Miracle-dz/UniFAR-FTUs huggingface dataset:
Translocation of 14C in ponderosa pine seedlings

The movement of 14C from the old needles to the roots, and later to the new needles, was measured in 2-year-old ponderosa pine seedlings. The seedlings were in one of three growth stages at the time of the feeding of 14CO2: 9 days before spring bud break with no root activity; 7 days before spring bud break with high root activity; and 7 days after spring bud break with moderate root activity. The form of the curves of count rate plotted against time are similar for a given plant part. Immediately after being fed 14CO2, year-old needles had high 14C count rates which dropped rapidly, leveled out within 7 to 10 days, and reached a steady state residual count rate after 10 to 20 days. The decrease in count rate from the old needles was followed by an increase in count rate by the root tip and (or) the new needles. The count rate of the root tips increased from background to a peak within 3 to 7 days, then decreased for the duration of the study. The details and timing of movement of 14C to and from plant pa.
Winter Resource Selection of Reintroduced Elk and Sympatric White-tailed Deer at Multiple Spatial Scales

Abstract Understanding limiting factors and interspecific interactions is fundamental to wildlife management and can be inferred from multiscale patterns of resource selection. We studied winter resource selection and overlap of white-tailed deer (Odocoileus virginianus) and translocated female elk (Cervus elaphus) over 2 winters in central Ontario, Canada. Microhabitat data were collected along 4 organism-centered spatial scales: site, trail, feeding station, and diet. Although winter conditions varied between years, white-tailed deer consistently traveled and fed in habitats with greater coniferous basal area than elk. Neither species demonstrated selection for coniferous basal area or snow depth across scales. At successively finer scales, female elk selected increased understory cover of trembling aspen (Populus tremuloides). For white-tailed deer, across-scale selection of sugar maple (Acer saccharum) understory cover was exhibited when winter conditions were more severe. Dietary overlap was moderate during both winters (50–57%) and coniferous forage was more important to deer than elk. Using canonical variate analysis, a gradient from shade-intolerant hardwoods to mature coniferous vegetation was found to discriminate significantly between elk and deer habitat use at trails and feeding stations. These results indicate that deer were closely associated with conifers regardless of winter conditions and that both ungulates may have been limited by forage abundance.
Carbapenem Susceptibility Testing Errors Using Three Automated Systems, Disk Diffusion, Etest, and Broth Microdilution and Carbapenem Resistance Genes in Isolates of Acinetobacter baumannii-calcoaceticus Complex

Carbapenem Susceptibility Testing Errors Using Three Automated Systems, Disk Diffusion, Etest, and Broth Microdilution and Carbapenem Resistance Genes in Isolates of Acinetobacter baumannii-calcoaceticus Complex Ana Elizabeth Markelz, Katrin Mende, Clinton K. Murray,* Xin Yu, Wendy C. Zera, Duane R. Hospenthal, Miriam L. Beckius, Tatjana Calvano, and Kevin S. Akers Brooke Army Medical Center, Fort Sam Houston, Texas, and Uniformed Services University of the Health Sciences and Infectious Disease Clinical Research Program, Bethesda, Maryland
Ubiquitins (polyubiquitin and ubiquitin extension protein) in marine sponges: cDNA sequence and phylogenetic analysis

