Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Near-Isogenic Line CBB23 with a New Resistance Gene to Bacterial Blight in Rice and Its Application

The near isogenic line (NIL) with a new gene Xa23 for resistance to bacterial blight (BB) was developed and designated as CBB23 in 1993-1998. A susceptible indica variety JG30 with improved plant type was used as a recurrent parent. The progenies derived from the cross JG30/H 4 harboring the gene Xa23 were developed by back cross until BC 5, and selfing for 4 times. Evaluation of the resistance gene Xa23 with specific strain P6 and selection of plant type successively were carried out till the line showing stable resistance and agronomic characters similar to the recurrent parent. Comparison of reaction for resistance spectrum to 20 strains including 10 Philippine races, 3 Japanese races, and 7 Chinese pathotypes between CBB23(carrying Xa23 )and IRBB21(carrying Xa21) was made. Xa23 is resistant to all 20 strains, and Xa21 is resistant to 19 strains and highly susceptible to the Philippine race 10. The NIL CBB23 was used to establish segregation populations of JG30/CBB23 for mapping the gene Xa23. The gene was located on rice chromosome 11 in the preliminary tagging by screening SSR. Three AFLP markers screened are closely linked with Xa23. The genetic distance between APKj23 and Xa23 is about 1.0 cM. The NIL is also valuable in rice breeding.
SOJOURN TIMES IN THE M/G/1 FB QUEUE WITH LIGHT-TAILED SERVICE TIMES

The asymptotic decay rate of the sojourn time of a customer in the stationary M/G/1 queue under the foreground–background (FB) service discipline is studied. The FB discipline gives service to those customers that have received the least service so far. We prove that for light-tailed service times, the decay rate of the sojourn time is equal to the decay rate of the busy period. It is shown that FB minimizes the decay rate in the class of work-conserving disciplines.
RETURNS TO EDUCATION AND CHANGES IN WAGE STRUCTURE: IS THERE AN UNSKILLED BIAS TECHNOLOGICAL CHANGE IN ITALY?

In this paper we analyse the role of education on the dynamics of wage structure in Italy. Using SHIW data over the period 1993-2004, we derive two main results in a quintile regression framework. First, returns to education decline over time almost uniformly across the wage distribution. Second, using a quintile decomposition method à la Machado-Mata we point out that the composition effect associated with the increased share of educated workers is positive, while the price effect of education is negative in the whole wage distribution. Assuming a standard demand and supply paradigm, this leads us to the conclusion that a sort of “unskilled” bias technological change could have been prevailing in the Italian labour market during last decade. JEL codes: J24, J31,
A combination of prebiotic short- and long-chain inulin-type fructans enhances calcium absorption and bone mineralization in young adolescents

BACKGROUND Short-term studies in adolescents have generally shown an enhancement of calcium absorption by inulin-type fructans (prebiotics). Results have been inconsistent; however, and no studies have been conducted to determine whether this effect persists with long-term use. OBJECTIVE The objective was to assess the effects on calcium absorption and bone mineral accretion after 8 wk and 1 y of supplementation with an inulin-type fructan. DESIGN Pubertal adolescents were randomly assigned to receive 8 g/d of a mixed short and long degree of polymerization inulin-type fructan product (fructan group) or maltodextrin placebo (control group). Bone mineral content and bone mineral density were measured before randomization and after 1 y. Calcium absorption was measured with the use of stable isotopes at baseline and 8 wk and 1 y after supplementation. Polymorphisms of the Fok1 vitamin D receptor gene were determined. RESULTS Calcium absorption was significantly greater in the fructan group than in the control group at 8 wk (difference: 8.5 +/- 1.6%; P < 0.001) and at 1 y (difference: 5.9 +/- 2.8%; P = 0.04). An interaction with Fok1 genotype was present such that subjects with an ff genotype had the least initial response to fructan. After 1 y, the fructan group had a greater increment in both whole-body bone mineral content (difference: 35 +/- 16 g; P = 0.03) and whole-body bone mineral density (difference: 0.015 +/- 0.004 g/cm(2); P = 0.01) than did the control group. CONCLUSION Daily consumption of a combination of prebiotic short- and long-chain inulin-type fructans significantly increases calcium absorption and enhances bone mineralization during pubertal growth. Effects of dietary factors on calcium absorption may be modulated by genetic factors, including specific vitamin D receptor gene polymorphisms.
Interactions between Germline and Somatic Mutated Genes in Aggressive Prostate Cancer

Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the USA. Advances in high-throughput genotyping and next generation sequencing technologies have enabled discovery of germline genetic susceptibility variants and somatic mutations acquired during tumor formation. Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic variation and their role in aggressive PCa remain largely unexplored. Here we investigated the possible oncogenic interactions and cooperation between genes containing germline variation from genome-wide association studies (GWAS) and genes containing somatic mutations from tumor genomes of 305 men with aggressive tumors and 52 control samples from The Cancer Genome Atlas (TCGA). Network and pathway analysis were performed to identify molecular networks and biological pathways enriched for germline and somatic mutations. The analysis revealed 90 functionally related genes containing both germline and somatic mutations. Transcriptome analysis revealed a 61-gene signature containing both germline and somatic mutations. Network analysis revealed molecular networks of functionally related genes and biological pathways including P53, STAT3, NKX3-1, KLK3, and Androgen receptor signaling pathways enriched for germline and somatic mutations. The results show that integrative analysis is a powerful approach to uncovering the possible oncogenic interactions and cooperation between germline and somatic mutations and understanding the broader biological context in which they operate in aggressive PCa.
Influence of Structure—Phase State of Nb Containing Zr Alloys on Irradiation-Induced Growth

On account of the search for the optimal composition and structure-phase state of Zr alloys much attention is paid to upgrade the E110 (Zr-1 %Nb) and E635 (Zr-1 %Nb-0.35 %Fe-1.2 %Sn) alloys that have proved well in terms of irradiation-induced creep and growth, high strength characteristics, and corrosion. The difference between the alloy properties is determined by their states related to their compositions. The structure-phase state of the Zr-Nb and Zr-Nb-Fe-Sn systems has been studied after heat treatment in the α-- and α + β- regions and its influence on the irradiation-induced growth (IIG) during BOR-60 irradiation at T =315–350 °C was investigated. A substantial difference has been shown in the deformation effected by IIG of those alloys, it is less for Zr-Nb-Fe-Sn alloys in dissimilar structure-phase states. The incubation period of the accelerated growth stage is determined by the α-matrix composition, the phase state and the initial dislocation structure. Neutron irradiation leads to a redistribution of alloying elements between the matrix and the precipitates, and to changes in the α-solid solution composition. These changes affect accumulation and mobility of irradiation defects, anisotropy and formation of vacancy c-component dislocation loops. The appearance of c-loops usually correlates with an axial direction acceleration of the IIG of tubes conforming to their texture. The basic regularities of the phase transformation have been established: a) β-Nb precipitates in Zr-Nb alloys are altered in composition to reduce the Nb content from 85–90 % to ∼ 50 %, fine precipitates likely enriched in Nb are formed; b) β-Zr precipitates are subject to irradiation-stimulated decomposition; c) Laves phase precipitates change composition (the content of Fe decreases) and crystal structure, HCP to BCC (β-Nb); d) (Zr,Nb)2Fe precipitates having the FCC lattice retain their composition and crystal structure; e) no amorphization of any secondary phase precipitates is observable under the given conditions of irradiation (T = 315–350 °C). Based on the dpa, the results were compared pertaining to Zr-alloy IIG deformation vs. fluence in various reactors at different energies of fast neutrons. The presented graphs enable comparison between the results of numerous experiments and enable predictions of Zr-material behavior in long-term operation and at high burn-up in commercial reactors.
Impact of explants and gamma irradiation dosage on In vitro mutagenesis in carnation (Dianthus caryophyllus L.).

Effect of gamma irradiation was studied on horizontally cut leaflets for their performance under in vitro conditions. With increased dosage of gamma irradiation, survivability decreased. Explant enlargement was noticed maximum in case of leaf tip explant but, this enlargement had no indication of survival percentage. Survival percentage was least in case of leaf tip, which reduced to nil by the end of 5th week of culture. Leaf expansion, formation of calli and regeneration was found to be dependent on explant used, media composition and their interaction. Maximum regeneration was noticed from leaf base. Regeneration was found to be dependent on irradiation dosage. Irradiation dosage had significant interaction with media and explant on survival, leaf expansion, calli formation and on regeneration.
Studies on genetic variability and heritability for quality traits of tomato (Lycopersicon esculentum Mill.) under heat stress conditions.

The present investigation was aimed to study the variation and heritability of quality characters in tomato genotypes raised under normal and high temperature conditions of Punjab. Fifteen advanced generation breeding lines of tomato along with four checks were evaluated for quality characters under normal and stress (high temperature) conditions. Maximum TSS, pericarp thickness, fruit firmness, acidity, lycopene content and dry matter was recorded in LT-36, LT-10, LT-39, LT-41, LT-16A and LT-36. Both genotypic and phenotypic components of variance were high during February planting for all the characters except for lycopene content and dry matter. High heritability coupled with low genetic advance for all the characters suggested the involvement of nonadditive gene action in their inheritance which can be exploited through heterosis breeding.
Effects of a Four-day Spaceflight and Recombinant Human Growth Hormone on Cancellous Bone Microarchitecture in Femoral Head of Rapidly Growing Male Rats

