Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence analysis of chromatin immunoprecipitation data for factors

Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis, and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses, and recommend strategies for effective motif discovery from these data.
IL-4 Induces In Vivo Production of IFN-γ by NK and NKT Cells1

Although IL-4 and IFN-γ often have opposite effects and suppress each other’s production by T cells, IL-4 can stimulate IFN-γ production. To characterize this, we injected mice with IL-4 and quantified IFN-γ production with the in vivo cytokine capture assay. IL-4 induced Stat6-dependent IFN-γ production by NK and, to a lesser extent, NKT cells, but not conventional T cells, in 2–4 h. Increased IFN-γ production persisted at a constant rate for >24 h, but eventually declined, even with continuing IL-4 stimulation. This eventual decline in IFN-γ production was accompanied by a decrease in NK and T cell numbers. Consistent with a dominant role for NK cells in IL-4-stimulated IFN-γ secretion, IL-4 induction of IFN-γ was B and T cell-independent; suppressed by an anti-IL-2Rβ mAb that eliminates most NK and NKT cells; reduced in Stat4-deficient mice, which have decreased numbers of NK cells; and absent in Rag2/γc-double-deficient mice, which lack T, B, and NK cells. IL-4-induced IFN-γ production was not affected by neutralizing IL-12p40 and was increased by neutralizing IL-2. IL-13, which signals through the type 2 IL-4R and mimics many IL-4 effects, failed to stimulate IFN-γ production and, in most experiments, suppressed basal IFN-γ production. Thus, IL-4, acting through the type 1 IL-4R, induces Stat6-dependent IFN-γ secretion by NK and NKT cells. This explains how IL-4 can contribute to Th1 cytokine-associated immune effector functions and suggests how IL-13 can have stronger proallergic effects than IL-4.
MOLECULAR CLONING, SEQUENCE ANALYSIS AND EXPRESSION OF THE GLYCYL-TRNA SYNTHETASE GENE (GLYS A) FROM BACILLUS SUBTILIS SADATA-73 -

: The glycyl-tRNA synthetase (β-subunit) gene from locally isolated and identified Bacillus subtilis sadata-73 was cloned in lambda ZAP XR genomic library XhoI and EcoRI digest. The complete open reading frame was obtained in two steps, sequenced and the GenBank gene for this aminoacyl-tRNA synthetase has an open reading frame of 1479 nucleotides. The supposed amino acid sequence encodes a protein of 492 amino acids with MW = 55,142. The protein sequence has extensive overall identity / similarity with the Bacillus subtilis subtilis 168, the Bacillus amyloliquefaciencs , Bacillus licheniformis ATCC 14580 and Bacillus pumilus glycyl-tRNA synthetases (98%, 98%, 78%, 69%, and 66%, respectively). The enzyme was overexpressed as a fusion protein in E.coli using pMal-c2 expression system containing the T7 RNA polymerase/ promoter. The predicted MW for the MBP gene product is in good harmony with the size of the fusion protein determined by SDS-PAGE (M(r) = 55) and the predicted protein has an isoelectric point 5.08.
Phylogenetic analysis based on chloroplast atpA gene sequences from Phyllostachys propinqua.

Based on the construction of chloroplast genomic library,the atpA gene was cloned from Phyllostachys propinqua chloroplast genome,and the atpA gene sequences were compared between P.propinqua and other 11 gramineous plant species collected from GenBank.The results showed that there were 110 single nucleotide polymorphisms(SNP) markers between the 12 atpA gene sequences.Among these SNP markers,there was only one SNP marker blasted atpA gene sequence of P.propinqua with atpA gene sequence of Oryza sativa Indica,O.sativa Japonica and O.nivara;there were two SNP markers existed in the sequences of P.propinqua,Zea mays,Sorghum bicolor,Saccharum officinarum and S.hybrid cultivar;however,there were more markers between atpA gene sequence of P.propinqua,Triticum aestivum,Hordeum vulgare subsp.vulgare,Agrostis stolonifera and Lolium perenne.The Neighbor-Joining phylogenetic trees based on the atpA gene sequences and coding amino acid sequences indicated that the 12 gramineous plant species could be divided into two major groups and four subgroups,the P.propinqua and rice were clustered together.It could be concluded from the results that the P.propinqua had the most closest phylogenetic relationship with O.sativa,the closer relationship was for P.propinqua,Z.mays,S.bicolor,S.officinarum and S.hybrid cultivar,but the phylogenetic relationship of P.propinqua with wheat and relatives of wheat was far away.
The role of Sox9 in heart valve development and disease

