. Gel spots were excised and analyzed by MALDI-ToF mass spectrometry, resulting in several protein identifications. The proteins identified all have functions unrelated to DNA replication. While some of these proteins may be due to contamination, it is possible that some of these proteins are dual-functional, playing direct roles in the regulation of DNA replication. Chapter 2 A 28 kDa soybean protein was isolated by sequence specific DNA affinity chromatography from total chloroplast protein isolations. Mass spectrometry analysis revealed that the 28 kDa protein contains some homology within an ssb domain of an Arabidopsis mitochondrial-targeted SSB (mtSSB) of approximately 21 kDa. N-terminal sequencing revealed that the 28 kDa soy protein is identical to a 36 amino acid region at the N-terminus of the Arabidopsis mtSSB. Protein fractions containing the 28 kDa protein shift oriA in electrophoretic mobility shift assays (EMSAs). Arabidopsis mtSSB fails to shift oriA in EMSAs run under identical conditions. Arabidopsis mtSSB causes a shift of ssDNA in EMSAs, while the ability of the 28 kDa soy protein to bind ssDNA is still unclear. Importantly, the 28 kDa soy protein was identified from total protein extracts obtained from intact chloroplasts, while in-vitro targeting experiments suggest that the Arabidopsis mtSSB localizes only to mitochondria and not to chloroplasts. BLAST searches of the available soybean genomic and EST databases do not produce any significant homologies to the 36 amino acid N-terminal sequence.
Genetic structure in striped skunks (Mephitis mephitis) on the southern high plains of Texas

—Genetic variation within populations reflects population-level social and demographic processes and influences how a population behaves as an evolutionary unit. We examined partitioning of genetic variation in striped skunks (Mephitis mephitis) from the Southern High Plains of Texas during 1994–1995. Sixty-nine male and 35 female skunks were sampled on four 12.8-km2 study plots. Plot centers ranged from 17.6 to 61.6 km apart. We used multi-locus DNA fingerprinting with 2 probes, pV47 and CTTxAGG, to test 3 hypotheses: (1) females are more genetically similar to other females than males are to other males on the same plot (indicating greater female philopatry than male philopatry), (2) genetic similarity is greater within plots than among plots (indicating partitioning of genetic variation in space), and (3) genetic similarity of males decreases as the distance separating males increases (indicating geographic distance affects rates of gene flow). In general, males on a plot had lower average genetic similarity than females. Genetic similarity within plots was not different from genetic similarity among plots for males or for females. Genetic similarity of males did not decrease with increasing distance among plots. The lack of geographical genetic structure in striped skunks suggests at the scale of this study (<60 km) that gene flow of biparentally inherited genes is not distance-mediated. However, the higher similarity values for females than for males on the same plot supports an effect of male-biased dispersal and female philopatry on partitioning of genetic variation between sexes.
JONGERENDAG - JOURNEE DES JEUNES – 2012 - Conchological differentiation in an ongoing radiation of Lanistes gastropods from ancient Lake Malawi: how adaptive is shell morphology?

