Miracle-dz/UniFAR-FTUs huggingface dataset:
Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme

The action of novobiocin and coumermycin (two coumarins which interact with the gyrB subunit of eubacterial DNA gyrase) and ciprofloxacin (a fluoroquinolone which interacts with the gyrA subunit of DNA gyrase) was tested on several archaebacteria, including five methanogens, two halobacteria, and a thermoacidophile. Most strains were sensitive to doses of coumarins (0.02 to 10 micrograms/ml) which specifically inhibit DNA gyrase in eubacteria. Ciprofloxacin inhibited growth of the haloalkaliphilic strain Natronobacterium gregoryi and of the methanogen Methanosarcina barkeri. In addition, ciprofloxacin partly relieved the sensitivity to coumarins (and vice versa). Novobiocin inhibited DNA replication in Halobacterium halobium rapidly and specifically. Topological analysis has shown that the 1.7-kilobase plasmid from Halobacterium sp. strain GRB is negatively supercoiled; this plasmid was relaxed after novobiocin treatment. These results support the existence in archaebacteria of a coumarin and quinolone target related to eubacterial DNA gyrase.
Shear strain localization in elastodynamic rupture simulations

We study strain localization as an enhanced velocity weakening mechanism on earthquake faults. Fault friction is modeled using Shear Transformation Zone (STZ) Theory, a microscopic physical model for non‐affine rearrangements in granular fault gouge. STZ Theory is implemented in spring slider and dynamic rupture models of faults. We compare dynamic shear localization to deformation that is uniform throughout the gouge layer, and find that localized slip enhances the velocity weakening of the gouge. Localized elastodynamic ruptures have larger stress drops and higher peak slip rates than ruptures with homogeneous strain.
Predicting costs with diabetes complications severity index in claims data.

OBJECTIVES To test the usefulness of the Diabetes Complications Severity Index (DCSI) without laboratory test results in predicting healthcare costs, for potential use in disease management programs. STUDY DESIGN Retrospective cohort study using up to 2 years of claims data from 7 health insurance plans. METHODS Individuals with diabetes mellitus and continuous enrollment were study subjects. The DCSI (sum of 7 diabetes complications graded by severity as 0, 1, or 2; range 0-13) and count of diabetes complications (sum of 7 diabetes complications without severity grading; range 0-7) were the main independent variables and were generated using only diagnostic codes. We analyzed 5 types of healthcare costs (ie, total costs, inpatient costs, hospital other costs, pharmacy costs, and professional costs) attributable to the DCSI and the complication count with linear regression models, both concurrently and prospectively. RESULTS The DCSI without laboratory data was a better predictor of costs than was complication count (adjusted R2 of total costs: 0.095 vs 0.080). The DCSI explained concurrent costs better than future costs (adjusted R2 of total costs: 0.095 vs 0.019). There were important differences in healthcare utilization among people stratifi ed by DCSI scores: 5-fold and 3-fold differences in concurrent and prospective total costs, respectively, across 4 DCSI groups. CONCLUSIONS The DCSI without laboratory data may be useful for stratifying individuals with diabetes into morbidity groups, which can be used for selection into disease management programs or for matching in observational research.
CORTISOL METABOLISM AFTER ORAL CONTRACEPTIVES: TOTAL PLASMA CORTISOL AND THE FREE CORTISOL INDEX

Plasma concentrations of cortisol, cortisol resin uptake ratio (cortisol RUR) and free cortisol index (FCI) were measured in women taking combined oestrogen/progestogen and progestogen only oral contraceptives. Compared to control subjects, women taking the combined pill had elevated cortisol and cortisol RUR values in both the morning and afternoon but there was no significant change in FCI. Women taking the progestogen only pill had essentially normal levels of cortisol, cortisol RUR and FCI at both times of the day. As far as could be judged, diurnal variation of total cortisol and FCI remained unimpaired in women taking both types of pill. The FCI measurements indicated that there was no significant increase in metabolically active cortisol in women taking either the combined oestrogen/progestogen or the progestogen only type of oral contraceptive.
Ethnography, co-design and emergence: Slow activism for sustainable design

