The paradigm of relevance: Is it time to kill the sacred cow?

Prior to embarking on further study into the subject of relevance it is essential to consider why the concept of relevance has remained inconclusive, despite extensive research and its centrality to the discipline of information science. The approach taken in this paper is to reconstruct the science of information retrieval from first principles including the problem statement, role, scope and objective. This framework for document selection is put forward as a straw man for comparison with the historical relevance models. The paper examines five influential relevance models over the past 50 years. Each is examined with respect to its treatment of relevance and compared with the first principles model to identify contributions and deficiencies. The major conclusion drawn is that relevance is a significantly overloaded concept which is both confusing and detrimental to the science.

Cow's milk allergy and the development of tolerance

Aims: To gain insight on the immunological processes behind cow’s milk allergy (CMA) and the development of oral tolerance. To furthermore investigate the associations of HLA II and filaggrin genotypes with humoral responses to early oral antigens. Methods: The study population was from a cohort of 6209 healthy, full-term infants who in a double-blind randomized trial received supplementary feeding at maternity hospitals (mean duration 4 days): cow’s milk (CM) formula, extensively hydrolyzed whey formula or donor breast milk. Infants who developed CM associated symptoms that subsided during elimination diet (n=223) underwent an open oral CM challenge (at mean age 7 months). The challenge was negative in 112, and in 111 it confirmed CMA, which was IgE-mediated in 83. Patients with CMA were followed until recovery, and 94 of them participated in a follow-up study at age 8-9 years. We investigated serum samples at diagnosis (mean age 7 months, n=111), one year later (19 months, n=101) and at follow-up (8.6 years, n=85). At follow-up, also 76 children randomly selected from the original cohort and without CM associated symptoms were included. We measured CM specific IgE levels with UniCAP (Phadia, Uppsala, Sweden), and β-lactoglobulin, α-casein and ovalbumin specific IgA, IgG1, IgG4 and IgG levels with enzyme-linked immunosorbent assay in sera. We applied a microarray based immunoassay to measure the binding of IgE, IgG4 and IgA serum antibodies to sequential epitopes derived from five major CM proteins at the three time points in 11 patients with active IgE-mediated CMA at age 8-9 years and in 12 patients who had recovered from IgE-mediated CMA by age 3 years. We used bioinformatic methods to analyze the microarray data. We studied T cell expression profile in peripheral blood mononuclear cell (PBMC) samples from 57 children aged 5-12 years (median 8.3): 16 with active CMA, 20 who had recovered from CMA by age 3 years, 21 non-atopic control subjects. Following in vitro β-lactoglobulin stimulation, we measured the mRNA expression in PBMCs of 12 T-cell markers (T-bet, GATA-3, IFN-γ, CTLA4, IL-10, IL-16, TGF-β, FOXP3, Nfat-C2, TIM3, TIM4, STIM-1) with quantitative real time polymerase chain reaction, and the protein expression of CD4, CD25, CD127, FoxP3 with flow cytometry. To optimally distinguish the three study groups, we performed artificial neural networks with exhaustive search for all marker combinations. For genetic associations with specific humoral responses, we analyzed 14 HLA class II haplotypes, the PTPN22 1858 SNP (R620W allele) and 5 known filaggrin null mutations from blood samples of 87 patients with CMA and 76 control subjects (age 8.0-9.3 years). Results: High IgG and IgG4 levels to β-lactoglobulin and α-casein were associated with the HLA (DR15)-DQB1*0602 haplotype in patients with CMA, but not in control subjects. Conversely, (DR1/10)-DQB1*0501 was associated with lower IgG and IgG4 levels to these CM antigens, and to ovalbumin, most significantly among control subjects. Infants with IgE-mediated CMA had lower β -lactoglobulin and α-casein specific IgG1, IgG4 and IgG levels (p<0.05) at diagnosis than infants with non-IgE-mediated CMA or control subjects. When CMA persisted beyond age 8 years, CM specific IgE levels were higher at all three time points investigated and IgE epitope binding pattern remained stable (p<0.001) compared with recovery from CMA by age 3 years. Patients with persisting CMA at 8-9 years had lower serum IgA levels to β-lactoglobulin at diagnosis (p=0.01), and lower IgG4 levels to β-lactoglobulin (p=0.04) and α-casein (p=0.05) at follow-up compared with patients who recovered by age 3 years. In early recovery, signal of IgG4 epitope binding increased while that of IgE decreased over time, and binding patterns of IgE and IgG4 overlapped. In T cell expression profile in response to β –lactoglobulin, the combination of markers FoxP3, Nfat-C2, IL-16, GATA-3 distinguished patients with persisting CMA most accurately from patients who had become tolerant and from non-atopic subjects. FoxP3 expression at both RNA and protein level was higher in children with CMA compared with non-atopic children. Conclusions: Genetic factors (the HLA II genotype) are associated with humoral responses to early food allergens. High CM specific IgE levels predict persistence of CMA. Development of tolerance is associated with higher specific IgA and IgG4 levels and lower specific IgE levels, with decreased CM epitope binding by IgE and concurrent increase in corresponding epitope binding by IgG4. Both Th2 and Treg pathways are activated upon CM antigen stimulation in patients with CMA. In the clinical management of CMA, HLA II or filaggrin genotyping are not applicable, whereas the measurement of CM specific antibodies may assist in estimating the prognosis.

