Miracle-dz/UniFAR-FTUs huggingface dataset:
IL-10 and TNF-α promoter haplotypes are associated with childhood Crohn's disease location

AIM: To determine the distribution and frequencies of the genotypes and haplotypes of the genes encoding for the glucocorticoid receptor (GR), the tumor necrosis factor (TNF)-α and the interleukin (IL)-10 in childhood Crohn’s disease (CD) and to assess the impact of the corresponding DNA variants on clinical and disease phenotypes. METHODS: Ten variants in GR, TNF-α and IL-10 were genotyped in 113 childhood CD cases and 95 healthy subjects, both of French-Canadian origin. RESULTS: For the GR polymorphisms (R23K and N363S) and IL-10 variants in the 5’flanking region (-1082 G > A, -819 T > C and -592 A > C), no difference was observed in allele and genotype frequencies between CD patients and controls. At the haplotype level, we found three IL-10 haplotypes previously described in Caucasians (GCC, ACC and ATA) and three novel haplotypes only present in IBD patients. When we analyzed the haplotype distribution with the anatomical location of the disease, the GCC haplotype was associated with the colonic and the ACC haplotype with the terminal ileum location, respectively. The genotyping of five polymorphisms in the promoter region of the TNF-α gene (-1031 T > C, -863 A > C, -857 T > C, -308 A > G and -238 A > G) revealed a significant overrepresentation of homozygous -1031 CC among CD patients (OR = 9.9) and an association with the colonic location. For TNF-α, eleven haplotypes were inferred, including two frequent ones, TCCGG and CACGG, which were significantly observed more frequently in controls and cases, respectively. CONCLUSION: This is one of the first studies investigating the association between haplotype structure and disease location in a CD pediatric cohort. Our results will help to increase our understanding of the genetic determinants of childhood CD.
Role of ubiquitination in Caenorhabditis elegans development and transcription regulation during spermatogenesis

Title of Dissertaion: Role of ubiquitination in Caenorhabditis elegans development and transcription regulation during spermatogenesis Madhura Kulkarni, Doctor of Philosophy, 2008 Dissertation Directed by: Dr. Harold Smith Center for Advanced Research in Biotechnology Regulation of gene function can be achieved through a variety of mechanisms. In this dissertation, I present the genetic and molecular characterization of two genes involved in two distinct mechanisms of control. Each gene was initially identified by its functional role in sperm development in the model organism Caenorhabditis elegans. The first gene, uba-1, is an essential enzyme involved in protein turnover through ubiquitin-mediated proteolysis. A temperature-sensitive allele, (uba-1)it129, was isolated in a classical genetic screen for mutations that cause sperm-specific sterility. The second gene, spe-44, encodes a putative transcription factor. Its identification by microarray screening for sperm-enriched genes led to the cytological analysis of the deletion allele spe-44(ok1400), by reverse genetics approach. it129 encodes a conditional allele of uba-1, the sole E1 ubiquitin-activating enzyme in C. elegans. E1 functions at the apex of the ubiquitin-mediated conjugation pathway, and its activity is necessary for all subsequent steps in the reaction. Ubiquitin is covalently conjugated to various target proteins. Poly-ubiquitination typically results in target protein degradation, which provides an essential mechanism for the dynamic control of protein levels. Homozygous mutants of uba-1(it129) manifest pleiotropic phenotypes, and include novel roles for ubiquitination in sperm fertility, control of body size, and sex-specific development. We propose a model whereby proteins normally targeted for proteasomal degradation instead persist in uba-1(it129) and impair critical cellular processes. The second gene, spe-44, was identified as a putative sperm gene regulator in C. elegans based on its up-regulated expression during spermatogenesis and its significant sequence homology to the DNA-binding SAND domain. Genetic analysis of a deletion allele of spe-44(1400) has revealed its functional role during sperm development. Cytological analysis of spe-44(ok1400) showed developmental arrest of spermatocytes prior to spermatid differentiation. spe-44 mRNA is expressed in a narrow spatial and temporal window, just prior to spermatocyte differentiation, consistent with its functional role during spermatogenesis. Future study will be directed to find putative targets of spe-44 and the mechanisms that regulate gene expression using microarray analysis and yeast-one hybrid screens. These studies will help to understand transcriptional regulatory aspects of spermatogenesis in C. elegans. ROLE OF UBIQUITINATION IN CAENORHABDITIS ELEGANS DEVELOPMENT AND TRANSCRIPTION REGULATION DURING SPERMATOGENESIS
Prospective Study for Antimicrobial Susceptibility of Escherichia coli Isolated from Various Clinical Specimens in India