In this article I take the novel step of examining how ethnographic understandings of the futures and intervention orientation of indirect forms of activism can inform design practice. To do this I focus on the example of the Slow City movement, specifically on its development across the UK, Spain and Australia. The focus on process and relationality that is part of the way that the movement works, creates forms of emergence that can lead to sustainability and resilience. Such processes are in many ways coherent with the principles of design anthropology and a phenomenological approach to co-design, and I suggest that by studying the success and limitations of Slow City examples we can see their work as a kind of living lab that brings new insights to design theory and practice for similar or parallel scenarios.
Overview: Helicobacter pylori and Extragastric Disease

Isolation of the gastric spiral bacterium Helicobacter pylori totally reversed the false dogma that the stomach was sterile. In addition to its causal role in peptic ulceration, the newly identified bacterium has now been implicated in other gastric and even extragastric diseases, including chronic atrophic gastritis, gastric MALT lymphoma, gastric cancer, functional dyspepsia, idiopathic thrombocytopenic purpura (ITP), iron deficiency anemia, chronic urticaria, ischemic heart disease, and others. The majority of the reports are anecdotal, epidemiologic, or eradication studies, but there are also relevant in vitro studies. ITP represents one disease showing a strong link with H pylori infection. There are also accumulating data on the role of H pylori infection in iron deficiency anemia and ischemic heart disease. In summary, the association between H pylori infection and other extragut diseases is still controversial but worthy of further investigation.
Induction of a Gradual, Reversible Morphogenesis of Its Host’s Epithelial Brush Border by Vibrio fischeri

ABSTRACT Bacteria exert a variety of influences on the morphology and physiology of animal cells whether they are pathogens or cooperative partners. The association between the luminous bacterium Vibrio fischeri and the sepiolid squid Euprymna scolopesprovides an experimental model for the study of the influence of extracellular bacteria on the development of host epithelia. In this study, we analyzed bacterium-induced changes in the brush borders of the light organ crypt epithelia during the initial hours following colonization of this tissue. Transmission electron microscopy of the brush border morphology in colonized and uncolonized hosts revealed that the bacteria effect a fourfold increase in microvillar density over the first 4 days of the association. Estimates of the proportions of bacterial cells in contact with host microvilli showed that the intimacy of the bacterial cells with animal cell surfaces increases significantly during this time. Antibiotic curing of the organ following colonization showed that sustained interaction with bacteria is essential for the retention of the induced morphological changes. Bacteria that are defective in either light production or colonization efficiency produced changes similar to those by the parent strain. Conventional fluorescence and confocal scanning laser microscopy revealed that the brush border is supported by abundant filamentous actin. However, in situ hybridization with β-actin probes did not show marked bacterium-induced increases in β-actin gene expression. These experiments demonstrate that the E. scolopes-V. fischeri system is a viable model for the experimental study of bacterium-induced changes in host brush border morphology.
Better Algorithms for Selective Sampling

We study online algorithms for selective sampling that use regularized least squares (RLS) as base classifier. These algorithms typically perform well in practice, and some of them have formal guarantees on their mistake and query rates. We refine and extend these guarantees in various ways, proposing algorithmic variants that exhibit better empirical behavior while enjoying performance guarantees under much more general conditions. We also show a simple way of coupling a generic gradient-based classifier with a specific RLS-based selective sampler, obtaining hybrid algorithms with combined performance guarantees.
Opportunistic Relay Selection with Cooperative Macro Diversity

We apply a fully opportunistic relay selection scheme to study cooperative diversity in a semianalytical manner. In our framework, idle Mobile Stations (MSs) are capable of being used as Relay Stations (RSs) and no relaying is required if the direct path is strong. Our relay selection scheme is fully selection based: either the direct path or one of the relaying paths is selected. Macro diversity, which is often ignored in analytical works, is taken into account together with micro diversity by using a complete channel model that includes both shadow fading and fast fading effects. The stochastic geometry of the network is taken into account by having a random number of randomly located MSs. The outage probability analysis of the selection differs from the case where only fast fading is considered. Under our framework, distribution of the received power is formulated using different Channel State Information (CSI) assumptions to simulate both optimistic and practical environments. The results show that the relay selection gain can be significant given a suitable amount of candidate RSs. Also, while relay selection according to incomplete CSI is diversity suboptimal compared to relay selection based on full CSI, the loss in average throughput is not too significant. This is a consequence of the dominance of geometry over fast fading.
Identification and characterization of epitopes shared between the mycobacterial 65-kilodalton heat shock protein and the actively secreted antigen 85 complex: their in situ expression on the cell wall surface of Mycobacterium leprae

