Miracle-dz/UniFAR-FTUs huggingface dataset:
IFN-γ and Fas Ligand Are Required for Graft-versus-Tumor Activity against Renal Cell Carcinoma in the Absence of Lethal Graft-versus-Host Disease1

To determine the mechanisms of graft-versus-tumor (GVT) activity in the absence of graft-versus-host disease (GVHD) against a solid tumor, we established two allogeneic bone marrow transplantation models with a murine renal cell carcinoma (RENCA). The addition of 0.3 × 106 donor CD8+ T cells to the allograft increased the survival of tumor-bearing mice without causing GVHD. The analysis of CD8+ T cells deficient in cytotoxic molecules demonstrated that anti-RENCA activity is dependent on IFN-γ and Fas ligand (FasL), but does not require soluble or membrane-bound TNF-α, perforin, or TRAIL. Recipients of IFN-γ−/− CD8+ T cells are unable to reject RENCA compared with recipients of wild-type CD8+ T cells and, importantly, neither group develops severe GVHD. IFN-γ−/− CD8+ T cells derived from transplanted mice are less able to kill RENCA cells in vitro, while pretreatment of RENCA cells with IFN-γ enhances class I and FasL expression and rescues the lytic capacity of IFN-γ−/− CD8+ T cells. These results demonstrate that the addition of low numbers of selected donor CD8+ T cells to the allograft can mediate GVT activity without lethal GVHD against murine renal cell carcinoma, and this GVT activity is dependent on IFN-γ and FasL.
Development of Male-Sterile Elite Lines using Marker-Assisted Backcrossing (MABC) in Tomato

Recurrent backcrossing is a traditional breeding method that is commonly employed to transfer alleles at one or more loci from a donor to an elite variety. In order to develop male-sterile elite tomato lines, marker-assisted foreground and background selections were performed during backcross breeding. Compared to conventional backcrossing, marker-assisted backcrossing (MABC) is extremely useful for recovery of a recurrent parent’s genetic background. For foreground selection, the tomato mutant anthocyanin absent (aa) presents a green hypocotyl during the seedling stage. Lines carrying the Aa genotype were selected from BC1F1 and BC2F1 populations using indel markers derived from the unique aa mutation of T2-517. This trait has been utilized in marker-assisted selection of male sterile 10 (ms10) at the seedling stage because their corresponding loci are closely linked on chromosome 2. For background selection, a total of 48 single nucleotide polymorphism (SNP) markers obtained from resequencing data between the MR10-3211 and T2-517 lines evenly distributed in the tomato genome were finally selected. BC1F1 and BC2F1 plants carrying the heterozygous (Aa) genotype were subjected to background selection using a set of 48 SNP markers. Multiple genotype analysis was done using a high-throughput genotyping system. As a result, one plant, 87.5% similar to the recurrent parent genome in the BC1F1 generation, and three plants with a 95.5% recovery rate of the recurrent parent genome in the BC2F1 generation, were selected. These selected plants were fixed in the BC2F2 and BC2F3 generations for the male sterile tomato elite line. We therefore demonstrate the utility of the MABC method for the recovery of recurrent parent genomes in tomato breeding strategies. Additional key words: background selection, foreground selection, marker-assisted selection (MAS), recurrent backcrossing, single nucleotide polymorphism (SNP) marker
The seagrass root microbiome: Micro-scale solutions for macro-scale resolutions

While light availability plays a critical role in seagrass growth and distribution, there is limited understanding of how changes in light exposure impact belowground processes. We investigated the effect of prolonged and fluctuating reductions in light on root growth and exudation by three colonizing seagrasses: Cymodocea serrulata, Halophila ovalis and Halodule uninervis. Seagrasses were grown in mesocosms under continuous full light (control), under continuous light reduction (medium or low), or under fluctuating light (10 days of low and four days of high light, repeated three times). Plants were harvested (i) six weeks after light treatments (impact), and (ii) after an additional four weeks of continuous full light (recovery). Root exudates were collected from trap solutions and measured for dissolved organic carbon (DOC), total dissolved nitrogen (TDN), and dissolved organic matter (DOM) excitation/emission fluorescence spectroscopy. Root biomass decreased in all shading treatments. The most notable impact of light treatment was an increase in root exudation of DOC, protein-like DOM and humic-like DOM under fluctuating light for all species. After four weeks of recovery, exudation of DOC, and protein-like DOM observed under fluctuating light returned to the control light levels. However exudation of DOC and protein-like DOM by H. ovalis grown in continuous low light remained greater than the
Identificatie van plantaardige eiwitten in magere melkpoeder