The aim of the present work was to study the prevalence of Extended-spectrum β-lactamases (ESBLs) and Metallo-β-lactamases (MβLs) among 464 E. coli clinical isolates obtained from various clinical specimens; and to study the susceptibility of various drugs against E. coli isolates. Phenotypic characterization and susceptibility studies were performed according to the methods described in Clinical and Laboratory Standards Institute guidelines (CLSI, 2010). The prevalence of ESBLs and MβLs was analyzed with Polymerase Chain Reaction (PCR), using the previously reported primers. Among the four hundred sixty four isolates, 186 (40.08%) isolates were ESBLs positive, 75 (16.16%) isolates were MβLs positive, and 80 (17.24%) were both ESBLs and MβLs positive. The remaining 123 (26.50%) were non ESBLs and MβLs. TEM-types ESBLs (blaTEM-1, blaTEM-2, and blaTEM-50) were found in approximately 57% isolates. The prevalence of SHV-types, CTX-M-types and OXA-type was 29.03, 11.82 and 2.15%, respectively. Among the MβLs, the frequency of distribution of NDM-1, IMP-1, VIM-1 and KPC-types was 37.39, 21.33, 18.66, and 22.66%, respectively. In general, 92.6% E. coli isolates were susceptible to ceftriaxone plus EDTA plus sulbactam (CSE1034), followed by meropenem (74.4%), imipenem (71.2%), piperacillin plus tazobactam (52.1%), cefoperazone plus sulbactam (46.0%) and amoxycillin plus clavulanic acid (23.6%). Similarly, amoxycillin plus clavulanic acid showed the highest percentage of resistance (72.8%), followed by cefoperazone plus sulbactam (43.6%), piperacillin plus tazobactam (39.3%), imipenem (23.3%), meropenem (20.3%) and ceftriaxone plus EDTA plus sulbactam (CSE1034) (2.5%). Results of the present study revealed that most of the clinical isolates were susceptible to ceftriaxone plus EDTA plus sulbactam (CSE1034), and can be a potent antibacterial agent for the treatment of severe bacterial infections caused by E. coli.
A Colloidal Approach of Milk Acidification by Glucono-Delta-Lactone

Abstract Colloidal techniques (laser Doppler electrophoresis, particle size analysis, and capillary viscosimetry) were used in combination with a turbidimetric method to study milk acidification by gluconodelta-lactone. In agreement with a previous paper (1), micellar phenomena as a whole can be related to the turbidimetric observations, and it appears possible to hypothesize a logical development of milk acidification at the micellar level. The observed electrokinetic and hydrodynamic comportment of micelles can be explained by the presence of an outer hairy layer. Then, as for renneting, ethanol, or thermal milk treatments, the micellar destabilization by acidification could largely depend upon the collapse of this outer hairy layer. Thermal motion should be a major factor for aggregation of particles because increasing temperature leads to increasing frequency of particle encounters. Casein solubilization from low temperature and acidification seems to act as an additional micellar destabilizing factor.
Synthesis and Conformation of Novel 4'-Fluorinated 5'-Deoxythreosyl Phosphonic Acid Nucleosides as Antiviral Agents

Efficient synthetic route to novel 4'-fluorinated 5'-deoxythreosyl phosphonic acid nucleosides was described from glyceraldehyde using Horner-Emmons reaction in the presence of triethyl α-fluorophosphonoacetate. Glycosylation reaction of nucleosidic bases with glycosly donor 14 gave the nucleosides which were further phosphonated and hydrolyzed to reach desired nucleoside analogues. Synthesized nucleoside analogues 18, 21, 25 and 28 were tested for anti-HIV activity as well as cytotoxicity. Adenine derivatives 18 and 21 showed significant anti-HIV activity up to 100 µM.
Body size evolution in insular vertebrates: generality of the island rule

