Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide association studies to dissect the genetic architecture of yieldrelated traits in maize and the genetic basis of heterosis

Advances in next generation sequencing (NGS) technologies and the development of appropriate populations and statistical approaches enable genomewide dissection of the genetic determinants of traits via genome-wide association studies (GWAS). Although multiple statistical approaches for conducting GWAS are available, there is not yet consensus about which approaches perform best. Kernel row number (KRN) trait data were collected from a set of 6,230 lines derived from four related maize populations. A set of ~13M variants (~2M of which were newly discovered) were projected and/or imputed onto the 6,230 lines. Three distinct approaches to GWAS were compared: 1) single-variant, 2) stepwise regression and 3) Bayesian-based multi-variant model fitting. In combination, these analyses identified associations in 764 100-kb chromosomal bins. A subset of these KRNassociated variants (KAVs) were subjected to cross-validation using three unrelated populations that were not included in the GWAS; approximately 50% of successfully genotyped KAVs were cross-validated in at least one unrelated population. Importantly, ~60% of cross-validated KAVs were identified by only one of the three statistical approaches. This finding demonstrates that the three GWAS approaches are complementary. These identified KAVs have the potential to enhance our understanding of maize domestication and the developmental steps involved in ear development.
Distinctive Characteristics of the Causality between the PPI and CPI: Evidence from Romania

This paper examines the causal relationship between the producer price index (PPI) and consumer price index (CPI) in Romania. The Granger full sample test shows unidirectional causality from PPI to CPI. The parameter stability test shows instability in the short run and the result is inappropriate for estimation due to the presence of structural changes. The Sub-sample rolling window test is used to address the time-varying, and it provides bi-directional causality at different sub-sample. The finding does not support the neoclassical profit-maximizing model, which states that PPI is not a single factor of fluctuation in CPI for Romania. It indicates the bidirectional relationship between the PPI and CPI, suggests that both these price indices play a significant role. The study implies policy-wise that PPI is a major factor in the price stability and should have been included in inflation targeting policy to curb the inflation in Romania.
Post-transcriptional Regulation of Gene Expression by Rod1

markdownabstract__Abstract__ The process of gene expression consists of several interconnected steps which ensure proper protein production from a specific gene. However, an extensive amount of transcripts containing premature termination codons (PTCs) are generated in cells, mainly through alternative splicing events. If translated, these transcripts could generate truncated proteins which are potentially deleterious to the cell. Nonsense-Mediated mRNA Decay (NMD) is a mechanism of mRNA degradation which eliminates these faulty transcripts, thus protecting the cell against abnormal protein functions. Chapter 2 of this thesis describes experiments aimed at finding new protein factors involved in NMD. Rod1 is found to be required for NMD in HEK293 cells and to regulate several potential NMD targets. In chapter 3, the role of Rod1 in erythroid cells, where it is highly expressed, is addressed. Rod1 is found to regulate Alternative Splicing (AS) together with Ptbp1 and Raver1. AS is a mechanism that regulates inclusion or skipping of thousands of exons and is therefore an important generator of protein diversity in metazoans. AS is regulated by a large number of factors, including core spliceosomal proteins and proteins that activate or repress specific exons. AS is regulated in a tissue-specific manner, and some AS factors, like Rod1, are expressed in restricted tissues as well. Chapter 3 also contains experiments aimed at finding RNAs associated with Rod1 and Ptbp1 in differentiated MEL (murine erythroleukemia) cells. In chapter 4, results from chapters 2 and 3 are discussed, as well as its implications. Future directions are also presented.
Developing a Mouse Model of Sensory and Cognitive Deficits for Multiple Sclerosis

Abstract : In this project, we have been developing a novel mouse model of MS with a focus on cognitive dysfunction and defective myelin using homologous recombination in embryonic stem cells. We obtained homologous recombinants at high frequency; however, difficulties in deriving mice from the ES cells delayed our progress. We repeated the recombination experiments and again obtained high level recombination from our screens of embryonic stem cell clones but could not derive animals from these cells. We have discontinued business with the company used for the embryonic stem cell work and we are currently testing another facility to determine if we can continue our project. Future experiments will be funded from internal funding sources to ensure that we obtain the mouse model proposed in the current project. In addition to generation of our novel model, we developed neurophysiological techniques to assess cognitive deficits in our novel mouse model. These experiments involve using the auditory pathway to test neural processing in the superior olivary complex We have published one of these studies.
Hongos micorrizógenos arbusculares y nutrimentos del suelo asociados a cuatro especies de helechos en dos ecosistemas de Oaxaca, México