In het kader van controle op gebruik van magere melkpoeder (MMP) in kunstmelkvoeder onderzoekt het RIKILT ca. 800 monsters per jaar. Er zijn aanwijzingen dat er plantaardige eiwitten en/of eiwithydrolysaten (bijvoorbeeld soja, tarwe, erwt, mais, etc.) worden toegevoegd aan het subsidiabel MMP terwijl dat niet is toegestaan. Deze eiwitten zijn niet toegestaan en kunnen met de huidige analysetechnieken niet of in onvoldoende mate worden gedetecteerd. Voor het kunnen screenen en identificeren van plantaardige eiwitten in MMP zijn een aantal technieken gekozen om nader te onderzoeken in de tweede helft van 2005. Dit betreft immunoblotting, voorscheidingen d.m. v. voorextractie of HPLC, MALDI TOF MS, targeted LC-MS, untargeted LC-MS(/MS) en capillaire electroforese
Modulation of Aromatase Expression in the Breast Tissue by ERRα-1 Orphan Receptor

We have previously identified a silencer element (S1) that is situated between promoters I.3 and II of the human aromatase gene and that down-regulates the action of these promoters. We recently applied the yeast one-hybrid approach to screen a human breast tissue hybrid cDNA expression library for genes encoding the proteins binding to the silencer region. Most proteins identified from this approach belong to the nuclear receptor superfamily. Fifty % of the positive clones encode for ERR alpha-1, and other positive clones include EAR-2, EAR-3 (COUP-TF1), RAR gamma, and p120E4F. Because ERR alpha-1 was found to be the major protein interacting with S1, we decided to examine the regulatory action of ERR alpha-1 on promoter I.3 of the human aromatase gene. Using a reporter plasmid that includes the aromatase genomic fragment containing promoter I.3 and S1, ERR alpha-1 was found to have a positive regulatory function in breast cancer SK-BR-3 cells. Gel mobility shift assays have confirmed that ERR alpha-1 binds to S1 in a dose-dependent manner, and DNase I footprinting analysis has revealed that ERR alpha-1 binds to a region, 5'-AAGGTCAGAAAT-3', which is within S1 and between 96 and 107 bp relative to the transcriptional start site of promoter I.3. In addition, despite the fact that the nuclear receptor SF1 was shown previously to bind to the same site and to mediate a cAMP response in ovary, our yeast one-hybrid screening did not find any SF-1 clones. Gel mobility shift assays further revealed that SF-1 can bind to the silencer element with an affinity comparable with ERR alpha-1. Because our reverse transcription-PCR analysis was not able to detect SF1 mRNA in breast cancer tissue or in SK-BR-3 cells, it is thought that SF1 protein is not expressed in breast cancer tissue. Two ERR alpha-1 RNA variants with differences at the 5'-end have been reported. Our reverse transcription-PCR analysis identified the shorter variant in 28 of 32 breast tumor specimens and the longer variant in only 1 specimen. In addition, the shorter variant was detected in breast cancer SK-BR-3 cells as well as in a breast tumor fibroblast line WS3TF. The results suggest that ERR alpha-1 is one of the nuclear proteins interacting with S1 in breast cancer tissue. It is thought that the silencer element in the human aromatase gene may function differently in different tissues because of distinct expression patterns of transcription factors.
In-vitro assay of some plant extracts against Fusarium oxysporum f. sp. lycopersici causal agent of tomato wilt

The effect of crude extracts of neem (Azadirachta indica) leaf, neem seed and garlic (Allium sativum) at concentrations ranging from 5% to 30% of the material in 100 ml of Potato Dextrose Agar on mycelial growth of Fusarium oxysporum f. sp. lycopersici was assessed. All the extracts inhibited mycel- lial growth at various levels. Dry neem seed extract gavel 100% inhibition of mycelial growth. Fresh neem leaf extract reduced mycelial growth with increasing concentration while in garlic there were no differences in growth inhibition among the various concentrations used. However garlic extracts de- creased sporulation with increasing concentration and cultures grown on extract amended agar plates remained viable.
Structural and Biologic Characterization of Pegylated Recombinant IFN-α2b