Aim My goals here are to (1) assess the generality of the island rule – the graded trend from gigantism in small species to dwarfism in larger species – for mammals and other terrestrial vertebrates on islands and island‐like ecosystems; (2) explore some related patterns of body size variation in insular vertebrates, in particular variation in body size as a function of island area and isolation; (3) offer causal explanations for these patterns; and (4) identify promising areas for future studies on body size evolution in insular vertebrates.
ISOLATION AND MOLECULAR CHARACTERIZATION OF SHIGA TOXIN PRODUCING E. COLI O157

Escherichia coli (E. coli) is normal inhabitant of all domestic animals and human beings. Its Sorbitol-non fermenting (SNF) biotype was detected in dung of buffalo (92 %), cattle (8 4 %), sheep (52 %) and goat (56 %). However, E. coli (SNF) was not detected in droppings of rural chickens, feces of donkeys and fresh aseptically collected milk and beef samples, whereas, the E. coli was detected in 96 percent market raw milk and 82 percent samples from beef shops. Eighty percent milk and 53 percent beef samples contained SNF isolates of E. coli. All isolates of SNF E. coli showing green metallic sheen on eosin methylene blue (EMB) agar were further characterized using polymerase chain reaction (PCR). The isolated DNA of 100 samples when amplified using universal, Stx1, Stx2 and O157 specific primers confirmed that 82 percent samples were positive for universal primers, 50 percent for O157, 60 percent for Stx1 and 51 percent for Stx2. It is concluded that E. coli O157 is normal inhabitant of intestinal tract of domestic ruminants and presumably animal feces are acting as main source of contamination of raw milk and beef.
Comparative Analysis of the $2\times 2$ Patch Antenna Array with Modified Fractal Antenna for 5G Communication and Wireless Applications

Modern communication demands wide bandwidth, high gain, and efficient reduced-size antennas to provide improved performance over a wide bandwidth range of the frequency spectrum. Here two antennas are taken, of which the first one is a fractal antenna and the second one is a $\mathbf{2}\times \mathbf{2}$ array antenna. This paper compares the performances of the modified fractal antenna and $\mathbf{2}\times \mathbf{2}$ patch array antenna. The modified fractal antenna has an FR-4 substrate with 2.4mm width and 2.4mm length and various rectangular slots through which the antenna has a wide bandwidth notch near 21 GHz with 2.77 GHz bandwidth, 25 GHz with 1.82 GHz bandwidth, 32 GHz with 4.23 GHz bandwidth, and 36.5 GHz with 2.94GHz bandwidth. It covers 5G applications in the range of 23.88-25.7GHz and 29.89-34.14GHz. On the other hand, the size of the $\mathbf{2}\times \mathbf{2}$ array antenna is less compared to the fractal antenna with FR-4 substrate, i.e., 1.5mm X 1.5mm. The array antenna has bandwidth notches near 15.3GHz with a bandwidth of 0.38GHz, 22.6GHz with a bandwidth of 2.55GHz, and 27.3GHz with a bandwidth of 3.13GHz and covers 5G applications in the range of 25.01-28.14GHz. Both antennas have an n258 band that covers a 5G millimeter wave, implemented using CST.
Raleio de cachos em vinhedos de altitude e qualidade do vinho da cultivar Syrah

The objective of this work was to evaluate the effect of different intensities of cluster thinning in mountain vineyards cv.Syrah on the evolution of phenolic compounds, during grape maturation. The experiment was carried out in the 2005/2006 and 2006/2007 crop seasons, at Sao Joaquim, SC, Brazil, at an average altitude of 1,230 m, on 'Syrah' grapevines that had been grafted on 'Paulsen 1103' root stock and trained out in vertical trellis system, spaced in 3x1.2 m and protected against hail. The cluster thinning was adjusted in the "veraison" corresponded to 15 Mg ha-1 (control), 13 Mg ha-1, 11 Mg ha-1 and 9 Mg ha-1, in a complete randomized blocks. The evolution of phenolic compounds was evaluated during the eight antecedent weeks to the harvest. The cluster thinning increased the content of anthocyanin in the grapes with a yield of 12 Mg ha-1, and improved their phenolic composition. These changes were favorable for the production of fine wines with excellent quality.
Systematic implications of butterfly leg structures that clean the antennae

