Miracle-dz/UniFAR-FTUs huggingface dataset:
Candida rishirensis sp. nov., a novel methylotrophic anamorphic yeast species isolated from soil on Rishiri Island in Japan.

Since the fi rst report of methanol-assimilating yeast by Ogata et al. (1969), a number of methanol-assimilating yeast species were reported. The majority of these yeast species are distributed into three clades, the Ogataea, the Kuraishia and the Komagataella, in the phylogenetic trees constructed from nucleic acid sequences (Péter et al., 2008a). In addition, all of the anamorphic methylotrophic yeast species are now placed in the genus Candida, most of which are closely related to the three teleomorphic genera mentioned above. Among these Candida species, the phylogenetic position of Candida pignaliae is not clear. Nagatsuka et al. (2008) reported that all of described species of the genus Ogataea excluding Ogataea nitratoversa (Péter et al., 2008b), three Pichia species and those anamorphic Candida species formed a cluster, the Ogataea cluster, in neighbor-joining and maximum parsimony trees based on the D1/D2 sequences of large-subunit (LSU) rRNA genes, and O. nitratoversa was included in the Pichia methanolica cluster. In their tree, C. pignaliae does not show a close relationship to any known species. During the course of a study of biodiversity of yeasts on Rishiri-tou (Rishiri Island), a small island located in the Japan Sea, two methylotrophic yeast strains, Y07-901-4 and Y07-901-7, were isolated from soil in a pine forest on Mt. Pon, in July 2007, by enrichment culture in media consisting of malt extract (5%), glucose (3%), chloramphenicol (100 μg/ml) and tetracycline (100 μg/ml), with pH 3.7. The two strains are closely related to C. pignaliae in the D1/D2 sequences of LSU rRNA genes but clearly separated from this species by phenotypic or genetic properties. They are described as Candida rishirensis sp. nov. in the present paper. Most of the morphological, physiological, and biochemical characteristics were examined by the methods described by Yarrow (1998). The maximum growth temperature was determined in YM broth using metal block baths at 1°C intervals. The ubiquinone system was analyzed according to the method described by Mikata and Yamada (1999). Nuclear DNA was isolated and purifi ed according to Holm et al. (1986). The DNA base composition was determined by HPLC after enzymatic digestion of DNA to deoxyribonucleosides as described by Tamaoka and Komagata (1984) using a DNA-GC Kit (Yamasa Shoyu Co., Ltd., Chiba, Japan). J. Gen. Appl. Microbiol. , 56, 169‒173 (2010)
Accuracy enhancement of an indoor ANN-based fingerprinting location system using Kalman filtering

This paper presents an accuracy enhancement solution to mobilepsilas location and tracking systems in indoor wireless local area network (WLAN) environments. The enhancement method consists of the Kalman filtering application to an artificial neural network (ANN) based fingerprinting location technique. The application of Kalman filtering has the advantage of using information about the mobilepsilas motion to reduce location errors (caused by the WLAN received signal strength- RSS variations) and to avoid trajectory discontinuities (caused by the static estimation of the ANN-based fingerprinting technique). To process the RSS-based fingeprinting location technique, two ANN-based pattern-matching algorithms have been examined: the generalized regression neural network (GRNN) and the multi-layer perceptron (MLP) and they have been compared to the classic K-nearest neighbors (KNN) method. Experimental results, conducted in a specific in-building environment, showed that the GRNN algorithm performs better than the MLP and KNN algorithms. The application of Kalman filtering to the considered GRNN-based fingerprinting location technique improved the location accuracy of about 22.4 % in terms of location mean error.
Characterization of early assembly intermediates of recombinant human keratins.