La abundancia y riqueza de hongos micorrizogenos arbusculares (HMA), asi como la micorriza arbuscular (MA) en las raices de cuatro especies de helechos (Cheilanthes myriophylla, Ch. bonariensis, Blechnum appendiculatum y Adiantum capillus-veneris) se evaluaron en relacion con la fertilidad del suelo durante febrero y diciembre. Los helechos se evaluaron en dos ecosistemas de Oaxaca, Mexico: Ch. myriophylla y Ch. bonariensis en el matorral xerofilo semiarido, y B. appendiculatum y A. capillus-veneris en el bosque mesofilo de montana. El suelo rizosferico de las cuatro especies tuvo mayor abundancia y riqueza de esporas de HMA que el suelo sin helechos. En total se registraron 13 generos y 32 morfoespecies de HMA. Las morfoespecies de Glomus se detectaron en ambos ecosistemas, mientras que Racocetra, Scutellospora, Diversispora y Gigaspora fueron exclusivas del bosque mesofilo. La baja micorrizacion arbuscular se atribuyo a los altos niveles de materia organica, N total y P inorganico; la MA fue mas activa en Ch. bonariensis, especie del matorral xerofilo, lo cual sugiere que la MA es regulada por la disponibilidad de recursos y la identidad del helecho. Las cuatro especies forman reservorios de HMA, lo que indica que los helechos podrian generar inoculos nativos utiles para la restauracion ambiental de sus ecosistemas.
Extraction and random primer PCR detection of genomic DNA of parasitic mites Demodex folliculorum and Demodex brevis (Acari: Demodicidae).

[Objective] To explore the extraction methods of genomic DNA of parasitic mites Demodex folliculorum (D.f.) and Demodex brevis (D.b.). [Methods] Mites were disrupted by repeated freezing and thawing in liquid nitrogen. Then,the improved DNA extraction method of mini-insects,alkaline lysis and the commercial extraction kit were used respectively to extract genomic DNA of D.f. and D.b. ,which had been kept freezing for ﹤5 or 8-10 months. [Results] The results of protein and nucleic acid radiometer showed the purity and quantity of genomic DNA extracted by the commercial kit were obviously better than those by other methods of mini-insects and alkaline lysis. Clear DNA fingerprints were found in the amplification results of random amplified polymorphic DNA (RAPD). There were obviously different banding patterns between D.f. and D.b. The freezing time affected the quantity of DNA extraction,but had only small effect on the purity and RAPD fingerprints of genomic DNA. The same species of mites had similar banding pattern even using different extraction methods. More and clear bands were detected by the commercial extraction kits and improved DNA extraction method of mini-insects. The bands detected by alkaline lysis method were less and obscure. [Conclusions] The application of repeated freezing-thawing in liquid nitrogen acts effectively to disrupt mites. The mites had better not be kept frozen more than 6 months. The commercial extraction kit is an effective approach to extract genomic DNA of mites. RAPD technique provides a simple method for detecting and classifying D.f. and D.b.
Overall Rates and Sample Selection: Inferring HIV Prevalence from a Selected Sample

This paper estimates HIV prevalence in Zambia from survey data that are subject to sample selection: some surveyed individuals do not consent to taking a HIV test. We introduce semiparametric estimators for an overall rate that incorporate recent developments in machine learning. The semiparametric estimators perform well in Monte Carlo experiments and obtain narrower confidence intervals than a fully parametric estimator when the model is misspecified. Our semiparametric estimates of the HIV rate are roughly equal to the rate in the selected sample. In contrast, recent parametric estimates find a higher rate--implying that some form of sample-selection correction is warranted.
Mitigations in Lipid Profile Levels with Duration-Dependent Exercise Intensities in Overweight and Obese Females