The foreleg tibial epiphyses of Lepidoptera are used to clean the antennae Jander 1966, ODe! et al. 1982 and included references. Among butterflies, the skippers Hesperiidae and swallowtails Papilionidae possess a tibial epiphysis Evans 1949, Ehrlich 1958, but other butterfly families do not. The absence of a tibial epiphysis in these families raises the question of how they clean their antennae. Jander1966 addressed this question and reported three kinds of cleaning behavior in butterflies. Hesperiids use their foreleg tibial epiphyses to comb antennae. Lycaenids and most nymphalids pull each antenna between a midleg tibia and femur. Satyrine nymphal ids clean antennae by sliding each against a midleg tarsus as they walk. Jander did not mention any special structures for cleaning antennae besides the tibial epiphysis. There is a hypothesized correlation between Jander's behavioral observations and midleg morphology in lycaenids, riodinids, liby theids, and nymphalids. Eliot 1973 reported that there are scale "brushes" on the midleg tibia and femur of virtually all lycaenids, that the function of these brushes is unknown, and that the brushes allow the midleg to be distinguished from the hindleg. Sorensen 1980 hypothesized that the midleg brushes are used by lycaenids to clean the antennae. Scott 1985 accepted this hypothesis, noted that Ehrlich 1958 had discovered a midleg tibial brush in the monarch Danaus plexippus Linnaeus, a danaiine nymphalid, and reported that similar brushes occur in many riodinids and nymphalids. The behavior of cleaning the antennae with the legs has been used in determining phylogenetic relations among the butterfly families. Kristensen 1976 proposed that the Nymphalidae including Liby theidae and Lycaenidae including Riodinidae form a monophy letie lineage, in part because both families use the midleg for
Foraging Ecology of Peregrine Falcons (Falco peregrinus) Along the Colorado River, Grand Canyon, Arizona

Abstract We compiled 355 observations of foraging events of peregrine falcons (Falco peregrinus) in Grand Canyon, downstream from Glen Canyon Dam on the Colorado River during 1973–1995, and documented abundance of prey, foraging behavior, and success in foraging. Peregrine falcons attempted to forage on ≥44 species, including ≥40 species of birds: swifts and swallows (29%), waterfowl (Anseriformes, Podicipediformes, and similar birds, 27%), other waterbirds (waders and other large, non-anseriform waterbirds, 11%), bats (10%), large wasps (8%), and other species (15%). Frequency of foraging during the breeding season was positively related to overall abundance of prey, but relative intensity of predation (ratio of relative frequency of attack on a species to mean abundance of that species) increased on most species of prey in the usually turbid lower reach, where prey were less abundant. Air-to-air strikes were most common (94% of 271 cases for which data were available), followed by air-to-water strikes (4%), and air-to-ground strikes (2%). Tandem attacks occurred in ≥43% of cases. Overall foraging success was ≥52%, and was highest on large wasps (100%) and bats (87%), intermediate on large waterbirds (63%), swifts, swallows, and small terrestrial birds (42%), and waterfowl (40%), and lowest on belted kingfishers (Ceryle alcyon; 18%) and small shorebirds (<3%). Foraging success was related to abundance of prey and number of co-foraging falcons, and was negatively related to relative body mass of prey. Most dietary biomass was derived from waterfowl (64%) and large waterbirds (25%), whereas swallows and swifts contributed only 3%. The low and variably turbid segment near the dam had greater abundance of prey and lower relative intensity of predation compared to the usually turbid segment downstream, but distribution and overall frequency and success of foraging by peregrine falcons were not affected by regulation of flow.
The 'Landcare' Approach to Soil Conservation in the Philippines: An Assessment of Farm-Level Impacts