The complete nucleotide sequences of twoSuberites domunculacDNAs and oneSycon raphanuscDNA, all encoding ubiquitin, have been determined. One cDNA fromS. domunculacodes for polyubiquitin with four tandemly repeated monomeric units and the second cDNA encodes ubiquitin fused to a ribosomal protein of 78 amino acids (aa). S. domunculapossesses at least one additional polyubiquitin gene, from which the last two monomers were also sequenced. All analysed genes fromS. domunculaencode identical ubiquitin proteins, with only one aa difference (Ala19) to the human/higher animals ubiquitin (Pro19). Ubiquitin inS. domunculais identical with the ubiquitin found in another Demospongia,Geodia cydonium. The cDNA fromS. raphanusencodes polyubiquitin with seven tandemly repeated units. All these gene monomers code for the same ubiquitin, which differs from the human/higher animals ubiquitin only at position 24 (Asp inSycon, Glu in others). However, ubiquitin fromS. raphanus(Calcarea) shows two aa differences (positions 19 and 24), when compared with the ubiquitin sequences from the two Demospongiae. In a phylogenetic tree constructed by multiple sequence alignment of all sponge ubiquitin gene monomers so far identified, all monomers from the same species cluster together, with the clear exception of the monomer fromS. domuncularibosomal protein fusion gene. This monomer branches off first from the tree and forms a separate line; this gives evidence for a very ancient split of ubiquitin-ribosomal-protein fusion genes from polyubiquitin encoding genes and their long separate coexistence in eukaryotes. The ubiquitin extension protein fromS. domunculais 78 aa long, displays all characteristics of 76–81 aa long ribosomal fusion proteins and shows 78% identity in the first 73 aa with the human S27a protein. However, its C-terminal sequence: 69-GLTYVYKKSD-78 is more similar to the plant consensus (69-GLTYVYQ/NK-76), than to the higher animal consensus (69-CLTYCFNK-76). This protein isolated from a sponge, belonging to the phylogenetically oldest multicellular animals, the Porifera, branches off first from the phylogenetic tree of metazoan ubiquitin extension proteins of the small ribosomal subunits.
Effect of iron limitation on cells of the diatom

The response of the Baltic diatom Cyclotella meneghiniana to iron deficiency was examined. The following growth parameters were measured: cell number, chlorophyll a and protein content. The results demonstrate the ability of this diatom to grow well with minimal iron availability; however, the rate of growth fell markedly at the lowest iron(III) concentration. The results of spectrophotometric chlorophyll a measurements and protein assays using the Lowry and Bradford methods indicated a significant decrease in their quantities. Iron may therefore be an important regulatory factor controlling the growth of diatom C. meneghiniana in an aquatic ecosystem.
Glucose deprivation regulates KATP channel trafficking via AMP-activated protein kinase (AMPK) in pancreatic β-cells Running Title : Regulation of KATP channel trafficking by AMPK

This is an uncopyedited electronic version of an article accepted for publication in Diabetes. The American Diabetes Association, publisher of Diabetes, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive publisher-authenticated version will be available in a future issue of Diabetes in print and online at http://diabetes.diabetesjournals. org. Diabetes Publish Ahead of Print, published online August 31, 2009
Analysis of the vaccine potential of nine MAP specific proteins, identified by immunoproteomics and in silico bio-informatic screening, in a murine model

OBJECTIVE Control of Mycobacterium avium subsp. paratuberculosis (MAP) is seriously hampered by the lack of adequate diagnostic tools, vaccines and therapies. In this study, we have evaluated the vaccine potential of nine MAP proteins: MAP3199, MAP2677c, MAP1693c, previously identified by immunoproteomic analysis of MAP secretome (Leroy et al., 2007) and Ag5, Ag6 (not-annotated), MAP1637c, MAP0388, MAP3743 and MAP3744 identified by bioinformatic in silico screening of the MAP genome.
The retinoblastoma gene family: its role in cancer onset and progression

In the recent past, a considerable amount of scientific literature has revealed impressive mechanisms that exist to safeguard development and homeostasis in high eukaryotes, and has identified a complex molecular machinery regulating proliferation, differentiation and cell death in mammalian cells. Alteration in at least two of these regulatory circuits is essential for transforming normal cells into malignant ones. During the second half of this century, research focused on the identification and characterisation of genes directly involved in malignant transformation and emphasised that tumourigenesis in humans is the result of a multi-step process reflecting genetic alterations, progressively pushing normal cells towards highly malignant derivatives. Because several human tumours involve loss of heterozygosity of tumour suppressor genes, it is now well accepted that mutations of these genes play a key role in malignant transformation. Current approaches in molecular research have aimed at developing more efficient therapies based on restoring the lost function of genes directly involved in malignant transformation. Since the retinoblastoma (RB) gene family, pRb/p105, pRb2/p130 and p107, has been shown to suppress neoplastic growth, these tumour suppressor genes offer an attractive therapeutic target for treating disorders involving cell growth. This review examines the functional regions of RB family members and the involvement of these genes in controlling cell cycle, apoptosis, differentiation and angiogenesis, highlighting the findings of in vitro and in vivo studies, and focusing on the role of RB proteins in tumourigenesis and in the design of potential approaches for gene therapy development.
Antifungal properties of lactic acid bacteria (LAB)isolated from Ricinus communis, Pentaclethramacrophylla and Yoghurts