Spaceflight results in reduced bone accrual and muscle atrophy in growing rodents. Some studies suggest that the detrimental effects of spaceflight are due, in part, to impaired growth hormone (GH) signaling. An experiment flown aboard STS-41 (October 6–10, 1990) evaluated the efficacy of recombinant human growth hormone (rhGH) in ameliorating the detrimental effects of spaceflight on the musculoskeletal system in male Sprague Dawley rats. The rats were 39 days old at launch and sacrificed following the 4–day flight. Ground controls (n=11/treatment group) and flight animals (n=8/treatment group) were treated with rhGH or excipient delivered using osmotic pumps implanted subcutaneously one day prior to launch. For the present examination, cancellous bone in the femoral head was evaluated using X-ray microtomography (microcomputed tomography), a technology not available when the study was performed. Spaceflight resulted in lower cancellous bone volume fraction, connectivity density, trabecular thickness and trabecular number, and higher trabecular separation. rhGH had no independent effect on cancellous bone architecture and there were no spaceflight by rhGH interactions. These findings suggest that a short interval of microgravity during rapid growth was sufficient to reduce accrual of cancellous bone and alter bone microarchitecture at an important weight bearing skeletal site. Additionally, increasing growth hormone levels was ineffective in preventing cancellous osteopenia in flight animals and did not increase cancellous bone volume fraction in ground controls.
CONSERVATION OF WET MEADOW SPECIES IN AN URBAN CONTEXT: LYCHNIS FLOS-CUCULI AS STUDY CASE

In urban areas, wetland habitats consist of small isolated remnants, embedded in an inhospitable human-used matrix, and incurring strong anthropogenic pres- sures (e.g., artificialization, pollution, eutrophication, and exotic species invasions). These can lead to detrimental genetic and demographic consequences for the populations, even for common species. This study investigated genetic variation and structure for 12 allozyme loci and reproductive fitness in populations of Lychnis flos-cuculi (Caryophyllaceae), an insect- pollinated perennial herb occurring in wetland fragments and along the Woluwe River, in Brussels urban zone (Belgium), in relation to population size. No effect of population size on genetic variation and usually low between-population genetic differentiation were found for urban populations of L. flos-cuculi. A significant pattern of isolation by distance indi- cated that beyond a certain distance, especially along the Woluwe, populations might still exchange genes. Floral display and fruit set increased with population size, but this relation- ship did not seem to be predominant. Significant differences found among populations sug- gest that other factors (e.g., plant density, neighbour competition and habitat quality) may have a stronger impact on reproductive fitness. Some of the small populations may also be still connected through pollen flow, increasing reproductive success and preventing inbreed- ing depression. The present findings suggest that populations of L. flos-cuculi in Brussels urban zone are not prone to the detrimental effects of habitat fragmentation, as we may have expected, despite the relative small size of the populations. These genetically diverse and productive populations can still be considered of conservation value, including the small ones, which within a certain spatial distance might be regarded as important connecting components of pollen-exchanging network of populations, buffering populations against the negative effects of small population size. The conservation of L. flos-cuculi in Brussels urban zone should favour the preservation of connected populations rather than only preserving isolated wetlands.
Visualização de dados genômicos do fungo Paracoccidioides brasiliensis

Genome sequencing projects developed worldwide produce an enormous and growing volume of information. These informations are usually described in text, HTML (Hypertext Markup Language) or XML (Extensible Markup Language) format, and they can be stored on hundreds or even thousands of pages. The storage and analysis of these information require computational tools and methods to facilitate and support the biological research. Besides the EST (Expressed Sequence Tags) information or genomic DNAs generated from the sequencing projects, other data such as genomic comparisons or differential gene expression, obtained from BLAST (Basic Alignment Search Tool) and cDNA macroarray experiments are available on text format which requires biological analysis. The work of the biologists can be supported if the available data is presented using graphics or tables. So, this work proposes two methods for visualizing data generated by the sequencing genome projects developed on the molecular biology of the University of Brasilia. Comparisons obtained by BLAST among the Paracoccidioides brasiliensis ESTs and the genomics DNAs of two others phylogenetic related fungi, Aspergillus fumigatus and Aspergillus nidulans, using a genomic visualization tool GBrowse, allow to infer the organization of the P. brasiliensis genes inside its chromosomes. Particularly, from the model A. fumigatus, synteny among the P. brasiliensis genes could be identified. The inferences obtained by these comparisons can greatly help to develop biological experiments to confirm the organization of the P. brasiliensis genes. Besides, to contribute for the analysis of the set of differentially expressed genes indicated by cDNA macroarray experiments, a tool named PathwayView was built, to locate the differential genes into the KEGG metabolic pathways maps. PathwayView contribute to process a great volume of data, making easier to find the pathways and the enzymes inside these pathways. In the particular case of the P. brasiliensis fungus, for example, this tool could be used to increase the knowledge of how biological adaptation of this pathogen occurs in humans, which in turn, could indicate new directions for the development of new drugs or fungicides.
Internet-based surveys: relevance, methodological considerations and troubleshooting strategies