'Landcare' is a group-based approach to the promotion of conservation farming. A case study of the Landcare program in Lantapan in the southern Philippines is presented to assess the farm-level impacts of this approach. The program was successful in promoting the formation of Landcare groups and a municipal Landcare association, resulting in rapid and widespread adoption of conservation practices, particularly among maize farmers. This in turn significantly reduced soil erosion, though the impact on crop yield and income was somewhat delayed. Adoption was thus not motivated primarily by short-term returns but by a concern to reduce soil erosion and provide a basis for diversification into agroforestry.
The Value of Natural Ecosystems: An Economic and Ecological Framework

Ecosystem values, and the functional roles of ecosystems in providing goods and services for Man, have been subjects of increasing discussion and controversy among ecologists and economists in recent years. Economists have developed economic theory based on a market model, and price or value has been set in the marketplace. However, the market system cannot account for all possible values, and fails to account for goods and services for which no market, or only imperfect markets, exist. These non-traded goods and services are termed nonmarket values, and are categorized in the scheme we have developed either as Value II (attributable or assignable values) or as Value III (intangible or non-assignable values). The true or total value of natural systems should include not only the market values (Value I) but also these two categories of non-market values whenever decisions are made about the alteration of natural systems. Usually, only market values are incorporated by decision-makers in the management strategies of natural systems, and as a result of their omission of non-market values, numerous natural systems are being degraded or destroyed through market-goods extraction. The examples of market and non-market values of tropical moist forests, demonstrate the range of nonmarket goods and services provided by natural ecosystems. Excessive alteration and destruction of tropical forests for extraction of market goods, damages the integrity of the forests and reduces or destroys the capacity of these ecosystems to provide valuable non-market goods and services. One can measure the value of these non-market goods and services by calculating the cost of providing them through technology. By not accounting for the public goods provided by forests, overall sustained-yield potential of the public and private goods produced by the system is reduced. These non-market values need to be incorporated in decisions about the fate of natural systems. An attempt has been made in this paper to establish a common understanding of value for both economists and ecologists. If the problems of value determination can be viewed with a joint understanding, the political process may be influenced to provide more efficient and wiser use of the products and services of natural systems.
The assessment of available manganese and aluminium status in acid soils under subterranean clover pastures of various ages

Summary-Three methods of estimating available manganese and aluminium status in acid soils were compared on three groups of soils from the Pejar district near Goulburn, New South Wales in which differences in pH had been brought about by different periods under subterranean clover pasture. Managanese extracted by 0.01 M calcium chloride gave the best correlation with the manganese concentration in rape and subterranean clover grown in pot culture, and provided the best index of available manganese. Soil solution manganese was inferior to CaCI,-extractable manganese and was more difficult to determine. Extraction with neutral ammonium acetate was unsatisfactory because this reagent overestimated available forms of manganese in soils containing high levels of reactive manganese. Aluminium extracted by 0.01 M CaCI, was well correlated with exchangeable aluminium and with percentage aluminium saturation of the effective cation exchange capacity. None of the three measures of aluminium status alone was an effective index for predicting lime response by rape on these soils because both manganese and aluminium status were involved in this response. These three parameters were equally effective in multiple regressions for yield responses of rape to lime. Because of its relative ease of determination, CaCI, extraction is preferred as a practical measure of aluminium status. Aluminium interacted with and increased the toxic effects of manganese in rape. Thus CaCI,-extractable manganese alone only provided a satisfactory index of a 'critical' value for manganese toxicity in rape for soils low in available aluminium. Subterranean clover was only slightly affected by aluminium and manganese levels in these soils, and manganese toxicity symptoms were only observed on soils containing 50 ppm or more CaCI,-extractable manganese. Nodulation failure in pots occurred in all soils with pH below 5.2 (water) or below 4.3 in CaCI,, whereas nodulation was normal when these soils were treated with CaCO, to raise the pH to 5.8-6.0 (water). With one exception nodulation appeared adequate at field sites from which soils showing nodulation failure in the glasshouse had been collected.