Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analyses for selecting effective siRNA sequences

Because the short interfering RNA (siRNA) widely used for studying gene functions in mammalian cells varies markedly in its gene-silencing efficacy, several siRNA design rules/guidelines have been reported recently. Analyzing the reported siRNA design guidelines from qualitative and quantitative points of views, we found that they were not always effective selection rules for many other mammalian genes. Though some rules from the guidelines are suitable for extracting effective sequences for specific genes, they might sometimes be unsuitable for selecting sequences for other genes. Since the gene-silencing efficacy depends very much on the target sequence positions selected from the target gene, we examined 860 effective siRNA sequences from 503 different mammalian cDNAs in the literature. As a result, we got many preferred and unpreferred nucleotides different from the ones used in the previous guidelines. These sequence-dependent nucleotides could be used as a more general guideline for selecting new siRNA sequences in target genes. We proposed a measure (score) for selecting effective siRNA candidates based on the positional features of specific significant nucleotides and demonstrated the effectiveness of the proposed measure compared with the recently reported other selection methods. In this paper we also discussed the elimination of ineffective siRNA sequences from target candidates and optimal GC content in siRNA sequences.
HARMONI MASYARAKAT SATU DESA TIGA AGAMA DI DESA PABIAN, KECAMATAN KOTA, KABUPATEN SUMENEP, MADURA

Tolerance and harmony has always been the basis for a society with religious diversity; this is especially true because religion is a way of life or a divine source of justice, truth and moral values. As a result, humans will always refer to and require religion. The community of Pabian village, Kalianget Sub Regency, Sumenep is a village located on the Eastern end of Madura Island with high levels of religious plurality. It is marked by the presence of three types of places of worship, including mosques, temples and churches. These places of worship are located very closely in distance, without conflict between the followers of each respective religions. The people visit each other, have social dialogues and participate in social activities together, resulting in a portrait of a religiously harmonious society throughout the history of the community.
Soil and Crop Parameters Related to Corn Nitrogen Response in Eastern Canada

Information regarding the relationships between soil properties and the economic optimum N rate for crop yield is needed to ensure profitable use ofN fertilizer. This study was conducted in 2007 and 2008 at 62 field sites in Qebec (eastern Canada) to assess corn (Zea mays L.) response to N fertilizer, to calculate the economically optimum nitrogen rate (EONR) and corn yield (EOY), and to relate these two parameters with soil and crop-based parameters. Yield response to N fertilizer rates (0-250 kg N ha ―1 ) at each site was fitted to a linear, quadratic, or quadratic-plus-plateau model. The EONR and yield (EOY) were related to 12 soil and crop-based parameters, and corn heat units (CHU). The quadratic-plus-plateau model best described the yield-fertilizer relationship at 43 of the 62 field sites. The values of EOY varied from 7.4 to 13.3 Mg ha ―1 in 2007 and from 5.2 to 11.2 Mg ha ―1 in 2008, while EONR was between 73 and 235 kg N ha ―1 in 2007 and from 48 to 200 kg N ha ―1 in 2008. Correlation and principal component analysis showed that dissolved nitrogen (DNc) and dissolved carbon (DOCc) extracted with cold water and pre-sidedress nitrate analyzed using nitrate test strips (PSNTts) were significantly and negatively related to EONR. In both years, PSNTts was consistently related to EONR, and CHU with EOY. While it remains challenging to predict EONR due to site-specific variability and fluctuations in growing conditions, the PSNTts test shows promise in predicting the EONR for corn production in Quebec.
Métodos para a estimativa do potencial de rendimento da soja durante a ontogenia

O objetivo deste trabalho foi estudar metodos para a estimativa do potencial de rendimento da soja durante a ontogenia. Os experimentos foram realizados em Eldorado do Sul, RS, durante as safras de 1996/1997, 1999/2000 e 2000/2001. Os tratamentos constaram de cinco cultivares de soja, FT-Saray, IAS 5, IAS 4, FT-Abyara e FEPAGRO RS-10. Cinco metodos foram utilizados para estimar o rendimento que seria obtido se todas as estruturas reprodutivas presentes no florescimento e no inicio do enchimento de graos, produzissem graos na maturacao. O potencial de rendimento no florescimento e no enchimento de graos, apresentou alta correlacao com o numero de flores e estruturas reprodutivas, respectivamente. Verificou-se, tambem, correspondencia entre os metodos. Nao houve, na maioria das vezes, correlacoes significativas entre o potencial, no florescimento e enchimento de graos, e o rendimento de graos na maturacao. Os metodos estudados constituem ferramentas importantes para o manejo, quando utilizados para comparar o potencial de rendimento durante a ontogenia.
Sharks of the Order Carcharhiniformes