Although known for its role in clogging arteries and pathogenesis of heart diseases and stroke, cholesterol (and similar lipids) is also useful in the bio-synthesis of sex and adrenal hormones. Studies have shown three forms of cholesterol-carrying proteins in the blood: high-density lipoproteins (HDL), low-density lipoproteins (LDL), and very low-density lipoproteins (VLDL). With LDL and VLDL being the “bad cholesterol”, this study investigated the effect(s) of a 10-week interval exercise training and a 10-week continuous exercise training on total body Cholesterol, HDL, LDL, VLDL and Triglycerides (TAGs) in obese and overweight females. To approach this, one hundred and eleven (111) overweight and obese female subjects (aged between 18-65 years) were ethically recruited and grouped into three of thirty-seven (37) subjects each; (CETG = Continuous Exercise Training Group, IETC = Interval Exercise Training Group, and CG = Control group). While CG had no form of exercise training, IETC received alternate intensity training in ratio 1:3 as 30 seconds of high-intensity exercise with an alternate 90 seconds of low-intensity exercise. Subjects in CETG received similar treatments as IETC but without the low-intensity phase. In both cases, exercise intensity was 65% of heart rate maximum for 20 minutes at the first 2 weeks and was subsequently increased by 5% intensity and 5 minutes duration every 2 weeks till the 10th week with proper profiling and record of serum lipid levels (cholesterol, LDL, VLDL, HDL and TAGs) in each case. Analysis of the differences in mean (ANOVA) for obtained records showed a statistically significant decrease in cholesterol, LDL, VLDL and TAGs after 10 weeks of high-intensity continuous exercise training and a statistically significant increase in HDL after 10 weeks of high-intensity interval exercise training. Thus, lipid profile levels were positively affected by continuous mode of aerobic exercise. Similar but advanced studies with dietetic implications are recommended for further explanation of the reasons for the observed differences.
Formation and Growth of Bryopsis hypnoides Lamouroux Regenerated from Its Protoplasts

Tissue culture, SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and spectra analysis were used for studying the aggregation mechanism of protoplasts from Bryopsis hypnoides Lamouroux and the discrepancy between the protoplast-regenerated plants and the wild type. The aggregation of protoplasts from B. hypnoides was observed in natural seawater and artificial seawater with different pH values, and the location and mechanism of the materials causing the aggregation were also studied. Results showed that the protoplasts could aggregate into some viable spheres in natural seawater and subsequently grow into mature individuals. Aggregation of the protoplasts depended exclusively upon the pH value (6-11), and the protoplasts aggregated best at pH 8-9. Some of the extruded protoplasts were separated into two parts by centrifugation: the pellet (PO) and the supernatant (PL). The PO could aggregate in artificial seawater (pH 8.3) but not in PL. No aggregation was found in PO cultured in natural seawater containing nigericin, which can dissipate the proton gradients across the membrane. These experiments suggest that the aggregation of protoplasts is proton-gradient dependent and the materials causing the aggregation were not in the vacuolar sap, but located on the surface or inside the organelles. Furthermore, the transfer of the materials across the membrane was similar to △pH-based translocation (△pH/TAT) pathway that occurs in the chloroplasts of higher plants and bacteria. Obvious discrepancies in both the total soluble proteins and the ratio of chlorophyll a to chlorophyll b between the regenerated B. hypnoides and the wild type were found, which may be related to the exchange of genetic material during aggregation of the organelles. In the process of development, diatom Amphora coffeaeformis Agardh attached to the protoplast aggregations, retarding their further development, and once they were removed, the aggregations immediately germinated, which showed that diatoms can affect the development of other algae.
Plasma Lipoproteins in Brain Inflammatory and Neurodegenerative Diseases

Functions of the central nervous system (CNS) are mainly performed by neurons and glial cells (astrocytes, oligodendrocytes and microglia). Microglia or microcytes have macrophage-like immune related functions; oligodendrocytes are the myelinating cells in the CNS; and astrocytes have diverse roles in synaptogenesis, neurotransmission, myelination and reactive mechanisms to injury. CNS tissue is separated from blood circulation by specialized cell barriers, the most extensive being the endothelium of the socalled blood-brain barrier (BBB).
Immunostimulatory effects and delivery of oligodeoxynucleotides containing CpG motifs (CpG-ODN) in neonatal broiler chickens