The intermediate filaments (IFs) form major structural elements of the cytoskeleton. In vitro analyses of these fibrous proteins reveal very different assembly properties for the nuclear and cytoplasmic IF proteins. However, keratins in particular, the largest and most heterogenous group of cytoplasmic IF proteins, have been difficult to analyze due to their rapid assembly dynamics under the near-physiological conditions used for other IF proteins. We show here that keratins, like other cytoplasmic IF proteins, go through a stage of assembling into full-width soluble complexes, i.e., "unit-length filaments" (ULFs). In contrast to other IF proteins, however, longitudinal annealing of keratin ULFs into long filaments quasi-coincides with their formation. In vitro assembly of IF proteins into filaments can be initiated by an increase of the ionic strength and/or lowering of the pH of the assembly buffer. We now document that 23-mer peptides from the head domains of various IF proteins can induce filament formation even under conditions of low salt and high pH. This suggests that the "heads" are involved in the formation and longitudinal association of the ULFs. Using a Tris-buffering protocol that causes formation of soluble oligomers at pH 9, the epidermal keratins K5/14 form less regular filaments and less efficiently than the simple epithelial keratins K8/18. In sodium phosphate buffers (pH 7.5), however, K5/14 were able to form long partially unraveled filaments which compacted into extended, regular filaments upon addition of 20 mM KCl. Applying the same assembly regimen to mutant K14 R125H demonstrated that mutations causing a severe disease phenotype and morphological filament abnormalities can form long, regular filaments with surprising efficiency in vitro.
P-Selectin Contributes to Severe Experimental Malaria but Is Not Required for Leukocyte Adhesion to Brain Microvasculature

ABSTRACT Plasmodium berghei-infected mice, a well-recognized model of experimental cerebral malaria (ECM), exhibit many of the hallmarks of a systemic inflammatory response, with organ damage in brain, lung, and kidneys. Identification of the molecules mediating pathogenesis of the inflammatory response, such as leukocyte adhesion, may lead to new therapies. Indeed, mice lacking the cell adhesion molecule P-selectin were significantly (P = 0.005) protected from death due to P. berghei malaria compared with C57BL/6 controls despite similar parasitemia (P = 0.6) being found in both groups of mice. P-selectin levels assessed by the quantitative dual radiolabeled monoclonal antibody technique increased significantly (P < 0.05) in several organs in C57BL/6 mice infected with P. berghei, supporting the concept of a systemic inflammatory response mediating malarial pathogenesis. Intravital microscopic analysis of the brain microvasculature demonstrated significant (P < 0.001) leukocyte rolling and adhesion in brain venules of P. berghei-infected mice compared with those found in uninfected controls. The maximum leukocyte adhesion occurred on day 6 of P. berghei infection, when the mice become moribund and exhibit marked vascular leakage into the brain, lung, and heart. However, P-selectin levels were significantly (P < 0.005) increased in brain, lung, and kidneys during P. berghei malaria in ECM-resistant BALB/c mice compared with those found in uninfected BALB/c controls, indicating that increased P-selectin alone is not sufficient to mediate malarial pathogenesis. Leukocyte adhesion to brain microvessels of P-selectin-deficient mice with P. berghei malaria was similar to that observed in control mice. Collectively, these results indicate that P-selectin is important for the development of malarial pathogenesis but is not required for leukocyte adhesion in brain.
Perceived Work Stress and Major Depressive Episodes in a Population of Employed Canadians Over 18 Years Old

Departments of Psychiatry and Community Health Sciences, Faculty of Medicine, University of Calgary, Calgary, Canada. The research and data analysis were performed using data from Statistics Canada. However, the opinions and views expressed do not represent those of Statistics Canada. Send reprint requests to Dr. JianLi Wang, Department of Psychiatry, Peter Lougheed Centre, Room 3645, 3500-26 Ave. NE, Calgary, Alberta, Canada T1Y 6J4. Copyright © 2004 by Lippincott Williams & Wilkins DOI: 10.1097/01.nmd. 0000110242.97744. bc
Topographic representations of object size and relationships with numerosity reveal generalized quantity processing in human parietal cortex

