Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil Analysis in Forensic Taphonomy : Chemical and Biological Effects of Buried Human Remains

Nature, Distribution, and Origin of Soil Materials in the Forensic Comparison of Soils, R.W. Fitzpatrick Cadaver Decomposition and Soil: Processes, D.O. Carter and M. Tibbett The Role of Soil Organisms in Terrestrial Decomposition, D.W. Hopkins Soil Fungi Associated with Graves and Latrines: Toward a Forensic Mycology, N. Sagara, Takashi, Yamanaka, and M. Tibbett The Role of Invertebrates in Terrestrial Decomposition Forensic Applications, I.R. Dadour and M.L. Harvey The Decomposition of Hair in the Buried Body Environment, A.S. Wilson The Decomposition of Materials Associated with Buried Cadavers, R.C. Janaway Decomposition Chemistry in a Burial Environment, S.L. Forbes Potential Determinants of Postmortem and Postburial Interval of Buried Remains, S.L. Forbes Principles and Methodologies of Measuring Microbial Activity and Biomass in Soil, P. Brookes Methods of Characterizing and Fingerprinting Soils for Forensic Application, L.A. Dawson, C.D. Campbell, S. Hillier, and M.J. Br ewer Index
Chemical constituents from Swartzia apetala Raddi var. glabra and evaluation of their antifungal activity against Candida spp.

From the hexanic extract of the stem from Swartzia apetala Raddi var. glabra were isolated one stilbene (1), one flavanone (2), one pterocarpan (3), one triterpene (4) and a mixture of three steroids (5 to 7). The crude extract and the compounds isolated were submitted to evaluation of the antifungal activity against nine yeast standard ATCC of the Candida genus. Among the compounds only the triterpene (4) and the mixture of steroids (5 to 7) showed no activity. The structures of the compounds were determined by spectral data analysis of GC/MS and 1H and 13C NMR (1D and 2D experiments), as well as comparison with literature values.
Biological control of vanilla anthracnose using Emericella nidulans.

Emericella nidulans was proved to be antagonistic to C lletotrichum gloeosporioides (Penz) causing anthracnose of Vanilla planifolia. Eight isolates of C. gloeosporioides were proved for pathogenecity. With this, isolate VP8 gave the high est virulence for disease incidence. E. nidulans was isolated from fallen leaves of Vanilla and tes ted against mycelial growth and sporulation of C. gloeosporioides VP8 by bi-culture and crude extract methods. Bi-cu lture test showed that E. nidulans could inhibit mycelial growth and sporulation at 4 9. 4% and 75.31%, respectively. Crude extracts were extracted from E. nidulans with hexane, ethyl acetate and methanol. Methanol crude extract inhibited the myce lial growth and sporulation at the concentration of 1,000 μg/ml and the effective dose (ED50) were 2,910 μg/ml and 0.0001 μg/ml, respectively.
Genetic effects and heterosis of the fibre colour and quality of brown cotton (Gossypium hirsutum)

With 1 figure and 8 tables Abstract The genetic effects and heterosis of the colour and quality of brown fibres were analysed in this paper through the complete 5 × 5 diallel crossing among two brown cotton cultivars and three white cotton cultivars in upland cotton (Gossypium hirsutum). Parents and F1 were arranged in a randomized block design in three locations. The results showed that the inheritability for all the traits has exceeded 50%, with significant dominance effect at the 0.01 level. The additive effect of fibre colour, lint percentage, elongation and strength was also significant at the 0.01 level, reaching 85.6%, 29.7%, 16.1% and 19.1%, respectively. The ratio of residual variance of lint percentage and fibre qualities was 29.5 – 45.9%, that of colour was only 1.1%. Fibre colour had significant negative correlation with lint percentage, fibre length, uniformity, elongation and strength. The mid-parent heterosis of fibre colour was negative, which was −0.7%; those of lint percentage, fibre length, uniformity and strength were 3.5%, 4.2%, 1.7% and 2.6%, respectively, reaching the significant level. The simple correlation coefficient between heterosis of fibre length and strength and SSR genetic distance was 0.718 and 0.724, respectively, with a significant level. For the heterosis utilizing, the fibre quality of F1 could be predicted via the mean value of the fibre qualities of parents or the SSR genetic difference among varieties (lines). Selection among the early hybrid generations was suggested. Regional planning could be applied to improve lint percentage and fibre qualities by taking advantage of environmental variation.
The identities of the Colombian frogs confused with Eleutherodactylus latidiscus (Boulenger) (Amphibia: Anura: Leptodactylidae)