Oligodeoxynucleotides containing CpG motifs (CpG-ODN) have been shown to stimulate the innate immune system against a variety of bacterial, viral, and protozoan infections in a variety of vertebrate species. The objectives of this study were to investigate the immunostimulatory effect of CpG-ODN against Salmonella Typhimurium infection and the formulation and delivery of CpG-ODN by the in ovo route. Day-old broiler chicks or embryonated eggs (day 18 of incubation) received either 50 μg of CpG-ODN, 50 μg of non-CpG-ODN, or saline. At day four-post hatch, all birds were subcutaneously inoculated by Salmonella Typhimurium. Clinical signs, pathology, bacterial isolations from the air sacs, and mortality were observed for ten days following challenge. The survival rate of the birds that received CpG-ODN via in ovo or in vivo treatments was significantly higher than the control group. Salmonella Typhimurium level in the peripheral blood and pathology were significantly lower (p < 0.001) in CpG-ODN group compared to the control group. In order to investigate the effect of formulation of CpG-ODN, embryonated eggs (day 18 of incubation) were inoculated with either 50 μg of CpG-ODN alone or CpG-ODN formulated with polyphosphazene, liposome, or Emulsigen®. Four days after administration of CpGODN formulations, the birds were challenged with E. coli by subcutaneous injection. Clinical signs, pathology, bacterial isolations from the air sacs, and mortality were observed for seven days following challenge. The birds that received either CpG-ODN or CpG-ODN formulated with polyphosphazene had significantly higher survival rates (30 and 60%) compared to the birds in groups receiving either non-CpG-ODN or saline.
Breeding cowpea (Vigna unguiculata (L.) walp.) for improved drought tolerance in Mozambique

A participatory rural appraisal (PRA), participatory varietal selection (PVS) and market price survey were conducted in Bilene, Boane and Chibuto districts and Maputo to assess farmers’ perceptions and preferences in cowpea varieties and to identify the major constraints affecting production. The study established that cowpea was an important crop, cultivated for its grain, leaves and fresh pods for household consumption and the market. Cowpea grain and leaves were important across the three districts in this study. Difference in accessibility to markets between districts determined differences in ranking of grain and leaves among districts. Grain was more important in Bilene and Chibuto districts which are situated far from the major urban centre of Maputo while leaves were more important in Boane, a district near the major market of Maputo. Fresh pods were important in Bilene district because it is situated in the main highway connecting Maputo and other provinces. Drought was the most important yield limiting constraint followed by aphids, bruchids and viral diseases. Farmers used various criteria to select cowpea varieties. These included high grain and leaf yield, large seed size, earliness, smoothness of the testa and potential marketability of the variety. The implication of this study for breeding is that different types of varieties need to be bred for different districts. Dual-purpose or grain type varieties need to be developed for districts situated far from the major markets while varieties for leaf production need to be developed for districts situated near urban centres. During the breeding process a selection index needs to be adopted whereby drought tolerance, high grain and leaf yield, large seed size, smooth testa, earliness, aphids and bruchids resistance should be integrated. High grain yield should receive high weight for varieties developed for the districts located far from major markets while high leaf yield would receive high weight for varieties developed for districts located near major markets.
Which words are most iconic

Some spoken words are iconic, exhibiting a resemblance between form and meaning. We used native speaker ratings to assess the iconicity of 3001 English words, analyzing their iconicity in relation to part-of-speech differences and differences between the sensory domain they relate to (sight, sound, touch, taste and smell). First, we replicated previous findings showing that onomatopoeia and interjections were highest in iconicity, followed by verbs and adjectives, and then nouns and grammatical words. We further show that words with meanings related to the senses are more iconic than words with abstract meanings. Moreover, iconicity is not distributed equally across sensory modalities: Auditory and tactile words tend to be more iconic than words denoting concepts related to taste, smell and sight. Last, we examined the relationship between iconicity (resemblance between form and meaning) and systematicity (statistical regularity between form and meaning). We find that iconicity in English words is more strongly related to sensory meanings than systematicity. Altogether, our results shed light on the extent and distribution of iconicity in modern English.
Aquatic Coleoptera response to environmental factors of freshwater ecosystems in Changbai Mountain, northeast China

