Miracle-dz/UniFAR-FTUs huggingface dataset:
The nature and mechanisms of human gene mutation

There are a variety of different types of mutations in the human genome and many diverse mechanisms for their generation. Single-base-pair substitutions account for the majority of gene defects. Among them, the hypermutability of CpG dinucleotides represents the most important and frequent cause of mutation in humans. Point mutations may affect transcription and translation, as well as mRNA splicing and processing. Mutations in regulatory elements are of particular significance, since they often reveal the existence of DNA domains that are bound by regulatory proteins. Similarly, mutations that affect mRNA splicing can contribute to our understanding of the splicing mechanism. We describe mechanisms of gene deletion and the DNA sequences that may predispose to such lesions, as well as potential mechanisms underlying insertions, duplications, or inversions, with representative examples. Retrotransposition is a rare but biologically fascinating phenomenon that can lead to abnormal phenotypes if the double-stranded DNA is inserted in functionally important regions of a gene. Long interspersed repeat elements (LINEs) and Alu repetitive elements and pseudogenes have been shown to function as retrotransposons, and their de novo insertion in the genome can produce disease. The expansion of trinucleotide repeats represents a relatively novel category of mutations in humans. There is a growing list of disorders that result from an abnormal copy number of trinucleotides within the 5′ or 3′ untranslated regions, coding sequences, and introns of genes. The pathophysiologic effects of the expansion of the trinucleotide repeat are unknown. Additionally, at least one disorder is caused by expansion of a 12mer repeat (progressive myoclonus epilepsy). The study of mutations in human genes is of paramount importance in understanding the pathophysiology of hereditary disorders, in providing improved diagnostic tests, and in designing appropriate therapeutic approaches.
Low protein diets for broilers

A review of the literature regarding Low Protein diets (LCP) for broilers reveals that by using crystalline amino acids, dietary CP could be reduced in each phase safely by a factor of 10% (a figure fairly consistent with turkeys but quite low with that found for ducks and swine) from the respective NRC (1994) levels; the calculated minimum dietary CP levels thus appeared to be 20.7, 18.0, and 16.2% respectively for 0–21, 21–42 and 42–56 days of age. It is, however, noted that the magnitude of protein reduction, without affecting the growth performance of broilers, could have been increased depending upon the EAA concentration and balance of LCP vs. control-CP diets as well as the response criteria used (gain vs. composition of gain). Further reduction in dietary protein results in depressed live/carcass yield in almost all cases. Depressed feed intake appears partially to explain the negative effect of LCP diets in some cases. Addition of NEAA-like glycine above the current NRC recommendations has shown partially to alleviate the negative effect of LCP diets indicating imprecision of our knowledge about NEAA (like glycine, serine and proline etc) requirements of broilers under these conditions. The dietary NEAA/EAA ratio seems to be an important, though poorly understood, factor in defining the performance of broilers fed on LCP diets. It seems that regardless of the absolute amounts of dietary amino acids, performance tend to be depressed when NEAA/EAA ratio is decreased from 50/50; thus the NEAA level of about 50% of protein seems “minimum” state of adequacy. More work is needed before a precise role of the ratio of nitrogen coming from NEAA vs. EAA is proposed. A wider NE:ME in LCP diets seems to explain the higher body fat accretion on these diets; more work on how dietary NE:ME ratio modulates the growth performance of broilers, and how it interacts with different genetic stocks (lean vs. fat lines) is warranted.
Viral aetiology of diarrhoea in puppies from a same shelter in Turkey : presence of mixed infections

SUMMARY This study was conducted to evaluate the prevalence of viral agents that cause enteritis in puppies. Prevalences of canine distemper virus (CDV), canine parvovirus (CPV) and canine rotavirus (CRV) were established using RT-PCR, PCR and polyacrylamide gel electrophoresis (PAGE) techniques respectively, in faecal samples from 1 to 2-month-old diarrheic puppies (n = 34) stemming from a same shelter. Twenty-nine samples (85.3%) were found positive for at least one enteritis virus: the prevalences of CDV and CPV infections were 44.1% and 76.5% respectively while no CRV was evidenced in any sample tested. On the other hand, 12 samples (35.3%) were positive for both CDV and CPV infections. These results demonstrate that the prevalence of viral infections in diarrheic puppies is strong and also that CDV and CPV infections, which may be simultaneously present with a high rate, should not be under-estimated particularly in shelters with a high animal population.
Stereotype Threat in a Video Game Context and Its Influence on Perceptions of Science, Technology, Engineering, and Mathematics (STEM): Avatar-Induced Active Self-Concept as a Possible Mitigator