of a dissertation at the University of Miami. Dissertation supervised by Professor Joy Lincoln. No. of pages in text. (91) Heart valve structures open and close during the cardiac cycle to provide unidirectional blood flow through the heart, critical for efficient cardiovascular function. Valve dysfunction results in either incomplete opening or incomplete closure of the valve. Both types of valve dysfunction decrease efficiency of blood flow, increasing the load on the myocardium and leading to secondary heart disease such as pathological hypertrophy and heart failure. There are currently no effective treatments to prevent or slow the progression of valve disease, and there are no pharmacological treatments for advanced valve disease. Although most valve disease is associated with aging, increasing evidence suggests that valve disease often has origins in development. Congenital valvuloseptal defects affect many newborns, ranging from life-threatening malformations requiring immediate repair to more subtle, often undiagnosed defects that increase susceptibility to valve disease later in life. Therefore, an improved understanding of the mechanisms of heart valve formation and maintenance of adult valves may serve as an important step in improving valve disease treatment options. In this work, the mechanisms of normal valve development and the role of Sox9 in developing and mature valves are further studied. The temporal and spatial expression of extracellular matrix genes and proteins are examined throughout normal murine valve development. Sox9 function in the processes of valve development and valve maintenance is examined using mouse models of conditional Sox9 loss-of-function. Heart valve phenotypes in mice with reduced Sox9 function are examined throughout development and in adult mice with resultant calcific valve disease. The possible causative mechanisms of calcific valve disease in mice with reduced Sox9 function are further investigated by identification of novel possible targets of Sox9 transcriptional regulation. Together these studies improve our understanding of heart valve development, characterize a model of heart valve calcification with genetic etiology, and identify and characterize novel targets of Sox9.
FT-IR and X-Ray Diffraction Characterization of Melanoidins Formed from Glucose and Fructose with Amino Acid Enantiomers in the Maillard Reaction

The objective of this study was to investigate Fourier transform infrared (FT-IR) spectrometry and the X-ray diffraction (XRD) characterization of melanoidins formed from glucose and fructose with amino acid enantiomers in the Maillard reaction. Before dialysis, FT-IR spectroscopy of all the samples showed that the characteristic absorption intensities appeared as a broad and intense band of the stretching vibration of the -OH group at 3,400/㎝ for a high pH. The absorption bands of the melanoidins sharply decreased in intensity after dialysis as compared to those before dialysis. In particular, the absorption bands at 992 and 575/㎝ disappeared. The XRD confirmed that the crystal structure of the melanoidins disappeared after dialysis and a new crystal structure was formed at 9 and 28° (2θ). In particular, broad diffraction peaks were formed in the 10-21° (2θ) range for a high pH, while other sharp diffraction peaks disappeared.
GridQTL: A Grid Portal for QTL Mapping of Compute Intensive Datasets.

INTRODUCTION. QTL mapping is an essential tool for the understanding of the genetic basis of complex traits, including health and production traits in farm animals and disorders and quantitative risk factors for disease in animal and human populations. QTL Express has provided a user-friendly and web-accessible analysis tool that has seen wide use for the analysis of experimental data, particularly from studies of outbred species. With the advent of microarrays, high-density multiple trait gene expression datasets are now prevalent. Paralleled with the availability of dense SNP marker maps for thousands of individuals this results in a computationally intensive and complex QTL mapping problem. The GridQTL project aims to provide an expanded and improved QTL analysis tool that harnesses Grid technologies to deal with greatly increased computational demands.
Vocal individuality in the roding calls of Woodcock Scolopax rusticola and their use to validate a survey method

The Woodcock Scolopax rusticola is a difficult species to survey in the breeding season because of its cryptic plumage and, with the exception of courtship flights, secretive behaviour. Sparse data from general bird surveys prohibit reliable estimation of population sizes and trends, and a new species-specific method to provide baseline information on population status and to enable reliable future monitoring is required. Counts of displaying, or ‘roding’, males at dawn or dusk potentially provide such a method but their value is unclear because it is impossible for an observer to distinguish different birds. We examined the vocal individuality of 39 roding males and were able to attribute calls to individuals correctly in 95% of cases on the basis of five parameters measured from spectrograms. Using calls, we determined the number of individual males at 43 sites. Roding activity differed between males at one site, with the two most active birds accounting for, on average, 55 and 27% of passes. There was no evidence of sequential roding by different males. We quantified the relationship between numbers of males and numbers of passes of roding birds during a 1-h period at dusk. This relationship was not affected by region, month, habitat or woodland size class. We conclude that counts of roding males provide a suitable index for monitoring populations of this species.
Harmonized System: Nomenclature Evolution at Its 20th Anniversary (1988–2008)