Significance Processing of quantities such as object sizes and numbers relies on analyses of sensory information and informs cognitive tasks such as decision making and mathematics. Whereas sensory processing is organized into topographic maps reflecting sensory organ structure, organization of cognitive processing is poorly understood. We demonstrate topographic representation of object size-tuned responses. This arises separately from object number tuning, but these two quantities are associated in overlapping maps. This generalized quantity representation may allow us to consider object size and number together when making decisions. Optimization of cognitive processing using topographic maps may be a common organizing principle in association cortex, as it is in sensory processing. Linking cognitive representations in maps of related features may support increasingly abstract cognition. Humans and many animals analyze sensory information to estimate quantities that guide behavior and decisions. These quantities include numerosity (object number) and object size. Having recently demonstrated topographic maps of numerosity, we ask whether the brain also contains maps of object size. Using ultra-high-field (7T) functional MRI and population receptive field modeling, we describe tuned responses to visual object size in bilateral human posterior parietal cortex. Tuning follows linear Gaussian functions and shows surround suppression, and tuning width narrows with increasing preferred object size. Object size-tuned responses are organized in bilateral topographic maps, with similar cortical extents responding to large and small objects. These properties of object size tuning and map organization all differ from the numerosity representation, suggesting that object size and numerosity tuning result from distinct mechanisms. However, their maps largely overlap and object size preferences correlate with numerosity preferences, suggesting associated representations of these two quantities. Object size preferences here show no discernable relation to visual position preferences found in visuospatial receptive fields. As such, object size maps (much like numerosity maps) do not reflect sensory organ structure but instead emerge within the brain. We speculate that, as in sensory processing, optimization of cognitive processing using topographic maps may be a common organizing principle in association cortex. Interactions between object size and numerosity maps may associate cognitive representations of these related features, potentially allowing consideration of both quantities together when making decisions.
A feasibility study to investigate the clinical application of functional electrical stimulation (FES), for dropped foot, during the sub-acute phase of stroke – A randomized controlled trial

Purpose Functional electrical stimulation (FES), for dropped foot, has been shown to have positive benefits in chronic stroke. It has been suggested that similar benefits may be seen earlier after stroke. The aim of this feasibility study was to evaluate the trial methodology of undertaking a randomized controlled trial (RCT) of FES in sub-acute stroke. Method: This was a randomized feasibility study with non-blinded outcomes at 6 and 12 weeks. Sixteen sub-acute stroke in-patients with dropped foot were randomized into two groups (control, n = 7; intervention, n = 9). Both groups received routine gait re-education and an orthotic device, the control group used an ankle foot orthosis and the intervention group used FES. Outcome measures included gait velocity and cadence, Functional Ambulation Classification, Visual Analogue Scale of perception of walking, and the Stroke Impact Scale. Results: Eligibility criteria developed for inclusion of participants in the trial were appropriate. Set-up of FES during sub-acute stroke was feasible but more challenging than with chronic patients. Outcome measures were suitable and have informed the choice of measures for future work. Conclusions: It is feasible to undertake a trial evaluating FES during the sub-acute phase of recovery after stroke. A larger RCT is required.
Review of Recent Developments and Shortcomings in the Characterization of Potential Atmospheric Ice Nuclei: Focus on the Tropics

In this paper, we summarize the four main ice nucleating aerosol types: mineral dusts, bioaerosols, soot, and glassy organics, with the aim of demonstrating the limitations in scientific literature regarding their ice nucleation properties. Because the tropics are largely associated with marine environments, such as the Atlantic, Pacifi c, and Indian Oceans, they are potential source of ice nuclei, and therefore ice clouds can form in regions of high convective uplift. As a result, these particles are able to infl uence both the planet’s radiative force and its hydrological cycle. Due to our limited understanding of these effects, we would like to encourage the scientifi c community to increase its efforts to study and characterize the tropical aerosol particles that may function as ice nuclei. Through such efforts, we may reduce uncertainties in climate predictions, and improve our understanding of global warming in the hopes of fi nding potential solutions to these issues.
Detection and Removing Cross Site Scripting Vulnerability in PHP Web Application

Cross Site Scripting (XSS) vulnerability acts as one of the chief widespread security issues in web applications. By reviewing the literature pertaining to XSS vulnerability, it has been found that many investigations have directed their energy only on XSS vulnerability detection, but not many studies have concentrated on removing XSS vulnerability. This paper embed the removal stage of XSS vulnerability to our previous approach of detection XSS vulnerability, in a way to make the approach fully to detect and remove XSS vulnerability from PHP source code. We conducted two experiments to detect and remove Reflected and Stored XSS vulnerability. The results show that our approach is able to detect and remove XSS vulnerability in PHP source code. More research is required in the field of removing XSS vulnerability from the application source code before deployment.
The expression of genetic information: a study with hybrid animal cells.