Aquatic Coleoptera (beetles) play a key role in freshwater ecosystems and are considered as a suitable bioindicator. Despite being widely distributed in China, there are few aquatic Coleoptera-based methods to assess ecological quality and environmental conditions. Changbai Mountain, with its distinct temperate and boreal forest ecosystems, provides an excellent opportunity to explore the influence of environmental features on aquatic beetles along altitude gradients. The objectives of the study were to investigate community structure and to determine the dominant factors controlling aquatic beetles in the montane environment. Study results showed that there were 8 families, 40 genera, and 72 aquatic beetle species on Changbai Mountain, and that Dytiscidae, Hydrophilidae and Haliplidae were the dominant families. Seven sensitive species of aquatic beetles could be considered as the candidate of indicator for environmental monitoring. Canonical correspondence analysis showed that water pH, concentrations of total organic matter and total phosphorus in sediment, water conductivity and water temperature had a significant impact on the community structure of aquatic beetles, and that water pH was the most important factor. Our results suggested that water quality played a key role in species richness of aquatic beetles, and that therefore they could be considered as an indicator organism of freshwater ecosystem health.
Emulsifying properties and structural characteristics of β-conglycinin and dextran conjugates synthesised in a pressurised liquid system.

Summary The purpose of this study was to characterise the Maillard reaction in a pressurised liquid system containing β-conglycinin and dextran. The rate of browning and the free amino content in this liquid system, with an initial pH of 7.2, were measured after reaction under atmospheric pressure and at 10 MPa. The secondary and tertiary structures of the conjugates were analysed by circular dichroism, showing that the increased pressure accelerated the reaction rate of the free amino groups and reduced the rate of browning. Significant structural changes occurred in the tertiary structure of the conjugates. Additionally, the emulsifying properties of the β-conglycinin–dextran conjugates produced were studied. The emulsifying properties of the conjugates produced at 10 MPa were higher than those made at atmospheric pressure.
Quantitative Fish Dynamics

1. Population Growth, Mortality, and the Fishing Process 2. Stock Productivity and Surplus Production 3. Stock and Recruitment 4. Growth and Fecundity 5. Delay-Difference Models 6. Age-Structured Models: Per Recruit and Year-class Models 7. Age Structured Models: Renewal Theory 8. Catch-Age and Age-Structured Assessment Models 9. Size Structured Models and Assessment Methods 10. Migration and Movement 11. Optimal Harvesting
On the histone acetyltransferase hMOF

7 TIIVISTELMÄ . 8 REVIEW OF THE LITERATURE . 9 STRUCTURE OF CHROMATIN . 9 BIOCHEMISTRY OF CHROMATIN . 12 CHROMATIN REMODELING ENZYMES. 13 HISTONE VARIANTS . 14 POST-TRANSLATIONAL MODIFICATIONS . 16 Acetylation-deacetylation as a charge switch . 18 Is there a histone code? 19 Histone modifications as signal transductors. 21 HISTONE ACETYLTRANSFERASES . 23 STRUCTURE OF HISTONE ACETYLTRANSFERASES . 23 HAT FAMILIES . 24 B-HATS. 25 A-HATS . 25 BIOLOGICAL FUNCTIONS OF HATS . 27 HISTONE ACETYLATION IN GENE REGULATION . 27 Thinking globally. 28 Acting locally . 30 DNA REPAIR . 31 DNA REPLICATION. 34 RECOMBINATION . 35 HATS IN DEVELOPMENT AND DISEASE . 37 LESSONS FROM MICE . 37 CHROMATIN AND DISEASE. 38 DOSAGE COMPENSATION AS A MODEL FOR CHROMATIN REGULATION . 40 MAMMALS: X = X(X). 41 NEMATODES: X = 1⁄2XX. 42 FRUIT FLIES: 2X = XX . 42 OTHER ORGANISMS: ? 44 AIMS OF THE STUDY. 45