This book is a general review, taxonomic revision, and phylogenetic analysis of the carcharhinoids, the largest group of living sharks, which comprises almost 60 percent or 200 of known shark species. Students of shark biology have been hampered by the lack of just such a comprehensive and rigorous account of shark morphology. With this work L.J.V. Compagno offers not only the most comprehensive and detailed account of this important but neglected group to date but also one of the most comprehensive modern anatomical and phylogenetic studies on cartilaginous fishes available. It will become an essential reference not only for researchers on carcharhinoids but also for those who study other families of sharks and for paleontologists interested in this ancient group of fishes. The book begins with a general account of carcharhinoid sharks. Chapters Two through Eleven include detailed discussions of character systems used in taxonomic and phylogenetic analysis of carcharhinoids. Chapter Twelve defines the Order Carcharhiniformes, lists its families, and includes a taxonomic key to the families. Chapters Thirteen through Twenty review the eight carcharhinoid families, and Chapter Twenty-One is an extended discussion of the phylogeny of carcharhinoids, with cladistic analysis of taxa at various levels.
Conceptual metaphor, human-computer interaction and music : applying conceptual metaphor to the design and analysis of music interactions

Interaction design for domains that involve complex abstractions can present significant challenges. This problem is particularly acute in domains where users lack effective means to conceptualise and articulate relevant abstractions. In this thesis, we investigate the use of domain-specific conceptual metaphors to address the challenge of presenting complex abstractions, using tonal harmony as an extended case study. This thesis presents a methodology for applying domain-specific conceptual metaphors to interactions designs for music. This domain involves complex abstractions where users with any degree of domain knowledge may have difficulty in articulating concepts. The methodology comprises several parts. Firstly, the thesis explores methods for systematically guiding conversation between musicians to elicit speech that describes music using conceptual metaphors. Recommendations for the most suitable methods are made. Secondly, the thesis presents a methodology for identifying image schemas and conceptual metaphors from transcriptions of conversations between musicians. The methodology covers rules for identifying source image schemas and extrapolating conceptual metaphors. Thirdly, the thesis presents a methodology for evaluating existing music interaction designs using domain-specific conceptual metaphors. We demonstrate that this approach can be used to identify potential areas for improvement as well as tensions in the design between certain tasks or abstractions. Fourthly, the thesis presents a case study for the development of a conceptual metaphor-influenced design process. In the case study, a set of materials are developed to be used by participants in the design process to facilitate the mapping of conceptual metaphors to elements of an interaction design without requiring knowledge of Conceptual Metaphor Theory. Finally, a pilot study is presented integrating the results of the conceptual metaphor-influenced design process into a consistent and useful prototype system. Compromises and refinements to the design proposals made during the design process are discussed and the resulting system design is detailed.
Secondary production of invertebrates in a Central European mountain stream (Steina, Black Forest, Germany)

We estimated macroinvertebrate production in the Central European mountain stream Steina over 3 years from November 1985 to October 1988 applying the increment-summation method and additional P/B ratios from literature. Total production differed little between the three study years, amounting to 19.0 (1986), 19.7 (1987) and 20.8 g m -2 y -1 (1988). Ephemeroptera, Trichoptera and Diptera contributed most to total invertebrate production. Whereas the production of Tricladida, Oligochaeta, Acari, Crustacea, and Coleoptera remained more or less stable over the three study years, it showed in part distinct trends or between-year variation in the three most dominant orders. Mayfly production increased from 4.7 to 7.2 g m -2 y -1 and stonefly production from 1.8 to 2.3 g m -2 y -1 . Caddisfly production showed a decreasing tendency from 1986 (6.8 gm -2 y -1 ) to 1988 (4.0 g m -2 y -1 ). Marked differences, increasing or decreasing values, occurred at some species level. Secondary production of all primary consumers in the Steina was 16.7 (1986, 1987) and 17.9 (1988) g m -2 y -1 over the three-year time span. Production of secondary consumers (predators) amounted to 2.3-3.0 g m -2 y -1 of total production, and was 2.7 g m -2 y -1 on average. Analysis of the portions of functional groups revealed that suspension feeders and predators accounted for only 12.8-17.8 % of total production, whereas the relative contribution of scrapers was about 24 % in 1986 and 1987, and even reached 38 % in 1988. Production of shredders and deposit feeders reached the same order of magnitude as scrapers, particularly in 1986. However, there was a decreasing tendency in production of shredders and deposit feeders and an increasing tendency in production of scrapers and suspension feeders towards the 3rd year.
Predation by cormorants, Phalacrocorax carbo (L.), on the salmonid populations of an Irish river