When the nucleus of a hen erythrocyte is introduced into the cytoplasm of a human or mouse cell in culture, it resumes the synthesis of RNA. The reactivated erythrocyte nucleus undergoes great enlargement, but it does not, for at least 2 or 3 days, develop nucleoli which can be discerned under the light microscope. During this period, the heterokaryon, although it may contain several active erythrocyte nuclei, does not synthesize any hen-specific surface antigens; and the hen-specific antigens introduced into the surface of the heterokaryon by the process of cell fusion are eliminated. But when, later, the erythrocyte nuclei do develop nucleoli, hen-specific antigens reappear on the surface of the heterokaryon and progressively accumulate. Before developing nucleoli, the erythrocyte nuclei synthesize little, if any, normal 28 s or 16 s RNA; but they do synthesize large amounts of the RNA which shows polydisperse sedimentation in conventional sucrose density gradients. Autoradiographic studies involving the use of a microbeam of ultraviolet light show, however, that this ' polydisperse' RNA is not transferred to the cytoplasm of the cell in detectable amounts so long as the erythrocyte nucleus lacks a definitive nucleolus. The inability of the erythrocyte nucleus at this stage to determine the synthesis of hen-specific surface antigens is thus attributable to the fact that it fails to transfer the RNA made on its chromosomes to the cytoplasm of the cell. When the erythrocyte nuclei develop nucleoli, however, the RNA which they make is transferred to the cytoplasm of the cell, and the synthesis of hen-specific surface antigens then begins. These experiments suggest that the nucleolus may play a decisive role in the transfer of information from nucleus to cytoplasm. The possible nature of this role is discussed.
Nuclear localization of the functional Bel 1 transactivator but not of the gag proteins of the feline foamy virus.

Interactions between host cells and foamy or spumaretroviruses are different from those of other known retroviruses. Previous work has suggested that the Gag and high-affinity DNA-binding Bel 1 transactivator of human foamy virus are localized in the nuclei of infected cells. Using two independent detection methods, we show here that the functionally active Bel 1 transactivator protein of feline foamy virus is of nuclear localization. In contrast to that reported for the human foamy virus Gag protein, the cat foamy virus Gag proteins exclusively localized in the cytoplasm close to perinuclear regions.
Increasing Data Resilience of Mobile Devices with a Collaborative Backup Service

Whoever has had his cell phone stolen knows how frustrating it is to be unable to get his contact list back. To avoid data loss when losing or destroying a mobile device like a PDA or a cell phone, data is usually backed-up to a fixed station. However, in the time between the last backup and the failure, important data can have been produced and then lost. To handle this issue, we propose a transparent collaborative backup system. Indeed, by saving data on other mobile devices between two connections to a global infrastructure, we can resist to such scenarios. In this paper, after a general description of such a system, we present a way to replicate data on mobile devices to attain a prerequired resilience for the backup.
Aminolevulinate synthase: functionally important residues at a glycine loop, a putative pyridoxal phosphate cofactor-binding site.