Eleutherodactylus latidiscus (Boulenger) is a lowland species found in western Ecuador and southwestern Colombia; the species is replaced geographically (to the north) by E. cruentus (W. Peters). Eleutherodactylus latidiscus is assigned to the E. cruentus species group. The records attributed to E. latidiscus in Andean Colombia apply to other species (mostly E. supernatis Lynch and E. permixtus sp. nov.). Eleutherodacty/us tamsilli Cochran and Goin is not a geographic race of E. latidiscus and is redescribed. Eleutherodacty/us permixtus, E. supernatis, and E. tamsilli are not each other's nearest relatives but are assigned to the E. devillei species group. At moderate and intermediate elevations on the western flanks of the Cordillera Occidental of Colombia and Ecuador, one finds a series of long-legged species (E. crenunguis Lynch, E. ocellatus Lynch and Burrowes, E. labiosus sp. nov., and E. orpacobates sp. nov.) allied to E. rubicundus (Jimenez de Ia Espada), a species found on the cis-Andean slopes of Ecuador. The Central American representative of this group is E. cerasinus (Cope). This series of six species is termed the E. cerasinus species group.
A bioinformatics meta-analysis of differentially expressed genes in colorectal cancer

BACKGROUND: Elucidation of candidate colorectal cancer biomarkers often begins by comparing the expression profiles of cancerous and normal tissue by performing high throughput gene expression profiling. While many such studies have been performed, the resulting lists of differentially expressed genes tend to be inconsistent with each other, suggesting that there are some false positives and negatives. One logical solution to this problem is to determine the intersection of the lists of differentially expressed genes from independent studies. It is expected that genes that are biologically relevant to cancer tumorigenesis will be reported most often, while sporadically reported genes are due to the inherent biases and limitations of each of the profiling platforms used. However, the statistical significance of the observed intersection among many independent studies is usually not considered. PURPOSE: To address these issues, we developed a computational meta-analysis method that ranked differentially expressed genes based on the following criteria, which are presented in order of importance: the amount of intersection among studies, total tissue sample sizes, and average fold change in expression. We applied this meta-analysis method to 25 independent colorectal cancer profiling studies that compared cancer versus normal, adenoma versus normal, and cancer versus adenoma tissues. RESULTS: We observed that some genes were consistently reported as differentially expressed with a statistically significant frequency (P < .0001) in the cancer versus normal and adenoma versus normal comparisons,
Prevalence, pathogenicity and cultivar resistance of Fusarium and Rhizoctonia species causing soybean root rot

Zhang, J. X. , Xue, A. G. , Cober, E. R. , Morrison, M. J., Zhang, H. J., Zhang, S. Z. and Gregorich, E. 2013. Prevalence, pathogenicity and cultivar resistance of Fusarium and Rhizoctonia species causing soybean root rot. Can. J. Plant Sci. 93: 221-236. Root rot complex, caused by Fusarium and Rhizoctonia species, is a major soybean disease in Canada. We isolated nine Fusarium and Rhizoctonia species including F. oxysporum (Fo), F. graminearum (Fg), F. solani (Fs), F. avenaceum (Fa), F. tricinctum (Ft), F. sporotrichioides (Fsp), F. equiseti (Fe), F. poae (Fp), and R. solani (Rs) from soybean roots in eastern Ontario, Canada. The isolation results indicated that Fo was the most prevalent species while Fa, Fsp, and Fp were the least frequent species in the soybean rhizosphere. Numbers of Fo, Fs, Fg, and Rs isolates recovered from adult plant roots were significantly greater than those from seedling roots (P<0.01). The Rs, Fg and Fsp isolates were significantly more abundant in the no-till field than in the tilled field (P<0.01). Based on the greenhouse assays, Rs, Fg, and Fa were the most pathogenic species, while Fe and Fsp were the least pathogenic to soybean. The field resistance evaluation, based on the root rot severity, identified 21, 17, 30, and 3 out of 70 cultivars among the most tolerant to Fg, Fo, Fs, and Rs, respectively. A few of the cultivars showed partial resistance to multiple species, based on root rot severity and reduction in their seedling emergence, plant height, and root dry weight, but no cultivar was found to partially resist all four species. There was no correlation (P>0.05) between root rot severity and the reduction in seedling emergence, plant height, or root dry weight.
Seasonal shifts in the diet of the big brown bat (Eptesicus fuscus), Fort Collins, Colorado