Sir Internet-based surveys have steadily gained popularity with researchers because of their myriad advantages such as ability to reach a larger pool of potential participants within a shorter period of time (vis-a-vis face-to-face surveys), study subjects who maybe geographically dispersed or otherwise difficult to access and efficiency of data management and collation.1 2 This is in addition to obvious reasons such as convenience, relative inexpensiveness and user-friendly features such as comfortable pace and enhanced sense of participant control. With the advent of the COVID-19 pandemic and dwindling opportunities for face-to-face data collection, internet-based tools offer a powerful alternative to rapidly collect data. Moreover, they could be useful tools from a public health perspective to track public perceptions, myths and misconceptions3 in times of disaster. Many methodological issues confront a prospective researcher while designing online questionnaires/surveys. A few of them and some corresponding suggestions for troubleshooting are outlined below: 1. Web or mailed questionnaire? —A meta-analysis of 39 studies4 concluded that response rates to mail surveys are, in general, higher than web surveys. Interestingly, two important factors underlying this variation were the type of respondents and medium of follow-up reminders. While college students were more responsive to web surveys, physicians and laypersons were found to be more receptive to mail surveys. Further, follow-up reminders were more effective when given by mail, probably owing to greater personalisation, than the web. Recently, a hybrid method called web-push surveys, wherein, initial and subsequent follow-up contacts are made by mail to request a response by web was found to be a parsimonious method to elicit responses.5 However, results …
Photoacoustic imaging for surgical guidance: Principles, applications, and outlook

Minimally invasive surgeries often require complicated maneuvers and delicate hand–eye coordination and ideally would incorporate “x-ray vision” to see beyond tool tips and underneath tissues prior to making incisions. Photoacoustic imaging has the potential to offer this feature but not with ionizing x-rays. Instead, optical fibers and acoustic receivers enable photoacoustic sensing of major structures—such as blood vessels and nerves—that are otherwise hidden from view. This imaging process is initiated by transmitting laser pulses that illuminate regions of interest, causing thermal expansion and the generation of sound waves that are detectable with conventional ultrasound transducers. The recorded signals are then converted to images through the beamforming process. Photoacoustic imaging may be implemented to both target and avoid blood-rich surgical contents (and in some cases simultaneously or independently visualize optical fiber tips or metallic surgical tool tips) in order to prevent accidental injury and assist device operators during minimally invasive surgeries and interventional procedures. Novel light delivery systems, counterintuitive findings, and robotic integration methods introduced by the Photoacoustic & Ultrasonic Systems Engineering Lab are summarized in this invited Perspective, setting the foundation and rationale for the subsequent discussion of the author’s views on possible future directions for this exciting frontier known as photoacoustic-guided surgery.
Antioxidant Properties Associated with the Biochemical Changes in the Development of African Pear (Dacryodes edulis) Fruit

DOI: 10.21276/sjbr.2018.3.2. 6 Abstract: The antioxidant properties of oil and fruit extracts of Dacryodes edulis (African pear) from four weeks after anthesis (WAA) to fruit maturation were assessed in this study. The oils from the fruits were extracted with chloroformmethanol 1:2 (v/v) using standard procedures. The in vitro antioxidant capacity of the oil extracts was determined by spectrophotometric methods using 2, 2-diphenyl-1picrylhydrazyl (DPPH) radical, H2O2 and malondialdehyde (MDA) assays. Results from the study indicated that DPPH and H2O2 scavenging capacity as well as percentage inhibition of MDA were significantly (P˂0.05) higher in oil at 20 WAA (45.47%, 45.1%, 18.3%), but with significant (P˂0.05) lesser percentage of inhibition at 4-12 WAA. The hepatoprotective effects of the extracts were examined in vivo in male wistar rats challenged with sodium arsenate. Results showed that the rats fed with the oil WAA had significant reduction (p<0.05) in lipid peroxidation, increase in superoxide dismutase (SOD) and catalase (CAT) activities especially relative to control values. African walnut extracts treated rats also showed similar decrease in serum AST (70.3±2.54U/L), ALT (63.7±2.34U/L±), ALP (59.3±0.60U/L) and GGT (230.8±1.12U/L) levels at 20 WAA when compared to 4 WAA extracts treated rats, AST (105.2±1.38U/L), ALT (73.0±1.12U/L), ALP (72.0±2.26U/L) and GGT (299.7±1.88U/L). The results suggest that the various fruit extracts possess varied degrees of potent antioxidant activity both in vitro and in vivo and may serve as important sources of antioxidants in food, cosmetics and pharmaceutical industries.