5-Aminolevulinate synthase catalyzes the first step of the heme biosynthetic pathway in nonplant higher eukaryotes. The enzyme functions as a homodimer and requires pyridoxal 5'-phosphate as its cofactor. Lysine-313 in murine erythroid aminolevulinate synthase has been identified as the residue involved in the Schiff base linkage with pyridoxal 5'-phosphate [Ferreira, G. C. , Neame, P. J., & Dailey, H. A. (1993) Protein Sci. 2, 1959-1965]. However, other residues involved in binding and orienting the cofactor remain unknown. We studied the informational content of each residue within an 11 amino acid glycine-rich region, which we propose to be part of the phosphate-binding motif, based on amino acid sequence comparison with other pyridoxal 5'-phosphate-dependent enzymes and nucleotide-binding proteins. Partial random mutagenesis of this region in murine erythroid aminolevulinate synthase gene was followed by an efficient biological selection, using a hemA- Escherichia coli strain to recover functional unnatural enzymes. Among the total of 5444 variants produced, 283 were found to be functional. DNA sequencing results of 226 functional mutants indicated that most residues in this region contained a low informational content, being able to tolerate several other amino acid substitutions. However, three residues, namely, Arg-149, Gly-142, and Gly-144, were found to contain high informational content; Arg-149 was conserved in all of the functional mutants sequenced, while Gly-142 and Gly-144 could only tolerate alanine replacement. Two codon-specific random libraries of Arg-149, and Gly-142 and -144, respectively, were constructed to test further the stringency of these three positions. (ABSTRACT TRUNCATED AT 250 WORDS)
Exploring the genetics underlying autoimmune diseases with network analysis and link prediction

Ever since the first Genome Wide Association Study (GWAS) was carried out we have seen an important number of discoveries of biological and clinical relevance. However, there are some scientists that consider that these research outcomes and their utility are far from what was expected from this experimental design. We instead believe that the thousands of genetic variants associated with complex disorders by means of GWASs are an extremely valuable source of information that needs to be mined in a different way. Based on this philosophy, we followed a holistic perspective to analyze GWAS data and explored the structural properties of the network representation of one of these datasets with the aim to advance our understanding of the genetic intricacies underlying autoimmune human diseases. The simplicity, computational efficiency and precision of the tools proposed in this paper represent a new means to address GWAS data and contribute to the better exploitation of these rich sources of information.
Metabolic differentiation in actively swarming Salmonella

Most current paradigms of microbial metabolism have been derived from studying cells grown under a variety of nutrient compositions in aqueous environments. With recent advances in genomics and experimental techniques, alternative forms of bacterial growth are increasingly being explored. When propagated on nutrient‐rich semi‐solid media, several species of bacteria undergo a morphological differentiation into swarmers that are capable of migrating on surfaces. Recent studies indicate that swarmer differentiation represents much more than a motility phenotype, as several clinically important attributes are also co‐regulated. We demonstrate that migrating swarmer cells of Salmonella are metabolically differentiated compared to the vegetative swimmer cells grown in the same nutrient environment. Furthermore, once the cells have differentiated, the swarmers remain in this physiological state under conditions that do not promote the initial differentiation. The bacterium's capacity to override some of the classic paradigms of metabolic regulation established in aqueous environments represents a unique physiological response by the pathogen that may be advantageous in polymicrobial environments such as the host.
Complete Genome Sequence and Comparative Genomics of a Streptococcus pyogenes emm3 Strain M3-b isolated from a Japanese Patient with Streptococcal Toxic Shock Syndrome

Epidemiologic typing of Streptococcus pyogenes (GAS) is frequently based on the genotype of the emm gene, which encodes M/Emm protein. In this study, the complete genome sequence of GAS emm3 strain M3-b, isolated from a patient with streptococcal toxic shock syndrome (STSS), was determined. This strain exhibited 99% identity with other complete genome sequences of emm3 strains MGAS315, SSI-1, and STAB902. The complete genomes of five additional strains isolated from Japanese patients with and without STSS were also sequences. Maximum-likelihood phylogenetic analysis showed that strains M3-b, M3-e, and SSI-1, all which were isolated from STSS patients, were relatively close.
Dostępność przestrzenna do usług publicznych w Polsce = Spatial accessibility to public services in Poland

PL ISSN 0373-6547 ISBN 978-83-61590-82-8 Zapewnienie odpowiedniej dostępności do usług publicznych jest jednym z podstawowych zobowiązań państwa względem ich obywateli. Współcześnie, istotnym problemem społecznym jest nie tyle brak zasobów, co raczej brak dostępu do tych zasobów, przy czym usługi publiczne mogą być traktowane jako jeden z rodzajów zasobów. Dostępność do usług publicznych należy zatem traktować jako kluczowe zagadnienie warunkujące jakość życia, stanowiące istotny czynnik determinujący nierówności społeczno-przestrzenne.