Defoliation and patchy nutrient return drive grazing effects on plant and soil properties in a dairy cow pasture

Large herbivores can influence plant and soil properties in grassland ecosystems, but especially for belowground biota and processes, the mechanisms that explain these effects are not fully understood. Here, we examine the capability of three grazing mechanisms-plant defoliation, dung and urine return, and physical presence of animals (causing trampling and excreta return in patches)-to explain grazing effects in Phleum pratense-Festuca pratensis dairy cow pasture in Finland. Comparison of control plots and plots grazed by cows showed that grazing maintained original plant-community structure, decreased shoot mass and root N and P concentrations, increased shoot N and P concentrations, and had an inconsistent effect on root mass. Among soil fauna, grazing increased the abundance of fungivorous nematodes and Aporrectodea earthworms and decreased the abundance of detritivorous enchytraeids and Lumbricus earthworms. Grazing also increased soil density and pH but did not affect average soil inorganic-N concentration. To reveal the mechanisms behind these effects, we analyzed results from mowed plots and plots that were both mowed and treated with a dung and urine mixture. This comparison revealed that grazing effects on plant attributes were almost entirely explained by defoliation, with only one partly explained by excreta return. Among belowground attributes, however, the mechanisms were more mixed, with effects explained by defoliation, patchy excreta return, and cow trampling. Average soil inorganic-N concentration was not affected by grazing because it was simultaneously decreased by defoliation and increased by cow presence. Presence of cows created great spatial heterogeneity in soil N availability and abundance of fungivorous nematodes. A greenhouse trial revealed a grazing-induced soil feedback on plant growth, which was explained by patchiness in N availability rather than changes in soil biota. Our results show that grazing effects on plant attributes can be satisfactorily predicted using the effects of defoliation, whereas those on soil fauna and soil N availability need understanding of other mechanisms as well. The results indicate that defoliation-induced changes in plant ecophysiology and the great spatial variation in N availability created by grazers are the two key mechanisms through which large herbivores can control grassland ecosystems.