More than 200 countries and economic regions worldwide are using the nomenclature of the Harmonized Commodity Description and Coding System (Harmonized System Convention, HS) and are basing their customs tariffs thereon. The number of HS headings (four–digit–code) and HS–subheadings (six–digit–code) is altered every four to six years, when the nomenclature is revised and updated due to trade patterns and technical development (HS 1988, HS 1992, HS 1996, HS 2002, HS 2007). More and more gaps are emerging within the nomenclature 34 headings are not in use in the HS 2007 for the next four to five years. This Column shows the history of HS revisions, the gaps within the nomenclature and the evolution of the HS nomenclature within the past 20 years (1988–2008).
Parallel SPARQL Query Optimization

Existing parallel SPARQL query optimizers assume hash-based data partitioning and adopt plan enumeration algorithms with unnecessarily high complexity. Therefore, they cannot easily accommodate other partitioning methods and only consider an unnecessarily limited plan space. To address these problems, we first define a generic RDF data partitioning model to capture the common structure of various state-of-the-art RDF data partitioning methods. Then we propose a query plan enumeration algorithm that not only has an optimal efficiency, but also accommodates different data partitioning methods. Furthermore, based on a solid analysis of the complexity of the plan enumeration algorithm, we propose two new heuristic methods that can consider a much larger plan space than the existing methods, and at the same time can still confine the search space of the algorithm. An autonomous approach is proposed to choose one of the two methods by considering the structure and the size of a complex SPARQL query. We conduct extensive experiments using synthetic and a real-world dataset, which show the superiority of our algorithms in comparing to existing ones.
Infectious diseases in camelids

Introduction Part 1 Bacterial Diseases: General survey Digestive system Respiratory system Urogenital system Integument Udder Nervous system Part 2 Viral Diseases: Viral infections causing disease Nonpathogenic viral diseases Part 3 Fungal Infections: Mycotic dermatitis Aspergillosis Candidiasis Coccidiodomycosis Mucormycosis Miscellaneous fungal infections Part 4 Vaccination Programs: Part 5 Parasitic Diseases: Protozoal infections Infestations with Ectoparasites Infections with Helminths Infections with cestodes Infections with trematodes Infections with hirudinea References Index
Giardiasis risk from an unfiltered, protected surface water source

This article describes the efforts of water utility personnel to determine whether the level of endemic giardiasis observed in their service area could be attributed to the surface water supply, which is chloraminated but not filtered. Comparison of epidemiological data for the county in which the utility is located with data from another county that used conventionally treated water showed similar incidence rates, partitioning into risk categories, and age distributions for giardiasis. There was no correlation between the location of a giardiasis case and disinfection contact time within the unfiltered water's distribution system.
Dichelobacter nodosus and Fusobacterium necrophorum in ruminants with lameness and footrot

of a thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy Dichelobacter nodosus and Fusobacterium necrophorum in ruminants with lameness and footrot By Grant Norman Bennett Footrot is a destructive hoof disease found predominantly in sheep and goats that is caused by Dichelobacter nodosus (D. nodosus), a gram-negative, anaerobic bacterium. It has been shown that D. nodosus requires a second, gram-negative, anaerobic bacterium, Fusobacterium necrophorum (F. necrophorum), to initiate footrot. However, once footrot is established, the role, if any, that F. necrophorum plays is unknown. In this thesis, the roles D. nodosus and F. necrophorum play in footrot were investigated. To facilitate the study of F. necrophorum a new diagnostic Polymerase Chain Reaction (PCR) specific for F. necrophorum was developed and tested. This method was used in combination with an existing D. nodosus-specific PCR to study the prevalence of D. nodosus and F. necrophorum in sheep and goats with footrot in the field. This found D. nodosus and F. necrophorum were associated with under-running footrot and tended to be detected together. This supported the contention that F. necrophorum acts cooperatively with D. nodosus to cause under-running footrot in sheep and goats as well as that ovine and caprine footrot have similar bacteriologies. To ascertain the possible roles D. nodosus and F. necrophorum play during footrot development, two footrot trials were conducted. These trials ran disease-free sheep and
Optimization of the Production Process of Yam and Honey Jelly

[Objective] To optimize the production process of yam and honey jelly. [Method] Using yam and honey as raw materials,the single factor test and orthogonal experiment were adopted to optimize the production technology of jelly. [Result] The optimum conditions for producing yam and honey jelly were:20.00% of yam juice,15.00% of mixed syrups(honey∶sugar=1∶1) ,0.20% of citric acid,and 1.00% of gelling agent(xanthan gum∶sodium alginate=1∶3) . [Conclusion] The study provided experimental basis for producing the yam and honey jelly with nice flavor and health-care function.
Conserved Features of Chromatin Remodeling Enzymes: A Dissertation