The antifungal activity of lactic acid bacteria (LAB) isolates from Ricinus communis (Ogiri), Pentaclethra macrophylla (Ugba) and Yoghurt samples against moulds associated with food spoilage Aspergillus niger, Aspergillus flavus, Aspergillus fumigatus, Mucor, Penicillium, Rhizopus and Aspergillus nidulans was investigated using agar diffusion technique. Aspergillus fumigatus was the most susceptible with inhibition zone diameters ranging from 8mm for Lactococcus lactis to 20mm for positive control fluconazole. Pediococcus spp had no antifungal effect on any of the test fungi. None of the LAB isolates had good activity against Aspergillus flavus and Rhizopus spp. Aspergillus niger was inhibited only by Lactococcus lactis. The present study indicates that the LAB isolates if optimized and improved could be used as a natural, food-grade biopreservative agent for management of fungal contamination and food spoilage, thus preventing problems associated with mycotoxins in food and feed products. It is suggested that effective GMP and HACCP application in handling the affairs of food and feed storage/production will no doubt make the use of LAB as preservative a lot easier.
Differential Protective Efficacy of DNA Vaccines Expressing Secreted Proteins of Mycobacterium tuberculosis

ABSTRACT The development of more-effective antituberculosis vaccines would assist in the control of the global problem of infection withMycobacterium tuberculosis. One recently devised vaccination strategy is immunization with DNA plasmids encoding individual microbial genes. Using the genes for the M. tuberculosis secreted proteins MPT64 (23 kDa), Ag85B (30 kDa), and ESAT-6 (6 kDa) as candidate antigens, DNA vaccines were prepared and tested for immunogenicity and protective efficacy in a murine model of aerosolized tuberculosis (TB). Intramuscular immunization with DNA-64 or DNA-85B resulted in the activation of CD4+ T cells, which produce gamma interferon (IFN-γ), and high titers of specific immunoglobulin G antibodies. Further, DNA-64 induced major histocompatibility complex class I-restricted CD8+cytotoxic T cells. The addition of a eukaryotic leader sequence tompt64 did not significantly increase the T-cell or antibody response. Each of the three DNA vectors stimulated a significant reduction in the level of M. tuberculosis infection in the lungs of mice challenged 4 weeks after immunization, but not to the levels resulting after immunization with Mycobacterium bovis BCG. The vaccines showed a consistent hierarchy of protection, with the most effective being Ag85B, followed by ESAT-6 and then MPT64. Coimmunization with the three vectors resulted in a greater degree of protection than that induced by any single vector. This protective efficacy was associated with the emergence of IFN-γ-secreting T cells earlier than in infected animals immunized with a control vector. The efficacy of these DNA vaccines suggests that multisubunit vaccination may contribute to future vaccine strategies against TB.
Genetic variation and recent population history of the tropical gar Atractosteus tropicus Gill (Pisces: Lepisosteidae)

The tropical gar Atractosteus tropicus belongs to one of the few extant lineages of early bony fishes. The genetic variation detected both within and among 11 natural populations of A. tropicus in Mesoamerica along with the implications for their recent history are presented. Sequences from cytochrome b (307 bp) and cytochrome oxidase subunit II (607 bp) were used as data sources. Apparently, the populations of this fish have decreased in size because of anthropogenic pressures, such as habitat degradation and destruction. The observed values for nucleotide diversity (0� 0016 � 0� 0018) and haplotype diversity (0� 477 � 0� 302) suggest low levels of genetic variation. Nonetheless, most of the populations studied are currently in a period of genetic stasis. Recent isolation by distance, reduced gene flow and translocation were inferred as the processes maintaining this stasis. Phylogenetic analyses showed reciprocal monophyly between the haplotypes from Guatemala and the other populations. This, together with the observed genetic variation, suggests that the Guatemalan haplotypes might represent a new species. The haplotypes, other than those from Guatemala, exhibited a geographic pattern consistent with two main reproductive populations, one from the Pacific and the other from the Gulf of Mexico–Caribbean slope of Mesoamerica. Pleistocene glacial and interglacial periods might be responsible for moulding the heterogeneity in the genetic structure observed during this study.
Reinforced Cementitious Composites Developed Using a Novel