Both mycobacterial hsp65 and the actively secreted antigen 85 complex of 30-kDa region proteins are considered to be major immune targets in mycobacterial diseases. In this study, by using a novel series of monoclonal antibodies (MAbs) directed to these antigens, we identified and partially characterized three unique epitopes (Rb2, Pe12, and A2h11) that are shared between mycobacterial hsp65 and the individual components of the antigen 85 complex. Dot blot assays with native purified proteins revealed that all three MAbs are strongly bound to hsp65 and antigens 85A (MPT44) and 85B (MPT59), while a weak reaction or no reaction was found with antigen 85C (MPT45). Immunoblotting showed that MAb Rb2 reacted strongly with both hsp65 and the antigen 85 complex proteins, whereas MAbs Pe12 and A2h11 reacted strongly with the former but weakly with the latter. Moreover, these MAbs did not react with other closely related MPT51 and MPT64 secreted proteins. Further characterization of these epitopes was performed by using recombinant fusion and truncated proteins of Mycobacterium bovis BCG hsp65 (MbaA) and the M. leprae 30- and 31-kDa antigen 85 complex fusion proteins. In hsp65, Rb2-Pe12- and A2h11-reactive epitopes were found to reside in the C-terminal region of amino acid residues 479 to 540 and 303 to 424, respectively. In the M. leprae 30- and 31-kDa antigen 85 complex, all three epitopes were located in an N-terminal region of amino acid residues 55 to 266, one of the known fibronectin-binding sites of the M. leprae antigen 85 complex. Comparison of these MAb-reactive amino acid sequence regions between mycobacterial hsp65 and the components of the antigen 85 complex revealed that these regions show certain amino acid sequence identities. Furthermore, by immunoperoxidase and immunogold ultracytochemistry, we demonstrated that Rb2-, Pe12-, and A2h11-reactive epitopes are expressed both on the cell wall surface and in the cytosol of M. leprae bacilli within the lesions of lepromatous leprosy patients and in M. leprae-infected armadillo liver tissue.
Probabilistic Latent Semantic Analysis (PLSA) untuk Klasifikasi Dokumen Teks Berbahasa Indonesia

One task that is included in managing documents is how to find substantial information inside. Topic modeling is a technique that has been developed to produce document representation in form of keywords. The keywords will be used in the indexing process and document retrieval as needed by users. In this research, we will discuss specifically about Probabilistic Latent Semantic Analysis (PLSA). It will cover PLSA mechanism which involves Expectation Maximization (EM) as the training algorithm, how to conduct testing, and obtain the accuracy result.
Loop program mapping and compact code generation for programmable hardware accelerators

We present a novel design methodology for the mapping of nested loops onto programmable hardware accelerators. Key features of our approach are: (1) Design entry in form of a functional programming language and loop parallelization in the polyhedron model, (2) the underlying accelerator architectures consist of lightweight, tightly-coupled, and programmable processor arrays, which can exploit both loop-level parallelism and instruction-level parallelism, (3) support of zero-overhead looping not only for inner most loops but also for arbitrarily nested loops. We implemented the proposed methodology in a prototype design tool and evaluated selected benchmarks by comparing our code generator with the Trimaran compilation framework. As the results show, our approach can reduce the size of the generated processor codes up to 64 % while at the same time achieving a significant higher throughput.
Automatic Technical Survey Creation using Citation Information

The number of research publications in various disciplines is growing exponentially. Researchers and scientists are increasingly finding themselves in the position of having to quickly understand large amounts of technical material. In this paper we present the first steps in producing an automatically generated, readily consumable, technical survey. Specifically we explore the combination of citation information and summarization techniques. Even though prior work (Teufel et al., 2006) argues that citation text is unsuitable for summarization, we show that in the framework of multi-document survey creation, citation text can play a crucial role.
Comparison of multiple Amber force fields and development of improved protein backbone parameters

The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over‐stabilization of α‐helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of “Amber” force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in Amber of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

ABSTRACT We report here the 4.7-Mb draft genome of Arthrobacter sp. SPG23, a hydrocarbonoclastic Gram-positive bacterium belonging to the Actinobacteria, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations.
Hierarchical network topographical routing