The connection between video games and science, technology, engineering, and mathematics (STEM) fields has become a key focus for education and game scholars alike. While games may have the power to bring more students toward STEM fields, gender stereotypes about gaming ability may hinder this potential. To examine this issue, two studies were conducted to investigate whether stereotype threat induced in a gaming context would affect players’ game performance and their perceptions of STEM fields. The first study found that priming gender stereotypes influenced female participants’ video game performance as well as interest in and perceptions of STEM fields. A second study investigated this relationship through the use of both overtly gendered and nongendered forms of stereotype threat as well as avatar-induced identity salience. Interaction effects found between implicit/explicit stereotype threat and identity salience suggest a relationship between forms of stereotype threat and active self-concept.
Callus Induction and Plant Regeneration from Mature Embryos of Glutinous Rice (Oryza sativa L.) Cultivar TDK1

The present study was conducted to determine the optimum in vitro conditions for callus induction and plant regeneration from mature embryos (seeds) of glutinous rice cultivar TDK 1. It was revealed that embryos cultured on Murashige and Skoog (MS) agar medium supplemented with 2 mg/l 2,4-D and 500 mg/l L-proline under light condition produced the highest percentage of callus formation (96.91 %). The average size of callus produced was large (6.02 mm). The calli dehydrated by placing in petridishes with covers for 7 days under light condition before transferring onto regeneration medium generated higher frequency of shoot regeneration than the calli cultured on regeneration medium without dehydration. The most suitable medium for plant regeneration from dehydrated calli was MS agar medium supplemented with 1 mg/l IAA, 4 mg/l BA and 800 mg/l casein hydrolysate which induced the highest percentage of calli forming shoots (45.00 %) and each callus produced the largest number of shoots (average 15 shoots). The shoots were rooted at the highest rate (100 %) when transferred onto MS agar medium supplemented with 1 mg/l NAA. The complete plantlets were thereafter transplanted to grow under greenhouse condition. They were morphologically normal and fertile.
IMMUNOPATHOLOGICAL EFFECT OF LEAD ACETATE ON HUMORAL AND CELL MEDIATED IMMUNE RESPONSES IN BROILERS

Lead acetate was given to group II and III broiler birds at dose level of 250 and 400 ppm from 2nd to 6th week while group I was served as control. Both humoral and cell mediated immune responses were evaluated in each group at the end of 6th week. Humoral immune responses were evaluated on the basis of HI titers against New Castle Disease viral antigen by beta procedure utilizing 4HA unit of LaSota strain. Cell mediated immune responses were evaluated using 2, 4, Dinitrochlorobenzene (DNCB) by skin hypersensitivity test in acetone vehicle. Six birds from each group were sacrificed at the end of 6th week and organ weights of bursa and thymus were recorded. Average log values of HI titers in group I were significantly higher than group II and III birds. Skin thickness (mm) and diameter area (cm) were found to be maximum at 24 hours post challenge in control and both treatment groups but differences between control and treatment group birds at 24 and 48 hours were found to be statistically significant. Both treatment group birds revealed significant decrease in bursa and thymus weights in dose dependent manner when compared with control group. Histopathological investigation of bursa and thymus in both treatment group birds revealed small size follicles with depletion of lymphoid population.
Effect of lead on some haematological and biochemical characteristics of Clarias gariepinus dietary supplemented with lycopene and vitamin E