Abstract Recent analyses suggest that the big brown bat (Eptesicus fuscus) may be less of a beetle specialist (Coleoptera) in the western United States than previously thought, and that its diet might also vary with temperature. We tested the hypothesis that big brown bats might opportunistically prey on moths by analyzing insect fragments in guano pellets from 30 individual bats (27 females and 3 males) captured while foraging in Fort Collins, Colorado, during May, late July–early August, and late September 2002. We found that bats sampled 17–20 May (n = 12 bats) had a high (81–83%) percentage of volume of lepidopterans in guano, with the remainder (17–19% volume) dipterans and no coleopterans. From 28 May–9 August (n = 17 bats) coleopterans dominated (74–98% volume). On 20 September (n = 1 bat) lepidopterans were 99% of volume in guano. Migratory miller moths (Euxoa auxiliaris) were unusually abundant in Fort Collins in spring and autumn of 2002 and are known agricultural pests as larvae (army cutworms), suggesting that seasonal dietary flexibility in big brown bats has economic benefits.
Photoselective Shade Nets Reduce Postharvest Decay Development in Pepper Fruits.

During two-year studies, we evaluated the influence of photoselective coloured shade nets on the quality of fresh harvested pepper fruits (Capsicum annuum) after prolonged storage and shelf life simulation. Pepper cultivar ‘Romans’ grown in a semi arid region under 35% pearl and yellow shade nets significantly maintained better pepper fruit quality after 16 days at 7°C plus three days at 20°C, mainly by reducing decay incidence during two consecutive years (2008 and 2009), compared to commercial black and red nets. No significant differences were observed in percentage of weight loss, firmness and total soluble solids in fruit harvested under the different coloured shade nets. The skin colour of fruit harvested under Pearl net was significantly lighter than that of fruit harvested under red and black shade nets and this fact can be associated with inhibition of fruit ripening during growth. After storability and shelf life simulation however skin colour was red to dark red under all shade nets. Pearl and yellow shade nets significantly reduced Alternaria spp. population in the field, which was evaluated with Alternaria-selective growing medium. The highest Alternaria population was found under red shade net. The significant low decay incidence in fruit harvested under pearl and yellow shade nets can be explained by the low inoculum level of Alternaria spp. in the field, and inhibition of fungal sporulation, and/or by a slowing of fruit ripening during its growth, reducing fruit susceptibility to fungal infection in the field due to the scattered light, its quality and the ratio between the light spectrum under the two shade nets.
Efferent ductules of the fan-throated lizard Sitana ponticeriana Cuvier: light and transmission electron microscopy study

Light microscopy histology of efferent ductules and the ultrastructural organization of their epithelium were studied in the fan-throated lizard Sitana ponticeriana Cuvier. The ductules of this lizard are extra-testicular and arise from an extra-testicular rete testis. A major portion of the ductules is intra-epididymal and occupies the cephalic end of the epididymis. The ductules differentiate histologically into proximal and distal portions. The epithelium is formed of two major tall columnar cell types, the non-ciliated and ciliated, and one minor cell type, the basal cells. Dark cells were also identified. The non-ciliated cells possess microvilli towards the luminal end, tubular coated pits at the bases of the microvilli, coated vesicles in the apical cytoplasm and multivesicular bodies, lysosomes and mitochondria in the supranuclear and perinuclear cytoplasm, which reflects their role in the uptake of the material they are processing. These cells also participate in spermiophagy. The ciliated cells reflect their role in mixing the luminal content and/or its transport to the distal parts of the male tract. The lizard efferent ductules share many features in common with those of mammals and a crocodile and several other features with birds and a turtle. Spermiophagy by the efferent ductules is reported here for the first time in a reptile.
Cellular stress responses in equine tendon fibroblast monolayers