The effects of stall surfaces and milk yield on the lying behavior of dairy cow

The importance of lying behavior to dairy cows and the feasible definition of lying has attracted many studies on the subject. Cattle show both behavioral and physiological stress responses when subjected to thwarting of their lying behavior. If cows are unable to lie down they later compensate for lost lying time when possible. Environmental factors such as housing and bedding systems have been noted to affect the time spent lying, but there is usually large variation in lying time between individuals. Internal factors such as the reproductive stage, age and health of cows affect their lying time and can cause variation. However, the effect of higher milk production on behavior has not previously been illuminated. The objective of this study was to provide data applicable for the improvement of resting conditions of cows. The preference of stall surface material, differences in normal behavior per unit time and various health measures were observed. The aim was to evaluate lying behavior and cow comfort on different stall bedding materials. In addition, the effect of milk yield on behavior was examined in a tie stall experiment. The preferences for surface materials were investigated in 5 experiments using 3 surface materials with bedding manipulations. According to the results, the cows preferred abundant straw bedding and soft rubber mats. However, they showed an aversion to sand bedding. Some individuals even refused to use stalls with sand when no organic bedding material was present. However, this study was unable to determine the reason for the avoidance, as neither the sand particle size nor thermal properties appeared critical. However, previous exposure to particular surface materials increased the preference for them. The amount of straw bedding was found to be an important factor affecting the preferences for stalls, and the lying time in stalls increased when the flooring softness was improved by applying straw or by installing elastic mats. Despite sand being the least preferred flooring material in preference tests, the health of legs improved during exposure to sand-floored stalls. Moreover cows using sand were cleaner than those that used straw stalls. Thus, sand bedding entailed some health benefits despite the contradictory results of preference tests, which more strongly reflected the perceptions of individual animals. Milk yield was observed to affect behavior by reducing the lying time, possibly due to factors other than longer duration of eating. High yielding cows seemed to intensify their lying bouts, as they were observed to lie with the neck muscles relaxed sooner after lying down than lower yielding cows. In conclusion, cows were found to prefer softer stall surface materials and organic bedding material. In addition, the lying time was reduced by a high milk yield, although the lying time seemed to be important for resting. Cows might differ in the needs for their lying environment. The management of dairy cows should eliminate any unnecessary prevention of lying, as even in tie-stalls high yielding cows seem to be affected by time constraints. Adding fresh bedding material to stalls increases the comfort of any stall flooring material.

Dietary aspects of cow's milk allergy in young children

Cow s milk allergy (CMA) affects about 2-6% of infants and young children. Environmental factors during early life are suggested to play a role in the development of allergic diseases. One of these factors is likely to be maternal diet during pregnancy and lactation. The association between maternal diet and development of CMA in offspring is not well known, but diet could contain factors that facilitate development of tolerance. After an established food allergy, another issue is gaining tolerance towards an antigen that causes symptoms. The strictness of the elimination depends on the individual level of tolerance. This study aimed at validating a questionnaire used to inquire about food allergies in children, at researching associations between maternal diet during pregnancy and lactation and subsequent development of cow s milk allergy in the offspring, and at evaluating the degree of adherence to a therapeutic elimination diet of children with CMA and factors associated with the adherence and age of recovery. These research questions were addressed in a prospective birth cohort born between 1997 and 2004 at the Tampere and Oulu University Hospitals. Altogether 6753 children of the Diabetes Prediction and Prevention (DIPP) Nutrition cohort were investigated. Questionnaires regarding allergic diseases are often used in studies without validation. High-quality valid tools are therefore needed. Two validation studies were conducted here: one by comparing parentally reported food allergies with information gathered from patient records of 1122 children, and the other one by comparing parentally reported CMA with information in the reimbursement records of special infant formulae in the registers of the Social Insurance Institution for 6753 children. Both of these studies showed that the questionnaire works well and is a valid tool for measuring food allergies in children. In the first validation study, Cohen s kappa values were within 0.71-0.88 for CMA, 0.74-0.82 for cereal allergy, and 0.66-0.86 for any reported food allergy. In the second validation study, the kappa value was 0.79, sensitivity 0.958, and specificity 0.965 for reported and diagnosed CMA. To investigate the associations between maternal diet during pregnancy and lactation and CMA in offspring, 6288 children were studied. Maternal diet during pregnancy (8th month) and lactation (3rd month) was assessed by a validated, 181-item semi-quantitative food frequency questionnaire (FFQ), and as an endpoint register-based information on diagnosed CMA was obtained from the Social Insurance Institution and complemented with parental reports of CMA in their children. The associations between maternal food consumption and CMA in offspring were analyzed by logistic regression comparing the highest and lowest quarters with two middle quarters of consumption and adjusted for several potential confounding factors. High maternal intake of milk products (OR 0.56, 95% CI 0.37-0.86 p = 0.002) was associated with a lower risk of CMA in offspring. When stratified according to maternal allergic rhinitis or asthma, a protective association of high use of milk products with CMA was seen in children of allergy-free mothers (OR 0.30, 95% CI 0.13 - 0.69, p < 0.001), but not in children of allergic mothers. Moreover, low maternal consumption of fish during pregnancy was associated with a higher risk of CMA in children of mothers with allergic rhinitis or asthma (OR 1.47, 95% CI 0.96 - 2.27 for the lowest quarter, p = 0.043). In children of nonallergic mothers, this association was not seen. Maternal diet during lactation was not associated with CMA in offspring, apart from an inverse association between citrus and kiwi fruit consumption and CMA. These results imply that maternal diet during pregnancy may contain factors protective against CMA in offspring, more so than maternal diet during lactation. These results need to be confirmed in other studies before giving recommendations to the public. To evaluate the degree of adherence to a therapeutic elimination diet in children with diagnosed CMA, food records of 267 children were studied. Subsequent food records were examined to assess the age at reintroduction of milk products to the child s diet. Nine of ten families adhered to the elimination diet of the child with extreme accuracy. Older and monosensitized children had more often small amounts of cow s milk protein in their diet (p < 0.001 for both). Adherence to the diet was not related to any other sociodemographic factor studied or to the age at reintroduction of milk products to the diet. Low intakes of vitamin D, calcium, and riboflavin are of concern in children following a cow s milk-free diet. In summary, we found that the questionnaires used in the DIPP study are valid in investigating CMA in young children; that there are associations between maternal diet during pregnancy and lactation and the development of CMA in offspring; and that the therapeutic elimination diet in children with diagnosed CMA is rigorously adhered to.