of the western branch of the East African Rift System (EARS). Like other extant lakes in the EARS and several paleolakes that occupied rift basins in the EARS before, Lake Malawi provides habitats for an extraordinary diversity of freshwater biota ranging from vertebrates, like the adaptive radiations in cichlid fish (e.g. Kocher, 2004), to the phytoplankton communities that provide nutrients to the benthic and pelagic ecosystems (e.g. Van Bocxlaer et al., 2012 and references therein). Major environmental changes in the Malawi Basin since the Middle Pleistocene, including fluctuations in the water level of Lake Malawi, are recognized in the sediments of drill cores and are considered to be a driving force for organismal evolution (Cohen et al., 2007), including the diversification of ampullarid gastropods of the genus Lanistes (Schultheiß et al., 2009). In the latest revisions of the Lanistes from the Malawi Basin (Mandahl-Barth, 1972; Berthold, 1990) five species (L. ellipticus Martens, 1866, L. ovum Troschel, 1845, L. solidus Smith, 1877; L. nyassanus Dohrn, 1865 and L. nasutus Mandahl-Barth, 1972) were recognized mainly based on anatomical traits and shell morphology, but further revision is required (Schultheiß et al., 2009). In any case, the extant Lanistes fauna of the Malawi Basin is a monophyletic, endemic clade (Schultheiß et al., 2009). The onset of molecular diversification in this clade is much younger (~0.6 Ma) than the first Lanistes fossils recorded in the basin, which are preserved in Unit 3A of the Chiwondo Beds (~3.75-1.80 Ma; Kullmer, 2008). However, the mechanisms of this young diversification event are poorly understood, as is the relation between molecular diversity and disparity in shell morphology. In this study we aim to get a better insight into the heritability of shell morphology.
Role of Wnt5a and Possible Pathway of Action Through Ror2 in Proximodistal Outgrowth of the Limb

Role of Wnt5a and Possible Pathway of Action through Ror2 in Proximodistal Outgrowth of the Limb Tiffanie M. Dahl Department of Physiology and Developmental Biology, BYU Master of Science Despite over 60 years of study, the molecular pathways and mechanisms governing limb outgrowth and patterning remain poorly understood. Fgfs expressed in the AER are known to be necessary and sufficient for proximodistal limb outgrowth and have been proposed to have a chemoattractive role. Wnt5a is a secreted factor which is expressed in a gradient in the distal limb with the highest concentration next to the AER. The presence of the AER is necessary to establish this gradient. Expression of Wnt5a in a concentration dependant manner can be induced in the limb through the implantation of a bead soaked in recombinant Fgf4 protein. This indicates that Fgfs from the AER may establish the gradient of Wnt5a in the limb mesenchyme. Wnt5a mutants exhibit severe shortening of the face, limbs, and body axis, with limbs being progressively truncated proximally to distally. In normal limb proximodistal outgrowth, cells are seen to grow directionally toward the AER. Previous studies done in the Barrow lab, as well as those done by myself, have shown that if a portion of the AER is removed and the cells proximal to this area are labeled, those which are close enough to intact AER will redirect their growth toward this intact AER. When Wnt5a secreting cells are implanted in the limb mesenchyme of the chick this ectopic source of Wnt5a is sufficient to redirect the growth of the mesenchyme cells toward the Wnt5a source. This indicates that the AER may mediate directed growth of limb mesenchyme cells through the establishment of the Wnt5a gradient which provides positional information to the cells. This Wnt5a gradient results in the recruitment of the mesenchyme cells toward the AER. The Ror2 receptor has been found to be involved in several different pathways involving Wnt5a which are involved in changes in polarity and migration. This makes Ror2 a likely candidate for causing changes in cell polarity and migration during distal outgrowth in the limb. To test whether Ror2 is necessary for the polarizing response of limb mesenchyme cells to the Wnt5a gradient in vivo I co-transfected a dominant-negative Ror2 (Ror2ΔC) and a GFP expression vector in the embryonic chick limb using sonoporation. Limb mesenchyme cells transfected with dominant-negative Ror2 grew as radial clones in contrast to the directional outgrowth of the control limb mesenchyme cells along the proximodistal axis. This indicates that cells expressing the dominant-negative Ror2 could no longer respond to the Wnt5a gradient in the limb mesenchyme. This supports a role for Ror2 as a receptor or coreceptor for Wnt5a in mediating directional growth and movement during proximodistal outgrowth and patterning in the limb.
A comparative study of renal cell tumor model systems