The present study aimed to investigate the potential protective effects of lycopene (9 mg/kg ) in comparison with vitamin E (50 mg/kg) against the impacts of lead (Pb) toxicity(7 mg/l: 1/4 of 96 h LC50) on fishes Pb exposed for 15 and 30 days. Pb impacts were evaluated in terms of haematological and biochemical characteristics. The activities of aspartate aminotransferase and alanine aminotransferase in serum were significantly increased due to Pb. Treatment with Pb caused a significant increase in mean corpuscular haemoglobin concentration, serum glucose, total lipid,urea and creatinine and Lipid peroxidation in liver,kidney and gills tissues. On the other hand, Pb significantly caused decline in serum total protein,albumin, blood haemoglobin, red blood cell count, haematocrit value, mean corpuscular volume and mean corpuscular haemoglobin . It was observed that supplementation of lycopene and vitamin E decreases the toxic effect of lead.
STUDIES ON THE EFFECTS OF PLANT VARIETY AND ROOT EXUDATE COMPOUNDS ON THE SOIL MICROBIAL COMMUNITY

OF DISSERTATION STUDIES ON THE EFFECTS OF PLANT VARIETY AND ROOT EXUDATE COMPOUNDS ON THE SOIL MICROBIAL COMMUNITY Plants modify the soil environment through their root system, changing its physical properties and exuding compounds that promote or inhibit the growth of certain microorganisms. Therefore the structure of the soil microbial community is different in the rhizosphere than in the bulk soil. This dissertation introduces three research projects that investigated the effects of specific root exudate compounds on the soil microbial community structure, and plant cultivar specific differences in the rhizosphere microbiota. The progenitor of maize is Balsas teosinte (Zea mays subsp. parviglumis). In a greenhouse experiment we compared the structure and function of its bacterial and fungal rhizosphere community with that of domesticated corn cultivars sweet corn and popping corn by terminal restriction fragment length polymorphism, fatty acid methyl ester analysis, and soil enzyme assays. The results allude to functional and structural differences in the rhizosphere microbial communities of the corn varieties that could lead to useful discoveries on how corn domestication has altered rhizosphere processes. To study how root exudate flavonoids 7,4′-dihydroxyflavone and naringenin influence the soil bacterial community structure we constructed model systems to approximate the flavonoid exudation of Medicago sativa roots. Soil samples from the model systems were subjected to ATP assays and 16S rRNA gene amplicon sequencing. Our results suggest that 7,4′-dihydroxyflavone can interact with a diverse range of soil bacteria, including members of Acidobacteria subdivision 4, Gaiellales, Nocardioidaceae, and Thermomonosporaceae and may have other functions in the rhizosphere in addition to nod-gene induction in the legume–rhizobia symbiosis. Hydroxyproline is the most common amino acid in plant cell wall proteins and serves as an important carbon and nitrogen source for soil bacteria. We treated soil with the L or the D enantiomer of hydroxyproline and collected samples for 16S rRNA gene amplicon sequencing three and seven days after the treatment. The Land D-hydroxyproline treatments induced very similar responses in the bacterial community structure, but there were several differentially abundant groups. Our results inform about the role of hydroxyproline in shaping the soil microbial community in the rhizosphere and about the catabolism of its enantiomers in the soil.
Effect of mowing on perennial sedges