Gene Expression Profiling of Preovulatory Follicle in the Buffalo Cow: Effects of Increased IGF-I Concentration on Periovulatory Events

The preovulatory follicle in response to gonadotropin surge undergoes dramatic biochemical, and morphological changes orchestrated by expression changes in hundreds of genes. Employing well characterized bovine preovulatory follicle model, granulosa cells (GCs) and follicle wall were collected from the preovulatory follicle before, 1, 10 and 22 h post peak LH surge. Microarray analysis performed on GCs revealed that 450 and 111 genes were differentially expressed at 1 and 22 h post peak LH surge, respectively. For validation, qPCR and immunocytochemistry analyses were carried out for some of the differentially expressed genes. Expression analysis of many of these genes showed distinct expression patterns in GCs and the follicle wall. To study molecular functions and genetic networks, microarray data was analyzed using Ingenuity Pathway Analysis which revealed majority of the differentially expressed genes to cluster within processes like steroidogenesis, cell survival and cell differentiation. In the ovarian follicle, IGF-I is established to be an important regulator of the above mentioned molecular functions. Thus, further experiments were conducted to verify the effects of increased intrafollicular IGF-I levels on the expression of genes associated with the above mentioned processes. For this purpose, buffalo cows were administered with exogenous bGH to transiently increase circulating and intrafollicular concentrations of IGF-I. The results indicated that increased intrafollicular concentrations of IGF-I caused changes in expression of genes associated with steroidogenesis (StAR, SRF) and apoptosis (BCL-2, FKHR, PAWR). These results taken together suggest that onset of gonadotropin surge triggers activation of various biological pathways and that the effects of growth factors and peptides on gonadotropin actions could be examined during preovulatory follicle development.

Analysis of 20alpha-hydroxysteroid dehydrogenase expression in the corpus luteum of the buffalo cow: effect of prostaglandin F2-alpha treatment on circulating 20alpha-hydroxyprogesterone levels