Chromatin structure plays an essential role in the regulation of many nuclear processes such as transcription, replication, recombination, and repair. It is generally accepted that chromatin remodeling is a prerequisite step in gene activation. Over recent years, large multisubunit enzymes that regulate the accessibility of nucleosomal DNA have emerged as key regulators of eukaryotic transcription. It seems likely that similar enzymes contribute to the efficiency of DNA replication, recombination, and repair. These chromatin remodeling complexes can be classified into two broad groups: (1) the ATP-dependent enzymes, which utilize the energy of ATP hydrolysis to increase the accessibility of nucleosomal DNA; and (2) histone modifying enzymes that phosphorylate, acetylate, methylate, ubiquitinate, or ADP-ribosylate the nucleosomal histones (for review see Kingston and Narlikar, 1999; Muchardt and Yaniv, 1999; Brown et al., 2000; Vignali et al., 2000; Strahl and Allis, 2000). The mechanism by which these two groups of large, multi-subunit enzymes function to alter chromatin structure is enigmatic. Studies suggest that ATP-dependent and histone acetyltransferase chromatin remodeling enzymes have widespread roles in gene expression and perform both independent and overlapping functions. Interestingly, although both groups of enzymes appear to be distinct, several features of these enzymes have been conserved from yeast to man. Thus, understanding the role of these similar features will be essential in order to elucidate the function of remodeling enzymes, their functional interrelationships, and may uncover the fundamental principals of chromatin remodeling. In this study, we use a combination of yeast molecular genetics and biochemistry to dissect out the function of individual parts of these chromatin remodeling machines and to understand how these large macromolecular assemblies are put together. In addition, we also investigate the mechanism by which the ATP-dependent enzymes exert their regulatory effects on chromatin structure. Structure/function analysis of Saccharomyces cerevisiae Swi3p (conserved in SWI/SNF complexes across all eukaryotic phyla) reveals a unique scaffolding role for this protein as it is essential for assembly of SWI/SNF subunits. We have also characterized a novel motif that has homology to the Myb DNA binding domain, the SANT domain, and that is shared among transcriptional regulatory proteins implicated in chromatin remodeling. Mutational analysis of this domain in yeast Swi3p (SWI/SNF), Rsc8/Swh3p (RSC), and Ada2p (GCN5 HATs) reveals an essential function for the SANT domain in chromatin remodeling. Moreover, our studies suggest that this novel motif may be directly involved in mediating a functional interaction with chromatin components (i.e. histone amino terminal domains). We have also directly compared the activities of several members of the ATP-dependent chromatin remodeling enzymes. Surprisingly, we find that these enzymes utilize similar amounts of ATP…
Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS)

Summary 1In recent years the use of species distribution models by ecologists and conservation managers has increased considerably, along with an awareness of the need to provide accuracy assessment for predictions of such models. The kappa statistic is the most widely used measure for the performance of models generating presence–absence predictions, but several studies have criticized it for being inherently dependent on prevalence, and argued that this dependency introduces statistical artefacts to estimates of predictive accuracy. This criticism has been supported recently by computer simulations showing that kappa responds to the prevalence of the modelled species in a unimodal fashion. 2In this paper we provide a theoretical explanation for the observed dependence of kappa on prevalence, and introduce into ecology an alternative measure of accuracy, the true skill statistic (TSS), which corrects for this dependence while still keeping all the advantages of kappa. We also compare the responses of kappa and TSS to prevalence using empirical data, by modelling distribution patterns of 128 species of woody plant in Israel. 3The theoretical analysis shows that kappa responds in a unimodal fashion to variation in prevalence and that the level of prevalence that maximizes kappa depends on the ratio between sensitivity (the proportion of correctly predicted presences) and specificity (the proportion of correctly predicted absences). In contrast, TSS is independent of prevalence. 4When the two measures of accuracy were compared using empirical data, kappa showed a unimodal response to prevalence, in agreement with the theoretical analysis. TSS showed a decreasing linear response to prevalence, a result we interpret as reflecting true ecological phenomena rather than a statistical artefact. This interpretation is supported by the fact that a similar pattern was found for the area under the ROC curve, a measure known to be independent of prevalence. 5Synthesis and applications. Our results provide theoretical and empirical evidence that kappa, one of the most widely used measures of model performance in ecology, has serious limitations that make it unsuitable for such applications. The alternative we suggest, TSS, compensates for the shortcomings of kappa while keeping all of its advantages. We therefore recommend the TSS as a simple and intuitive measure for the performance of species distribution models when predictions are expressed as presence–absence maps.
Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota, Manis spp.)

Thirty-four polymorphic dinucleotide microsatellite loci were developed in the Malayan pangolin Manis javanica. Of the 34 markers, 32 and 18 were also amplified, respectively, in the Chinese pangolin (Manis pentadactyla) and the African tree pangolin (Manis tricuspis). Analysis of 24 Malayan, 12 Chinese and 2 African tree pangolins showed high levels of variability (heterozygosity ranging from 0.321 to 0.708). These are the first available microsatellite markers in Pholidota and will be an invaluable tool for evolutionary and conservation genetic studies in pangolins.