10 The present paper reports the first attempt of developing carbon nanotube (CNT) reinforced 11 cement composites through a short dispersion route using Pluronic F-127 as a novel 12 dispersing agent. Optimum concentrations of Pluronic for various types of CNT were 13 determined, and the influences of Pluronic and CNT on the microstructure and mechanical 14 properties of cementitious composites were thoroughly investigated. Pluronic with optimized 15 defoamer concentration significantly improved the bulk density and mechanical properties of 16 cement mortar. Further, dispersion of 0.1% single walled nanotube (SWNT) improved 17 flexural modulus of mortar by 72% and flexural and compressive strengths by 7% and 19%, 18 respectively after 28 days of hydration. Flexural and compressive strengths with 19 functionalized SWNT increased with the hydration period up to 17% and 23% after 56 days, 20 respectively. All CNT reinforced samples exhibited significantly higher stiffness, fracture 21 energy and ductility as compared to plain mortar and composite samples prepared using a 22 common surfactant. 23 24
Essential Role of β-Catenin in Postnatal Bone Acquisition*

Mutations in the Wnt co-receptor LRP5 alter bone mass in humans, but the mechanisms responsible for Wnts actions in bone are unclear. To investigate the role of the classical Wnt signaling pathway in osteogenesis, we generated mice lacking the β-catenin or adenomatous polyposis coli (Apc) genes in osteoblasts. Loss of β-catenin produced severe osteopenia with striking increases in osteoclasts, whereas constitutive activation of β-catenin in the conditional Apc mutants resulted in dramatically increased bone deposition and a disappearance of osteoclasts. In vitro, osteoblasts lacking the β-catenin gene exhibited impaired maturation and mineralization with elevated expression of the osteoclast differentiation factor, receptor activated by nuclear factor-κB ligand (RANKL), and diminished expression of the RANKL decoy receptor, osteoprotegerin. By contrast, Apc-deficient osteoblasts matured normally but demonstrated decreased expression of RANKL and increased osteoprotegerin. These findings suggest that Wnt/β-catenin signaling in osteoblasts coordinates postnatal bone acquisition by controlling the differentiation and activity of both osteoblasts and osteoclasts.
Association between Helicobacter pylori Virulence Factors and Gastroduodenal Diseases in Okinawa, Japan

ABSTRACT The incidence of gastric cancer in Okinawa is lowest in Japan. Some previous reports using small number of strains suggested that the high prevalence of Helicobacter pylori with Western-type cagA in Okinawa compared to other areas in Japan might contribute to the low incidence of gastric cancer. It has still not been confirmed why the prevalence of Western-type cagA strains is high in Okinawa. We examined the association between the virulence factors of H. pylori and gastroduodenal diseases in Okinawa. The genotypes of cagA and vacA of 337 H. pylori strains were determined by PCR and gene sequencing. The genealogy of these Western-type cagA strains in Okinawa was analyzed by multilocus sequence typing (MLST). Overall, 86.4% of the strains possessed cagA : 70.3% were East-Asian type and 16.0% were Western type. After adjustment by age and sex, the presence of East-Asian-type cagA / vacA s1m1 genotypes was significantly associated with gastric cancer compared to gastritis (odds ratio = 6.68, 95% confidence interval = 1.73 to 25.8). The structure of Western-type CagA in Okinawa was different from that of typical Western-type CagA found in Western countries. Intriguingly, MLST analysis revealed that the majority of Western-type cagA strains formed individual clusters but not hpEurope. Overall, low prevalence of gastric cancer in Okinawa may result from the high prevalence of non-East-Asian-type cagA strains. The origin of Western-type cagA strains in Okinawa may be different from those of Western countries.
A Location Analytics Method for the Utilization of Geo-tagged Photos in Travel Marketing Decision-Making, Journal of Information and Knowledge Management (

Location analytics offers statistical analysis of any geo-or spatial data concerning user location. Such analytics can produce useful insights into the attractions of interest to travelers or visitation patterns of a demographic group. Based on these insights, strategic decision-making by travel marketing agents, such as travel package design, may be improved. In this paper, we develop and evaluate an original method of location analytics to analyze travelers’ social media data for improving managerial decision support. The method proposes an architectural framework that combines emerging pattern data mining techniques with image processing to identify and process appropriate data content. The design artifact is evaluated through a focus group and a detailed case study of Australian outbound travelers. The proposed method is generic, and can be applied to other specific locations or demographics to provide analytical outcomes useful for strategic decision support.
Listeria monocytogenes -patogeenin tunnistusmenetelmiä elintarviketuotannossa