Background: During female reproductive cycles, a rapid fall in circulating progesterone (P4) levels is one of the earliest events that occur during induced luteolysis in mammals. In rodents, it is well recognized that during luteolysis, P4 is catabolized to its inactive metabolite, 20alpha-hydroxyprogesterone (20alpha-OHP) by the action of 20alpha-hydroxysteroid dehydrogenase (20alpha-HSD) enzyme and involves transcription factor, Nur77. Studies have been carried out to examine expression of 20alpha-HSD and its activity in the corpus luteum (CL) of buffalo cow. Methods: The expression of 20alpha-HSD across different bovine tissues along with CL was examined by qPCR analysis. Circulating P4 levels were monitored before and during PGF2alpha treatment. Expression of 20alpha-HSD and Nur77 mRNA was determined in CL at different time points post PGF2alpha treatment in buffalo cows. The chromatographic separation of P4 and its metabolite, 20alpha-OHP, in rat and buffalo cow serum samples were performed on reverse phase HPLC system. To further support the findings, 20alpha-HSD enzyme activity was quantitated in cytosolic fraction of CL of both rat and buffalo cow. Results: Circulating P4 concentration declined rapidly in response to PGF2alpha treatment. HPLC analysis of serum samples did not reveal changes in circulating 20alpha-OHP levels in buffalo cows but serum from pseudo pregnant rats receiving PGF2alpha treatment showed an increased 20alpha-OHP level at 24 h post treatment with accompanying decrease in P4 concentration. qPCR expression of 20alpha-HSD in CL from control and PGF2alpha-treated buffalo cows showed higher expression at 3 and 18 h post treatment, but its specific activity was not altered at different time points post PGF2alpha treatment. The Nur77 expression increased several fold 3 h post PGF2alpha treatment similar to the increased expression observed in the PGF2alpha-treated pseudo pregnant rats which perhaps suggest initiation of activation of apoptotic pathways in response to PGF2alpha treatment. Conclusions: The results taken together suggest that synthesis of P4 appears to be primarily affected by PGF2alpha treatment in buffalo cows in contrast to increased metabolism of P4 in rodents.

Assessment of phytostabilization of Pb/Zn mine soils with organic amendments and a native metallicolous ecotype of Festuca Rubra l.: implications for amendment selection and recovery of soil health

La contaminación del suelo es una de las principales amenazas para los ecosistemas y la salud humana. Actualmente, desde un punto de vista tanto económico como ambiental, la fitoestabilización es la mejor tecnología para remediar suelos contaminados con elevadas concentraciones de metales como son los suelos mineros. La fitoestabilización asistida consiste en el empleo de plantas y enmiendas orgánicas y/o inorgánicas con el fin de reducir la movilidad y la biodisponibilidad de los contaminantes y recuperar la salud de suelo. En este trabajo se han realizado ensayos en microcosmos y en campo centrándonos en la salud del suelo minero contaminado con Pb y Zn durante un proceso de fitoestabilización empleando enmiendas orgánicas (purines vacunos, gallinaza, estiércol de oveja y lodos de papelera mezclados con gallinaza) y/o la especie metalífera Festuca rubra con el objetivo de (i) estudiar las interacciones suelo-enmienda responsables de los cambios inducidos por el proceso de quimioestabilización en las propiedades físicoquímicas y biológicas del suelo, (ii) evaluar la efectividad del proceso de fitoestabilización sobre suelos vegetados y de la revegetación sobre suelos desnudos (iii) valorar la idoneidad de distintos indicadores químicos y biológicos (parámetros microbianos y de la vegetación) para monitorizar la efectividad de la fitoestabilización asistida en términos de reducción de la biodisponibilidad de metales en el suelo, mejora de la vegetación y de la recuperación de la salud del suelo. La aplicación de enmiendas al suelo minero supone una entrada de materia orgánica y nutrientes que conduce a una disminución de la biodisponibilidad de metales, facilitando la colonización de las plantas y el crecimiento de la vegetación nativa, además de estimular la actividad microbiana del suelo. El pH del suelo es un factor crítico que condiciona la movilidad de los metales y la toxicidad del suelo. Las poblaciones microbianas de las enmiendas no modificaron la diversidad funcional de las comunidades microbianas nativas de la mina. Los purines vacunos y los lodos de papelera mezclados con gallinaza son los tratamientos más efectivos en el proceso de fitoestabilización asistida bajo condiciones de campo. La gallinaza fue el tratamiento que más estimuló el crecimiento de la vegetación nativa y la colonización en los suelos desnudos. El bioensayo de elongación radical de lechuga es un test sensible, sencillo y barato para evaluar la biodisponibilidad de metal y la ecotoxicidad del suelo. Los tocoferoles son biomarcadores de exposición a metales con potencial para su implementación en bioensayos de toxicidad. Este trabajo permite concluir que la población metalífera de F. rubra, combinada con enmiendas orgánicas, es una excelente candidata para los proyectos de fitoestabilización asistida. Además, la monitorización simultánea de los parámetros fisicoquímicos y microbiológicos del suelo y de su ecotoxicidad permite una evaluación adecuada de la salud del suelo, así como la selección de enmiendas apropiadas para el desarrollo de un proceso fitoestabilizador.