The superficial digital flexor tendon (SDFT) is one of the most frequently injured tendons in Thoroughbred racehorses. Exercise associated factors including hyperthermia are thought to lead to cellular dysfunction and cell death of the resident tendon fibroblasts, the cells responsible for the repair of the tendon lesions. The main aim of this thesis was to investigate the sensitivity of SDFT fibroblasts to hyperthermia and to compare this with the deep digital flexor tendon (DDFT), a non-injury prone tendon. Understanding the physiological mechanisms of the heat shock response in these cells e.g. the use of protein markers will allow preventative strategies to be devised to protect these cells from damage. I determined whether thermotolerance associated with the induction of heat shock proteins (a survival mechanism that allows cells to withstand a subsequent lethal shock) could be induced with both heat and cold shock in these cells. Firstly, the basal DNA damage levels were quantified in both SDFT and DDFT fibroblasts as the cell culture environment is known to damage cells. My research showed both SDFT and DDFT fibroblasts were susceptible to replication induced DNA damage in vitro. The SDFT in particular had high levels of DNA damage when cultured on a fibronectin matrix in ambient oxygen. SDFT and DDFT fibroblasts were shown to be susceptible to a lethal heat shock (52oC). When a preconditioned sub-lethal heat shock was given to both tendons, induction of thermotolerance occurred and these cells survived a lethal heat shock. Thermotolerance was induced in preconditioned cold shocked SDFT fibroblasts but not in DDFT fibroblasts. Finally, a useful protein marker, DAXX (that is involved in cellular stress pathways as a transcriptional repressor and in apoptosis) was shown to disperse into the nucleoplasm during a mild heat shock in SDFT fibroblasts. One of the limitations of this thesis is that sample size was small and as a result, larger numbers of animals will be required for future experiments to determine whether my results are of biological significance.
Why Monogamy? Comparing House Wren Social Mating Systems In Two Hemispheres

Northern and southern temperate passerines differ in life-history traits, with southern species generally characterized by higher adult and juvenile survival, smaller clutches, and longer incubation and nestling periods. High adult survival is often associated with low rates of social and genetic polygamy, hence monogamy is expected to be more common in southern temperate birds. The broad distribution of the house wren (Troglodytes aedon) provides a distinctive opportunity to study geographic variation in life-history traits. Here we compare life-history traits and mating systems between a northern and a southern house wren population studied over a five-year period. As predicted, southern house wrens laid smaller clutches (4.86 vs 5.92 eggs), and had longer incubation (15.27 vs 13.89 days) and nestling periods (17.04 vs 15.89 days). Per-nestling parental effort was significantly higher for southern wrens, but the average number of feeding trips to the nest (trips/hour) did not differ significantly. Social polygyny was extremely rare in the southern house wren (1%) while relatively frequent in the northern house wren (18%). A smaller proportion of southern house wren nests contained extra pair young compared to northern house wrens (32% vs. 54%, respectively) but the overall proportion of extra-pair young per brood did not significantly differ. Northern house wren territories were distributed
HIV-2: Testing Specificities

Two years after the isolation of the first AIDS virus in 1983 (Barre-Sinoussi et al. 1983), a simian virus inducing a similar pathology was described in rhesus monkeys in captivity (Letvin et al. 1985). Apparently healthy individuals living in Senegal had antibodies that reacted better with the antigens of the simian virus than with those from the human virus (Barin et al. 1985). At the same period, two patients originating from West Africa were hospitalized in France and in Portugal with typical symptoms of AIDS, whereas their serology was negative for the human virus now called HIV-1. The second virus causing AIDS was isolated in 1986 (Clavel et al. 1986). It was then described in various countries of West Africa, and was later called Human immunodeficiency virus type 2 (HIV-2) (BrunVezinet et al. 1987; Clavel et al. 1987). It is classified in the Retroviridae family within the lentivirus genus. Among the lentiviruses, the two HIV are phylogenetically closer to simian lentiviruses than those infecting other animal species, explaining the antibody crossreactivity observed at first (Chakrabarti et al. 1987). The HIV-2 genome is closest to SIVsm infecting sooty mangabeys (Hirsch et al. 1989), whereas HIV-1 is closest to SIVcpz infecting chimpanzees (Huet et al. 1990).
Ontogeny of the Lim Code in the Mouse Gonads