The type I interferon-α (IFN-α) family is a family of natural small proteins that have clinically important anti-infective and antitumor activity. We have developed a semisynthetic protein-polymer conjugate of IFN-α2b (Intron® A) by attaching a 12,000-Da monomethoxypolyethylene glycol (PEG-12000) polymer to the protein. PEG conjugation is thought to increase the serum half-life and thereby prolong patient exposure to IFN-α2b without altering the biologic potency to the protein. Matrix-assisted laser desorption ionization/mass spectrometry (MALDI-MS), high-performance size exclusion chromatography (HPSEC), circular dichroism (CD) analysis and tryptic digestion peptide analysis of PEG Intron demonstrated that the IFN-α2b protein was approximately 95% monopegylated and that the primary, the secondary, and the tertiary structures were unaltered. Pegylation did not affect the epitope recognition of antibodies used for Intron A quantitation. An extensive analysis of the pegylated positional isomers revealed tha.
In the beginning was the worm : finding the secrets of life in a tiny hermaphrodite

This is the story of how three men won the Nobel Prize for their research on the humble nematode worm C. elegans; how their extraordinary discovery led to the sequencing of the human genome; how a global multibillion-dollar industry was born; and how the mysteries of life were revealed in a tiny, brainless worm. In 1998 the nematode worm-perhaps the most intensively studied animal on earth-was the first multicellular organism ever to have its genome sequenced and its DNA mapped and read. "When we understand the worm, we will understand life," predicted John Sulston, one of the three Nobel laureates, and his prediction proved astonishingly accurate. Four years later, the research that led to this extraordinary event garnered three scientists a Nobel Prize. Along with Robert Horvitz and Sydney Brenner, Sulston discovered the phenomenon of programmed cell death in the worm, an essential concept that explains how biological development occurs in animal life and, as Horvitz later showed, how it occurs in human life. C. elegans is about as simple as an animal can be, but understanding its genetic organization is helping to reveal the mechanisms of life and, by extension, the mechanisms of our own lives. In the Beginning Was the Worm shows that in order to unlock the secrets of the human genome we must first understand the worm. But this story is about more than just the worm. It is about how an eccentric group of impassioned scientists toiled in near anonymity for years, driven only by a deep passion for knowledge and scientific discovery. It is the story of countless hours of research, immense ambition, and one of the greatest discoveries in human history.
Transcriptome of the eastern oyster Crassostrea virginica in response to bacterial challenge

The Eastern oyster Crassostrea virginica, an ecologically and economically important estuarine organism, suffers mortalities as high as 90-100% in affected areas due to Roseovarius Oyster Disease (ROD), caused by the bacterial pathogen, Roseovarius crassostreae. Advanced genotypic breeding techniques necessitate information regarding markers and genes associated with disease resistance. As yet, the host-pathogen interaction between C. virginica and R. crassostreae is poorly understood at the molecular level. The identification of potential genes and pathways responsible for an effective host defense response in the Eastern oyster to R. crassostreae is important not only to provide a basis for enhanced breeding techniques, but also to enhance understanding of innate immunity in a broader, evolutionary sense. The present study proposed to uncover not only genes and general processes potentially involved in disease resistance to ROD in the Eastern oyster, but also diversified gene families. To that end the present study entailed a disease challenge exposing RODresistant and ROD-susceptible families of oysters to R. crassostreae, highthroughput cDNA sequencing of samples from several timepoints throughout the disease challenge, assembly of sequence data into a reference transcriptome, analysis of the transcriptome through differential gene expression and gene family similarity clustering, and single nucleotide polymorphism (SNP) detection to identify candidate gene markers. Oyster resistance to R. crassostreae was found to involve extracellular matrix remodeling, cell adhesion, inflammation, metabolism, and other processes. Several gene families identified as putatively diversified and important in the oyster host defense response were enumerated and described, including serine proteases, serine protease inhibitors, c-type lectins, C1q domain-containing proteins, fibrinogen domain-containing proteins, scavenger receptors with class B SRCR domains, interferon-induced protein 44 (IFI44) family proteins, and GTPase of the immunity associated protein (GIMAP) family proteins. Further, similarity clustering of proteins and translated transcripts from diverse invertebrates suggested that GIMAP proteins are expanded in molluscs and IFI44 proteins are expanded in bivalves.
The use of the Hurst exponent to investigate the quality of forecasting methods of ultra-high-frequency data of exchange rates