Abstract Field studies were conducted in 1996 and 1997 to determine the response of Cyperus rotundus and Cyperus esculentus, Kyllinga brevifolia, and Kyllinga gracillima to mowing regimens common to recreational turfgrass. Treatments were selected to simulate Cynodon dactylon golf course management and included mowing at 1.3 and 3.8 cm with mowing frequencies of three times per week and once a week, respectively. A nonmowed check was included for comparison. Reductions in C. rotundus shoot number were observed beginning 6 wk after initial treatment (WAIT) in 1996 and 9 WAIT in 1997 for the 1.3-cm mowing regime. The 3.8-cm mowing regime did not reduce C. rotundus shoot number until the final evaluation of each year. Reductions in C. rotundus rhizome length, tuber number, and tuber size were observed for both mowing regimes in both years. Cyperus esculentus shoot number was reduced by the 1.3-cm treatment at each evaluation date in 1996 and 1997. Cyperus esculentus shoot number reductions in the 3.8-cm regime were first observed 4 and 6 WAIT in the 2 yr and continued until termination. The 1.3-cm regime reduced C. esculentus spread beginning 6 WAIT in 1996 and 3 WAIT in 1997. Cyperus esculentus spread was also reduced by the 3.8-cm treatment, but reduction began at later evaluations (8 and 9 WAIT). Tuber production by C. esculentus was completely inhibited by the two mowing regimes in both years. The only treatment effect observed in K. brevifolia and K. gracillima in 1996 was a reduction in internode length of K. gracillima by the 1.3-cm mowing regime. In 1997, the 1.3-cm regime reduced K. brevifolia shoot number at 15 and 18 WAIT and plant spread beginning 6 WAIT and continuing until termination. The 3.8-cm treatment did not affect K. brevifolia shoot number and reductions in spread were only observed at the final evaluation. Kyllinga gracillima shoot number and plant spread were reduced by the 1.3-cm mowing regime at each 1997 evaluation. Reductions in K. gracillima shoot number occurred at the final evaluation, and reductions in spread began 12 WAIT when subjected to the 3.8-cm treatment. Both mowing regimes reduced K. brevifolia and K. gracillima internode length. Kyllinga brevifolia total rhizome length and total node number were reduced by the 1.3-cm regime only. Kyllinga gracillima rhizome length, internode length, and node number were reduced by both regimes in 1997. Nomenclature:Cynodon dactylon (L.) Pers. , bermudagrass; Cyperus rotundus L. CYPRO, purple nutsedge; Cyperus esculentus L. CYPES, yellow nutsedge; Kyllinga brevifolia Rottb. KYLBR, green kyllinga; Kyllinga gracillima Miq. KYLGR, false green kyllinga.
Statistical interrelation of length, growth, and scale circulus spacing: appraisal of a growth rate estimator for fish

Biological and statistical properties of spacing of the marginal circuli of scales (CIRC) were examined in an experimental population of tilapia (Oreochromis mossambicus/hornorum) hybrids. Biological, or "causal," interrelationships of body length, growth, and CIRC were analysed by maximum likelihood solution of a simultaneous equation model involving the three variables. Spacing varies directly with growth rate and inversely with fish length, and growth varies inversely with length. Consequently, spacing is relatively constant along the radial axis of the scale except where variation in ration level or other factors varies the rate of growth as a function of length. The correlation of CIRC with current growth rate in populations of mixed parentage, sizes, and ages is sufficiently high (r = 0.65–0.71) to render it a useful growth estimator in aquaculture and natural situations where ages are unknown and sequential size measurements are difficult to obtain. Statistical and procedural conditions for maximiz.
SCREENING OF PROMISING CLONES IN EARLY CLONAL GENERATIONS FROM POOL OF SACCHARUM COMPLEX HYBRIDS

Eighty four clones including three checks in first and second consecutive clonal generations were undertaken with the objective to identify reliable yield attributing traits for formulation of selection indices and selection of suitable clones in early clonal generation. A consistent trend for the significance of mean sum of square due to checks, entries, check vs. entries, range of variation and coefficient of variation was observed in both clonal generations. Correlation coefficient study revealed that only three quantitative traits i.e., number of shoots at 120 days, number of millable cane at harvest and single cane weight showed consistent trend of significant association with cane yield in both the clonal generations. Path coefficient analysis revealed that number of millable cane at harvest and single cane weight were major direct contibutor in both clonal generations. Multiple regression analysis revealed that single cane weight act as most reliable traits in predicting performance in early clonal generations. Preliminary selection in early clonal generation should be based on quantitative traits i.e. single cane weight, number of shoots at 120 days and number of millable canes and quality traits should be delayed to latter generation till the character stabilize.
Measuring the Success of Wildlife Community Restoration

It is difficult to measure the success of wildlife community restoration when the restoration goal concerns a relatively broad geographic area, rather than a particular piece of land, since many restored sites need to be compared to many reference sites simultaneously. A review of the methods used to measure success in previous restoration efforts indicated the potential value of multimetric methods to make the comparison. We designed a new method that retains some of the advantages of multimetric methods but also removes some of the associated problems. The new method was applied to data from 30 restored sites (phosphate-mined land) and 30 reference sites in central Florida (USA), and it showed the difference in wildlife composition between restored and reference sites to be large, relative to the maximum possible difference. Alternative methods were applied to the same data. Multivariate methods were unable to measure success adequately. Percentage similarity analysis yielded results seemingly comparabl.
VARIATION IN MASS OF FEMALE PROTHONOTARY WARBLERS DURING NESTING