Effects of fish-meal, cow blood-meal, and sorghum diets on food utilization and growth of cage cultured Sarotherodon niloticus

The growth responses and feed utilization of Sarotherodon niloticus held in metal cages in a pond and fed diets containing fish-meal, cow blood-meal or sorghum was studied. Results indicate that the best growth, feed conversion and protein efficiency ratio were obtained with the diet containing 60% fish-meal. The growth performance of fish on 40% fish-meal, and 40% and 60% blood meal were not significantly different, and were quite close to the performance with 60% fish-meal. The growth and food utilization of fish on 84% sorghum diet was significantly lower than the rest. The Caged fish without supplemental feeding had a light gain in weight. All fish with supplemental feeding appeared healthy. It is concluded that cow blood meal at 40% or 60% inclusion in diet can adequately replace fish-meal in S. niloticus supplemental diet in pond culture

Study on the biomass yield of Duckweed (Lemna minor) (L.) in hydroponic cultures containing different concentrations of aquaeous extract of chicken manure

The biomass yields of duck week (Lemna minor(L) was monitored in hydroponic media prepared by variously extracting 0.50, 1.00 and 2.00g of dried chicken manure per liter of city water (tap water) supply. The culture media consisting of aqueous extract of the various manure treatments were made up to 12 liters in all cases with tap water as control. Plastic baths of 25 liters capacity with 0.71 super(m2) surface area were used as culture facility. Each bath was stocked at a density of 30g super(m-2) with fresh weed samples (i.e 21.30g/bath). Maximum yields were obtained at all treatment levels and control on day 3 and based on the highest yield of 0.37gm super(-2)d super(-1) (dry matter) obtained at 1.00gL manure treatment which was however not significantly higher (P>0.05) than the 0.36gm super(-2)d super(-1) (dry matter) at 0.05gl super(-1) media manure content, an average manure level of 0.75l super(-1) was selected and used to determine the operational plant density. Thus fresh weights of 30 to 300gm super(-2) was grown in triplicate at 30g intervals for a period of 3 days. A regression equation of Y=2.6720+0.0021x with a corresponding maximum density or operational plant density of 266gm super(-2) and yield of 0.98gm super(-2), d super(-1) (dry matter) were obtained. Further growth trials were carried out at the operational density and manure levels of 0.50, 0.75, 1.00, 1.25, 1.50, 1.75 and 2.00gl super(-1) media manure concentration giving a significantly higher yield (P<0.05) of 17gm super(-2), d super(-1) (dry matter). This yield was however doubled to between 2.21 and 2.24gm super(-2) d super(-1) (equivalent to 7.96 to 8.06mt.ha-1, Yr-1 dry matter on extrapolation) if 25% and 75% respectively of the total weed cover were harvested daily within the experimental period. The role of some dissolved plant nutrients (DPN) were also discussed

Some potential occupational and environmental hazards associated with fish pond production in Nigeria

The paper highlights the concept of information and the significance of environmental and occupational hazards associated with pond fish production in Nigeria and discuss the possible options for the ways forward. The major raw material used in fish production system is the organic manure (cow dung, poultry droppings, porcine manure etc) that serves as substrate for heterotrophic production of bacteria and protozoa, which act as food for zooplankton and the fish. The pathogenic organisms (viruses, bacteria, protozoa's, and parasites), are noted for the potential hazard to the fish handlers and consumers. Nine species from seven genera of bacteria associated with fish diseases are found to have association with diseases of human such as typhoid fever, bacillary dysentery and other gastrointestinal tract related problems. Also the environmental contaminants in pond fish production become important because of its significance to consumers' acceptance of the fish products