Over the last century a variety of methods have been used for forecasting financial time data series with different results. This article explains why most of them failed to provide reasonable results based on fractal theory using one day tick data series from the foreign exchange market. Forecasting AMAPE errors and forecasting accuracy ratios were calculated for statistical and machine learning methods for currency time series which were divided into sub-segments according to Hurst ratio. This research proves that the forecasting error decreases and the forecasting accuracy increases for all of the forecasting methods when the Hurt ratio increases. The approach which was used in the article can be successfully applied to time series forecasting by indicating periods with the optimal values of the Hurst exponent.
Functional identity is more important than diversity in influencing ecosystem processes in a temperate native grassland

1 Experimental studies have provided significant knowledge of how biodiversity can influence ecosystem processes. However, there is a growing need to relate these findings to natural communities. 2 Here we identify two major hypotheses for how communities may influence ecosystem processes: the ‘diversity hypothesis’ (the diversity of organisms in a community influences ecosystem processes through mechanisms such as complementary resource use), and the ‘mass ratio hypothesis’ (ecosystem processes are determined overwhelmingly by the functional traits of the dominant species). We then test which of these two hypotheses best explain variation in ecosystem properties and processes (biomass pools and fluxes, water use, light interception) in a temperate native grassland. We do this by applying various measures of diversity, functional diversity, and functional identity, whose significant relations with ecosystem processes would support either of the competing hypotheses. 3 Mean trait values best explained variation in five of the eight ecosystem processes examined, supporting Grime's mass ratio hypothesis, which proposes that the functional identities of the dominant species largely determine ecosystem processes. 4 Multi‐trait functional diversity indices also explained large amounts of variation in ecosystem processes, while only weak relationships were observed between species richness and ecosystem processes. 5 To explore the mechanistic interactions between variables, we developed structural equation models (SEMs), which indicated that many of the community diversity and trait properties significantly influenced ecosystem processes, even after accounting for co‐varying biotic/abiotic factors. 6 Synthesis. Our study is one of the first explicit comparisons of the ‘diversity’ and ‘mass ratio’ hypotheses, and our results most strongly support the mass ratio hypothesis, that is, the traits of the dominant species most influenced the ecosystem properties and processes examined. Our results suggest that the management of communities for the maintenance of ecosystem processes should focus on species dominance hierarchies.
Pekerja efektif dan kecekapan teknik firma pembuatan di Malaysia

Kualiti pekerja amat penting dalam meningkatkan kecekapan sesebuah organisasi. Pekerja yang berkualiti sering dikaitkan dengan kecekapan dan produktiviti yang tinggi yang akhirnya meningkatkan daya saing sesebuah organisasi dan sektor. Dalam konteks Malaysia, kecekapan teknik sektor pembuatan amat penting diteliti memandangkan sumbangannya yang sangat signifikan kepada Keluaran Dalam Negara Kasar (KDNK). Sektor ini juga merupakan pemacu guna tenaga yang pantas, malah, beberapa subsektor di dalamnya disenaraikan dalam Bidang Ekonomi Keutamaan Negara (NKEA). Kualiti pekerja boleh diukur melalui pelbagai kaedah yang secara umumnya bersandarkan kepada pencapaian modal manusia individu. Ukuran yang sering digunakan dalam literatur adalah seperti tingkat pencapaian pendidikan dan kategori pekerjaan. Namun, ukuran ini mengabaikan peranan upah yang menggambarkan produktiviti seseorang pekerja. Kebanyakan kajian lepas tidak mengukur kualiti pekerja secara komposit apabila melihat pengaruhnya terhadap kecekapan teknik. Artikel ini bertujuan menganalisis tahap kualiti pekerja secara komposit atau dikenal sebagai pekerja efektif dan meneliti pengaruhnya terhadap kecekapan teknik firma pembuatan di Malaysia. Analisis berdasarkan kepada data 1077 firma pembuatan yang disediakan oleh Jabatan Perangkaan Malaysia bagi tahun 2009 melalui Penyiasatan Industri Pembuatan 2010. Dapatan kajian ini menunjukkan tahap pekerja efektif dan kecekapan teknik firma pembuatan masih berada pada peringkat sederhana, malah, amat rendah bagi firma bersaiz mikro. Penentu ketakcekapan teknik yang penting adalah pekerja efektif, perbelanjaan teknologi maklumat dan komunikasi (ICT), perbelanjaan latihan dan perbelanjaan penyelidikan dan pembangunan (R&D). Implikasi daripada dapatan ini adalah firma pembuatan masih perlu meningkatkan pelaburan modal manusia pekerjanya serta meningkatkan perbelanjaan terutamanya dalam latihan pekerja dan R&D.
Growth interactions between raphidophytes chattonella antiqua and Heterosigma akashiwo