Counts were made of cormorants, Phalacrocorax carbo (L.), feeding on the River Bush. County Antrim. Northern Ireland during the post-dawn period on three occasions. Two of the counts during May 1986 indicated that up to 264 birds may have been feeding at least once per day throughout the catchment during the salmon, Salmo salar L. , smolt run. The number of feeding birds had dropped to an estimated 61 by the time of the third count on 1 July 1986. Stomach samples from shot birds showed that upstream feeding was concentrated on wild smolts and brown trout. Salmo trutta L. However, cormorant predalion downstream from the salmon hatchery at Bushmills was restricted solely to hatchery smolts. Estimates of the total daily predation rates were calculated at 653–1214 wild smolts. 107–231 hatchery smolts and 422–785 brown trout. The possible impact of this level of predation on the salmonid stocks of the river was assessed.
Homocysteine Inhibits TNF-α-Induced Endothelial Adhesion Molecule Expression and Monocyte Adhesion via Nuclear Factor-κB Dependent Pathway

Abstract Cellular adhesion molecules play a pivotal role in the pathogenesis of atherosclerosis by mediating the adherence of blood leukocytes. Since hyperhomocysteinemia appears to be an independent risk factor for the development of atherosclerosis, in this study we investigated the effect of homocysteine on basal and TNF-α-induced expression of intercellular adhesion molecule-1 (ICAM-1), vascular cell-adhesion molecule-1 (VCAM-1), and endothelial leukocyte adhesion molecule-1 (E-selectin) on human umbilical-vein endothelial cells. Incubation of endothelial cells with homocysteine resulted in dose-dependent reduction in TNF-α-induced (5 ng/ml) expression of VCAM-1, E-selectin, and ICAM-1 (the latter less pronounced). This effect was found to be specific since other thiol compounds—cysteine and glutathione—did not mimic homocysteine activity. Homocysteine attenuated TNF-α-stimulated U-937 adhesion to the endothelial monolayer and reduced TNF-α-induced activation of the transcription factor NF-κB, indicating that NF-κB inhibition may play a role in inhibiting expression of adhesion molecules in endothelial cells.
Economic Importance and Growth Rate of Broiler Chickens Fed with Water Leaf ( Talinum triangulare ) Meal Supplements

An 8-week experiment was conducted to assess the weight gain and the economic importance of broiler chickens fed with Water Leaf Meal Supplements (WLM). One hundred and fifty day-old Anak 2000 broiler chicks were randomly distributed to 5 treatments which contained 0, 3, 6, 9 and 12% of WLM for A, B, C, D and E, respectively, in a completely randomized design. Each treatment was
Seasonal life‐history models for the integrated management of the invasive weed nodding thistle Carduus nutans in Australia