Abstract Over an 18-year period (1987–2004), we examined variation in body mass of female Prothonotary Warblers (Protonotaria citrea) captured throughout their nesting cycle. As is typical for many small passerine birds, body mass was greatest during egg laying and decreased throughout incubation and feeding of young. Mass decreased significantly between the onset of incubation and fledging of both first and second broods. Mass loss was gradual during incubation, noteworthy during the first 2 days of feeding nestlings, but did not continue to decrease throughout the feeding period. Mass lost while raising the first brood was regained before initiating the second brood. Mass of female warblers, adjusted for effects of nest attempt, year, clutch size, and day and stage of nesting, increased slightly with age. Body mass of nesting female warblers varied significantly with day of the nest cycle during incubation but not during egg laying or feeding of young. Mass was associated with clutch size during incubation in both first and second broods, but was not associated significantly with brood size when females were feeding nestlings. Frequency of food delivery to nestlings was associated negatively with female body mass. Females typically made more feeding trips per day than males. Feeding rates were correlated among pairs; that is, females with higher rates of delivery were mated to males that made a higher number of trips.
Wetlands and invertebrate disease hosts: are we asking for trouble?

Wetlands provide a range of benefits to society, and yet in South Africa wetlands continue to be affected by human activi ties. Considerable effort is now being directed towards rehabilitation of degraded wetlands and the construction of artificial systems to treat effluent and stormwater. At the same time, wetlands provide potential habitat for vectors or intermediate hosts (collectively referred to in this document as ‘invertebrate disease hosts’: IDHs), of parasites implicated in the transmission of such important diseases as malaria and schistosomiasis (bilharzia). The present review considers, for the 2 major IDHs (mosquitoes and schistosome-transmitting snails), the type of habitat required by the water-dependent life stage and the ways in which wetland degradation, rehabilitation and creation may affect the availability of suitable habitat. General practical measures for minimising pest species, particularly mosquitoes, are included. This review also highlights other issues that require research and testing in the South African context, including: the IDHs implicated in less well-known diseases (both of humans and animals) and the control of mosquitoes and schistosome-transmitting snails through biomanipulation. We conclude that in regions of the country where the diseases are prevalent there is the likelihood that wetland rehabilitation and creation could inadvertently encourage the IDHs responsible for transmitting malaria and schistosomiasis. Assessment of the potential risks and benefits of a proposed wetland modification needs to be undertaken in a holistic manner using an adaptive framework that recognises the critical need to balance human and environmental health. Possible ways of controlling IDHs both in an environmentally- and socio-friendly manner need to be investigated using a multidisciplinary approach engaging invertebrate biologists, health care officials, wetland scientists and also sociologists and economists.
Zooplankton assemblages in the Ohio River: seasonal, tributary, and navigation dam effects

Ohio River Zooplankton were collected monthly or quarterly for 1 yr from littoral and pelagic (main channel) areas in three navigation pools (constricted and floodplain) with four intrapool locations (lower pool and above, below, and within major tributaries). Total densities were minimal (1.64/L) when discharge and turbidities peaked (December–April) but were relatively high otherwise (21.63/L). Seasonal rises in rotifer density preceded increases in cladocerans and copepods; rotifers were nearly twice as abundant as cladocerans and copepods. Diversity (species richness) was not correlated with temperature, velocity, or turbidity. Density was positively linked with temperature and negatively correlated with river velocity and turbidity. Diversities in littoral and pelagic areas were not different, but densities were higher nearshore (mostly copepods and cladocerans); rotifers were usually more common in the main channel. Neither proximity to low-head navigation dams nor channel morphology had detectable .
A study on the Braconidae (Hymenoptera: Ichneumonoidea) from Ilam province, Iran

The family Braconidae (Hymenoptera) includes several parasitoid species with an efficient role in the biological control of pests. The fauna of these beneficial insects was studied in Ilam province of Iran. A total of 35 species from 26 genera and subgenera, and 6 subfamilies (Agathidinae, Alysiinae, Braconinae, Doryctinae, Microgastrinae, Rogadinae) were collected from different regions of Ilam province. Among these species, 2 species, Leluthia paradoxa (Picard) and Spathius maderi Fahringer are new records for the fauna of Iran.