The rat renal cell carcinoma system as described by deVere White and Olsson in 1980, is used widely as a model for its human counterpart. The tumor arose spontaneously in a male Wistar Lewis rat and its behaviour has been shown stable during multiple passages. We have compared this tumor with the human renal cell carcinoma using a multidisciplinary approach. Light microscopy and electron microscopy showed a great resemblance of this rat tumor to a human renal cell carcinoma of the clear cell type with the ultrastructural presence of desmosomes. With the use of tissue specific antibodies against intermediate filament proteins it could be shown that their expression is comparable to human renal cell carcinoma, i.e. coexpression of vimentin and different cytokeratins in the tumor cells. The cells could also be shown to contain cytokeratin 18. An aneuploid cell population in the tumor, expressing both vimentin and keratin, could be characterized by DNA flow cytometry in double labeling experiments. Comparison of normal and malignant rat kidney tissue by Northern blot analysis revealed increased levels of vimentin mRNA. In the double layer soft agar human tumor cloning system rat renal cell tumors showed a positive growth capacity. In conclusion this tumor model seems to have several histological and biological properties in common with the human renal tumor.
An investigation into normative values for fine hand dexterity and its relation with pinch and grip strength among healthy young Indian adults

An investigation into normative values for fine hand dexterity and its relation with pinch and grip strength among healthy young Indian adults. Evaluation of hand function is a crucial component to assess prognosis in hand pathologies. Examinations of dexterity provide unique way of evaluating neuro-motor function of entire hand. There is scarcity of literature on reference values for fine hand dexterity among healthy young adults. To explore normative values for fine hand dexterity and its relation with pinch and grip strength. The 9-Hole Pegboard Test was administered for evaluation of fine hand dexterity among healthy young adults (n= 256) of age group 18 to 35 with the mean age of 20.53 (±2.02). The task was demonstrated and both hands were assessed. Grip and pinch strengths were measured in both hands in a consistent manner. A dynamometer was used for grip strength and a pinch meter was used to measure key (lateral) and tripod pinch and tip to tip pinch strengths. Normative value for fine hand dexterity of dominant hand among males (n= 125) is 19 (± 2.18) and among females (n= 126) is 19.5 (± 2.59) and there was no significant correlation between fine hand dexterity with grip and pinch strength. Normative values generated in this study can be used for clinical reference in the evaluation of hand function to that of normal subjects of the same age and gender.
Evolution of Overlapping Genes: Comparative Genomics of Mycoplasma genitalium and Mycoplasma pneumoniae

Many overlapping genes have been identi ed in the genomes of procaryotes, bacteriophages, animal viruses, and mitochondria, some of which have been reported to have functional roles [1], but their evolutionary origin is not clearly understood. We systematically analyzed all overlapping genes in the genomes of two closely related species, Mycoplasma genitalium [2] and Mycoplasma pneumoniae [3]. In particular, careful comparisons were made for the homologous genes that are overlapped in one species but not in the other.
Typing of Legionella pneumophila and its Role in Elucidating the Epidemiology of Legionnaires’ Disease

The main reason for typing Legionella pneumophila is to help identify environmental sources giving rise to cases of legionellosis, thus allowing control measures to be implemented and further cases to be prevented in a timely manner. Monoclonal antibody (mAB) subgrouping is probably the most rapid and reliable phenotypic method available and is excellent for initial screening of isolates. Only a few of the many genotypic methods described have been shown to meet these exacting requirements. Of these, pulsed-field gel electrophoresis is the most widely applied, but others have also been used. For example, a restriction-fragment length polymorphism (RFLP) typing method was used as the standard method in the United Kingdom for almost 20 years. Investigation of travel-associated legionellosis requires even more rigorously standardized systems, as not only must the types be clearly defined but they also must be recognizable and reproducible in laboratories in different countries (different laboratories, different times). The standardized sequence-based typing (SBT) method targets part of six genes (flaA, pilE, asd, mip, mompS, proA), each of which shows considerable allelic variation, thus providing an extremely discriminatory typing system. Furthermore, of the seven major-outbreak-associated strains for which SBT data are available, five are SBT 3,4,1,1,14,9. However, if substantiated, these observations have important and widespread implications for our understanding of the epidemiology of legionellosis and for the monitoring and control of L. pneumophila in the built environment.