Summary 1 It is widely accepted that combining several control options into integrated pest management strategies is the most effective way to provide long-term suppression of pest populations. However, full factorial field trials of all single and integrated control options for a pest species would be prohibitively expensive and time consuming. Methods to allow triage of the huge array of management options would be of great value in streamlining the decision-making process. 2 We present a seasonally structured, individual-based model, specifically designed to compare and rank detailed management strategies for a noxious pasture weed. The model structure is determined in part by the demographic data available, and in part by the management options under consideration. The case study is for nodding thistle Carduus nutans in Australia. Eight years of demographic data, for more than 8000 mapped plants, were used to parameterize the model, which is age-, size- and density-dependent and incorporates individual variation. Management options for this plant include three biocontrol agents, as well as conventional herbicide and grazing management strategies, which can be used alone or in a variety of combinations. Data on management impacts were drawn from multiple studies. 3 The model predicts that the root-crown weevil Trichosirocalus mortadelo will more effectively suppress weed populations than either of the two flowerhead-feeding insect agents Urophora solstitialis and Rhinocyllus conicus. Crash grazing (up to four times the regular grazing pressure) in any single season, or when most effectively applied across spring and summer, is less effective than T. mortadelo, while combinations of crash grazing and biocontrol agents strongly decrease weed population persistence. However, lethal herbicide is the best single strategy, while spring spray–grazing (a combination of non-lethal herbicide and grazing) is the best integrated weed management strategy. 4 Synthesis and applications. The model is structured by, and serves to integrate, available information on demography and management from multiple sources. The subset of strategies that performed well forms the focus for fewer, more thorough, field trials. The decision-making approach illustrated here is also applicable to any species and any array of management options.
Hb COLIMA [β49(CD8)Ser→Cys]: A NEW HEMOGLOBIN VARIANT

Hb Colima was found in a 52-year-old Mexican Mestizo female, who was born in Colima, Mexico. This variant was observed during a population screening for the main hemoglobinopathies in the state of Colima, performed at the Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico. The hematological data of the proband, obtained by an electronic ABX-VEGA counter, were as follows: RBC 4.29610=L, Hb 13.6 g=dL, MCV 96.9 fL, MCH 32.0 pg, RDW 13.3%, and the reticulocyte count was normal. Biochemical analysis was done by conventional methods: Hb F 1.1%, Hb A2 3.4%, and Hb X 29.3%, that migrated faster than Hb A and Hb Fannin-Lubbock on cellulose acetate electrophoresis at pH 8.6. Hb X was quantified by DEAE cellulose chromatography of the stored hemolysate (at 15 C for two weeks). The isopropanol and butanol stability tests were normal. Isoelectrofocusing (IEF) was performed on a PhastSystem using PhastGel (Amersham Biosciences, Piscataway, NJ, USA) IEF media 5–8, and showed an X band that focused towards the anode from Hb A. DNA was extracted from the buffy coat by the salting-out method. Direct DNA sequencing of the b-globin gene showed a C! G substitution at codon 49 (Fig. 1), that results in the replacement of the serine residue by a cysteine in the b-globin chain. The entire b-globin gene was sequenced by ABI PRISM BigDye Terminator chemistry on an Applied BioSystems 3100 sequencer (Applied BioSystems, Foster City, CA, USA). The heterozygosity for the C! G
An assessment of the modifying effect of kinetin on in vitro tuberization of induced and non-induced tissues of Solatium tuberosum

‘Katahdin’ potato plants (Solatium tuberosum L.) were grown under inducing (26 °C day −12 °C night with an 8-h photoperiod) and non-inducing (28 °C day −25 °C night with a 16-h photoperiod) conditions. Apical, medial, and basal nodal stem segments from each plant harvested were surface sterilized and aseptically transferred to culture flasks containing Murashige and Skoog's medium with and without kinetin. After culturing in dark for 4 weeks at 24 °C, percentage tuberization of segments from induced plants was significantly greater than for non-induced segments. Addition of kinetin to the culture medium eliminated this effect of induction. Apical segments from induced plants tuberized more frequently than those from non-induced plants and those from lower on stem. Addition of kinetin eliminated this stem position effect. Percentage elongation was significantly greater in segments from non-induced than induced plants. Addition of kinetin reduced percentage elongation in non-induced segments to that for ind.
Distribution and Diversity of Oligochaetes in Selected Ponds of Thiruvananthapuram District, Kerala, South India

The present study was carried out to evaluate the distribution and diversity of oligochaete fauna in selected ponds of Thiruvananthapuram district in Kerala, South India. The sediment samples were collected from three ponds seasonally during the period December 2006 to November 2008. In the study, 10 oligochaete species which belong to 8 genera were identified in three selected ponds. These include Dero digitata, Dero nivea, Dero obtusa, Pristina longiseta, Aulophorus furcatus, Stylaria fossularis, Chaetogaster spp. , Aeolosoma spp. , Tubifex tubifex and Limnodrilus hoffmeisteri. Tubifex tubifex and Limnodrilus hoffmeisteri are the pollution-indicator oligochaete species identified in the fresh water ponds, which reveals that the studied ponds are subjected to pollution.
Squamosal Ontogeny and Variation in the Pachycephalosaurian Dinosaur Stegoceras validum Lambe, 1902, from the Dinosaur Park Formation, Alberta