We investigated growth interactions between the raphidophytes Chattonella antiqua (Hada) Ono and Heterosigma akashiwo (Hada) Hada ex Hara et Chihara using bi-algal cultures under axenic conditions. The growth of C. antiqua and H. akashiwo each tended to be strongly suppressed when the other species reached early stationary phase. A mathematical model was used to simulate the growth interactions of C. antiqua and H. akashiwo in bi-algal cultures. The model showed that C. antiqua outcompetes H. akashiwo over time in bi-algal cultures under all experimental conditions. Furthermore, despite re-enrichment with nutrients, the filtrate from dense cultures of C. antiqua reduced the maximum growth rate of H. akashiwo and filtrate from dense cultures of H. akashiwo reduced both the maximum growth rate and maximum yield of C. antiqua.
Vulnerability to Agricultural Drought in Western Orissa: A Case Study of Representative Blocks §

The nature of vulnerability to agricultural drought in three study blocks of Bolangir district in western Orissa has been analysed. The indexing and vulnerability profile method have been used for assessing the nature of drought vulnerability, coping capacity and risk. The study has revealed that the three most influential biophysical factors of drought vulnerability are: rainfall variability, drought intensity and shortage of available waterholding capacity of soil and the three most influential socioeconomic factors are: low irrigation development, poor crop insurance coverage and smaller forest area. It is found that while drought risk varies widely across the study blocks and drought vulnerability and physical exposure to drought vary moderately, the coping capacity of study blocks differ marginally. However, the level of coping capacity has been found significantly lower than the level of drought risk and vulnerability in the study blocks.
Population Genetic Structure of Bromus tectorum in the American Desert Southwest

Population Genetic Structure of Bromus tectorum in the American Desert Southwest Desiree R. Lara Department of Plant and Wildlife Sciences, BYU Master of Science Following its introduction to North America in the late nineteenth century, Bromus tectorum L. , an inbreeding invasive winter annual grass, has become dominant on millions of hectares of sagebrush steppe habitat throughout Intermountain Western North America. It appears that within the last 30-40 years, B. tectorum has expanded its range southward into the Mojave Desert and also into more climatically extreme salt desert environments. Previous research using microsatellite markers and experimental studies has suggested that lineages found in desert habitats are genetically distinct from those found in the sagebrush-steppe habitat and possess suites of traits that pre-adapt them to these environments. To provide additional support for our hypothesis that desert habitat-specific haplotypes dominate and are widely distributed across warm and salt desert habitats, we genotyped approximately 20 individuals from each of 39 B. tectorum populations from these habitats and adjacent sagebrush steppe habitats using 71 single nucleotide polymorphic (SNP) markers. Our data clearly demonstrate that populations throughout the Mojave Desert region, as well as in salt desert habitats further north, are dominated by a small number of closely related SNP haplotypes that belong to the desert clade. In contrast, populations from adjacent environments are largely dominated by haplotypes of the common clade, which is widely distributed throughout the North American sagebrush steppe. Populations across all habitats were usually dominated by 1-2 SNP haplotypes. This suggests that inbreeding B. tectorum lineages can often maintain their genetic integrity. It also explains the strong association between marker fingerprints and suites of adaptive traits in this species.