Lim genes are developmentally regulated transcription factors involved in tissue specification and cell differentiation. Several Lim genes are present in the mammalian genome and each tissue expresses a unique pattern of Lim genes giving rise to the Lim code and it is believed that the Lim code is the determinant of the cell fate decisions taken by the tissue. In the developing mouse, Lhx9 and Lmo4 have been identified to play a key role in gonad specification and testis development; however the presence of other Lim genes and its co-regulators has not been reported. Recent evidences also suggest that the Lim genes are also expressed in other adult tissues. However, the presence of Lim genes in adult gonads has not been reported. In the present study we report the expression profiles of Lhx9, Lmo 1-4 and Clim 1 and 2 in the developing, neonatal and adult mouse gonads. Our results show that along with Lhx9, all the Lmos and Clims are expressed by the developing and adult gonads. With the exception of Lmo4, the expression of all these factors is sexually dimorphic with higher expression in the female gonads as compared to male gonads. Our results indicate that the Lim gene activity may be vital for ovarian development and functioning. It will be interesting to study the gonadal phenotypes of the Lim mutants to define their specific roles in the gonads.
Composition and temporal change of the forest in 18Th century Shrewsbury, Massachusetts1

Abstract By the middle of the 19th century, nearly all of central Massachusetts, USA, was cut at least once and 80% deforested. When did deforestation begin? We recorded all the trees and other corner markers used in 18th century proprietors' surveys of Shrewsbury, MA. From 1718–1799, the percentage of corner markers that were “trees” declined from 45% to 20%, and the relative abundance of white oak tended to decrease. Unexpectedly, the relative abundance of white pine more than doubled. Overall, deforestation and alteration of species composition were already occurring in the 18th century due to changing conditions, selective harvest, and differences in the resilience of the dominant trees. Proprietors' records can provide data on forest change as well as forest composition.
The role of small GTPase Rac1 in stress signaling

The heat shock response, one of the most studied cellular homeostatic mechanisms, is involved in the maintenance of cell functionality during stress. Yet, the whole stress signaling pathway has not been elucidated. In line with the membrane thermosensor model, mild stress, or “membrane defects” caused by different disease states, is sensed by changes in the fluidity and microdomain structure of membranes, influencing membrane localized signaling activities. In favor of this model, our group exposed different mammalian cells to various membrane fluidizers or drugs with the ability to interact with certain membrane lipids and found substantial modulation of heat shock protein (HSP) expression. One possible signaling pathway originating from plasma membrane involves the lipid kinase, PI3kinase, which in turn activates the small GTPase, Rac1. Through downstream signaling cascade to MAP kinases, the main transcription factor, HSF1 is activated leading to HSP synthesis. It was shown that Rac1 translocation to the plasma membrane is essential for activating downstream effectors and its membrane binding is determined at least in part by membrane lipids. In favor of “membrane stress sensor” model, our working hypothesis was that Rac1 pathway is involved in stress signaling through the effect of stress on membrane microdomain organization. As a proof of concept, well established Rac1 specific inhibitor NSC23766 along with 2-bromopalmitate - which blocks Rac1 palmitoylation necessary to interact Rac1 with the liquid ordered membrane domains - have been investigated. We have shown that using specific Rac1 inhibitor, NSC23766 and 2-Brp, the heat shock response decreased remarkably in dose dependent manner. Moreover, elevated levels of heat shock response achieved by addition of HSP co-inducer, BGP15 is diminished by NSC23766. We showed, that palmitoylation affects Rac1 relocalization under stress conditions and, the p38 MAPK pathway has a key role in the Rac1 actions, described. Not only the relocalization of Rac1 to the plasma membrane but also its capacity for microdomain remodeling have been documented. Besides, cytoskeletal changes upon heat treatments and inhibitor administrations have been shown by taken SEM photos. Data gained above are further confirmed by the generation of stable clones with palmitoylation deficient, constitutively active and dominant negative Rac1 mutations. As a conclusion, Rac1 is a major mediator of heat stress signal transduction between plasma membrane and prominent HSP genes tested, in melanoma cells. This small GTPase is directly involved in the modulation of HSP expression through controlling the stress induced remodeling of membrane microdomains.