ABSTRACT The pachycephalosaurian squamosal is one of the most diagnostic bones in this enigmatic group of dinosaurs, but little is known about variation in its morphology. Despite this, features of squamosal morphology are often used in diagnoses and phylogenetic studies. The recently proposed hypothesis of an ontogenetic transition from Dracorex to Pachycephalosaurus implies a large amount of ontogenetic variation in squamosal ornamentation that has not been well documented due to the small number of squamosals for these taxa. Stegoceras validum provides an important model for examining variation in squamosal morphology due to the large number of squamosals available. Here we examine the morphology of 14 S. validum squamosals both qualitatively and quantitatively. We find that although both node number and shape vary considerably, there is no clear ontogenetic pattern, which suggests a high degree of individual variation. The ornamental pattern, however, is maintained throughout the sample. Increase in node size is isometric for the enlarged medial node and normal posterior nodes, but negatively allometric for the vertex node. The squamosal bar is taller laterally than medially in nearly all specimens and increases in height with positive allometry at the same rate medially and laterally. We found no correlation between the width of the supratemporal fenestra on the squamosal and the size of the squamosal itself. Rather, this feature appears to exhibit a large degree of individual variation. Overall, these findings have implications for previous hypotheses of ontogenetic growth and function of the ornamentation, as well as the construction of phylogenetic characters.
Inheritance of Russian Wheat Aphid Resistance in Spring Barley Germplasm Line STARS‐9577B

The Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko), has become a major pest of barley (Hordeum vulgare L.) in the western USA. STARS-9577B (PI 591617), a six-rowed, spring barley germplasm line with a high level of resistance to RWA, was recently released to barley breeders for barley improvement. Understanding the inheritance of RWA resistance in this germplasm line is necessary for breeders to develop an effective strategy for utilization of this germplasm in their breeding programs. This greenhouse study was conducted to determine the genetic control of RWA resistance in STARS-9577B. Crosses were made between 'Morex', a susceptible, six-rowed, malting barley cultivar, and STARS-9577B. Genetic analyses were performed on reaction to RWA of parents, F 1 , reciprocal F 1 , F 2 , backcrosses (BC 1 F 1 ) to both parents, and F 2 -derived F 3 families. Reaction was based on a visual rating scale of 1 to 9 (1 = no damage, 9 = dead plant). Segregation in the F 2 and BC 1 F 1 populations indicated multiple gene control. Seventy-seven F 3 families were found to be homozygous resistant and 18 homozygous susceptible, indicating two gene control of RWA resistance in STARS-9577B. Analysis of data from F 2 and BC 1 F 1 populations suggested RWA resistance in STARS-9577B is controlled by dominant alleles at two loci, with alleles at one locus conferring a high level of resistance and alleles at the other locus conferring an intermediate level of resistance only when recessive alleles are present at the first locus.
‘Candidatus Phytoplasma pini’ affecting Taxodium distichum var. imbricarium in China

Suspected phytoplasma symptoms were observed in Taxodium distichum var. imbricarium at the Nanyang Normal University campus, Nanyang City, Henan, China. The major symptoms consisted of little necrotic leaves, abnormal proliferation of twigs and overall necrotic appearance of the whole tree. Nested PCR was performed to confirm the association of phytoplasmas with symptomatic T. distichum var. imbricarium. PCR amplification using universal phytoplasma primers P1/P7 followed by R16F2n/R2, amplifying 16S ribosomal gene, yielded positive results. Amplified products were cloned and sequenced. Blast analysis showed 99% sequence identity with several ‘Candidatus phytoplasma pini’. Phylogenetic analysis confirmed the close relationship of the phytoplasma from T. distichum var. imbricarium with ‘Ca. P. pini’ belonging to 16SrXXI group. Hence this is the first report of association of ‘Ca. P. pini’ with a disease of T. distichum var. imbricarium tree in China.