Food is an important source of microbes, such as bacteria and viruses that causes foodborne diseases. Particularly zoonotic bacteria, such as Campylobacter jejuni, Salmonella enterica, Listeria monocytogenes, Escherichia coli O157:H7 and other shiga-toxin producing E. coli –strains, and Vibrio spp. are the pathogens that have caused the majority of food borne diseases during the last twenty years. Microbial pathogen tests have an important role in assuring food safety in the food chain. However, traditional official methods are laborious and time-consuming. Therefore, immunology and molecular biology based rapid methods have been developed in order to get results quickly. Although the detection result is achieved in hours or even in minutes, pre-analytical sample processing is still needed to some extend. L. monocytogenes is a pathogen that is able to live and survive in different host animals and environments. It can cause a severe illness, called listeriosis which is among the four main food borne illnesses in Finland. L. monocytogenes can befound in uncooked and processed food that is contaminated during or after processing. The pathogen can tolerate a wide range of pH and salt content. Additionally, it can multiply in refrigerate temperature and in anaerobic and aerobic conditions. For these reasons, this challenging bacterium has to be monitored in the food chain. In this article, the analysis methods for L. monocytogenes are reviewed. In particular, the focus is in alternative rapid methods by which the results can be obtained in < 2 days and that have been tested with contaminated food items. Both officially validated tests and selected examples described in the literature will be presented. Additionally, the analysis methods used in food industry will be discussed briefly.
Molecular Cloning of a Trypanosoma cruzi Cell Surface Casein Kinase II Substrate, Tc-1, Involved in Cellular Infection

ABSTRACT In this work, we report the cloning and characterization of the first cell surface casein kinase II (CKII) substrate (Tc-1) of Trypanosoma cruzi, the causative agent of Chagas' disease. Analysis of the gene sequence revealed a 1,653-bp open reading frame coding for 550 amino acid residues. Northern blot analysis showed a 4.5-kb transcript that is expressed in invasive trypomastigotes but not in noninvasive epimastigote forms of T. cruzi. Southern blot analysis indicates that Tc-1 is a single-copy gene. At the amino acid level, Tc-1 displayed 95% and 99% identity to two hypothetical proteins recently reported by the T. cruzi genome project. Analysis of the translated amino acid sequence indicates that the Tc-1 gene has a putative transmembrane domain with multiple cytoplasmic and extracellular CKII phosphosites. Exogenous human CKII was able to phosphorylate serine residues on both recombinant Tc-1 and Tc-1 of intact trypomastigotes. This phosphorylation was inhibited by the CKII inhibitors heparin and 4,5,6,7,-tetrabromo-2-azabenzimidazole. Immunoblots of solubilized trypomastigotes, epimastigotes, and amastigotes probed with anti-recombinant Tc-1 immunoglobulin G revealed a 62-kDa protein that is expressed only in infective trypomastigotes. Immunoprecipitation of labeled surface proteins of trypomastigotes indicated that the 62-kDa protein is a surface protein, and we found that the protein is uniformly distributed on the surface of trypomastigotes by direct immunofluorescence. Antibodies to Tc-1 effectively blocked trypomastigote invasion of host cells and consequently reduced parasite load. Preincubation of either trypomastigotes or myoblasts with CKII inhibitors blocked T. cruzi infection. Thus, for the first time, we describe a cell surface CKII substrate of a protozoan parasite that is phosphorylated by human CKII and that is involved in cellular infection.
Epidermal Deletion of HIF-2a Stimulates Wound

Wound closure requires a complex series of micro-environmentally influenced events. A key aspect of wound closure is the migration of keratinocytes across the open wound. It has been found previously that the response to hypoxia via the HIF-1a transcription factor is a key feature of wound closure. The need for hypoxic response is likely due to interrupted wound vasculature, as well as infection, and in this work we investigated the need for a highly related hypoxic response transcription factor, HIF-2a. This factor was deleted tissue specifically in mice, and the resulting mice were found to have an accelerated rate of wound closure. This is correlated with a reduced bacterial load and inflammatory response in these mice. This indicates that manipulating or reducing the HIF-2a response in keratinocytes could be a useful means to accelerate wound healing and tissue repair.