Within the last 10 years the content consumption model that underlies many of the assumptions about traffic aggregation within the Internet has changed; the previous short burst transfer followed by longer periods of inactivity that allowed for statistical aggregation of traffic has been increasingly replaced by continuous data transfer models. Approaching this issue from a clean slate perspective; this work looks at the design of a network routing structure and supporting protocols for assisting in the delivery of large scale content services. Rather than approaching a content support model through existing IP models the work takes a fresh look at Internet routing through a hierarchical model in order to highlight the benefits that can be gained with a new structural Internet or through similar modifications to the existing IP model. The work is divided into three major sections: investigating the existing UK based Internet structure as compared to the traditional Autonomous System (AS) Internet structural model; a localised hierarchical network topographical routing model; and intelligent distributed localised service models. The work begins by looking at the United Kingdom (UK) Internet structure as an example of a current generation technical and economic model with shared access to the last mile connectivity and a large scale wholesale network between Internet Service Providers (ISPs) and the end user. This model combined with the Internet Protocol (IP) address allocation and transparency of the wholesale network results in an enforced inefficiency within the overall network restricting the ability of ISPs to collaborate. From this model a core / edge separation hierarchical virtual tree based routing protocol based on the physical network topography (layers 2 and 3) is developed to remove this enforced inefficiency by allowing direct management and control at the lowest levels of the network. This model acts as the base layer for further distributed intelligent services such as management and content delivery to enable both ISPs and third parties to actively collaborate and provide content from the most efficient source.
DBSI server: DNA binding site identifier

UNLABELLED : Protein-nucleic acid interactions are among the most important intermolecular interactions in the regulation of cellular events. Identifying residues involved in these interactions from protein structure alone is an important challenge. Here we introduce the webserver interface to DNA Binding Site Identifier (DBSI), a powerful structure-based SVM model for the prediction and visualization of DNA binding sites on protein structures. DBSI has been shown to be a top-performing model to predict DNA binding sites on the surface of a protein or peptide and shows promise in predicting RNA binding sites. AVAILABILITY AND IMPLEMENTATION Server is available at http://dbsi.mitchell-lab.org CONTACT jcmitchell@wisc.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Bafilomycin A1 Treatment Retards Transferrin Receptor Recycling More than Bulk Membrane Recycling*

Treatment of Chinese hamster ovary cells with the vacuolar proton pump inhibitor bafilomycin A1 causes a 2-fold retardation in the rate of recycling of transfected human transferrin receptors back to the cell surface as measured using biochemical assays (Johnson, L. S., Dunn, K. W., Pytowski, B., and McGraw, T. E. (1993) Mol. Biol. Cell 4, 1251–1266). We have used quantitative fluorescence microscopy to determine which step(s) in the endocytic recycling pathway are affected. We show that removal of transferrin from sorting endosomes and accumulation in the peri-centriolar endocytic recycling compartment takes place normally in bafilomycin A1-treated cells. However, the rate constant for exit of transferrin receptors from recycling endosomes (k e ) is reduced from 0.063 min−1 in untreated cells to 0.034 min−1 in the presence of bafilomycin A1. This retardation appears to be dependent on the presence of internalization motifs in the cytoplasmic domain since modified receptors lacking these oligopeptide motifs do not show as large a decrease in recycling rate in the presence of bafilomycin A1. Bulk membrane recycling (measured by efflux of an internalized fluorescent lipid analog, 6-[N-[7-nitrobenzo-2-oxa-1,3-diazol-4-yl]-amino]hexoyl-sphingosylphosphorylcholine) is slowed from an exit rate constant of 0.060 min−1without drug to 0.046 min−1 in the presence of bafilomycin A1. We conclude that bafilomycin A1 slows bulk membrane flow, but it causes additional inhibition of receptor recycling in a manner that is dependent on a peptide motif on the cytoplasmic domain.
Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

Family studies of individual tissues have shown that gene expression traits are genetically heritable. Here, we investigate cis and trans components of heritability both within and across tissues by applying variance-components methods to 722 Icelanders from family cohorts, using identity-by-descent (IBD) estimates from long-range phased genome-wide SNP data and gene expression measurements for ∼19,000 genes in blood and adipose tissue. We estimate the proportion of gene expression heritability attributable to cis regulation as 37% in blood and 24% in adipose tissue. Our results indicate that the correlation in gene expression measurements across these tissues is primarily due to heritability at cis loci, whereas there is little sharing of trans regulation across tissues. One implication of this finding is that heritability in tissues composed of heterogeneous cell types is expected to be more dominated by cis regulation than in tissues composed of more homogeneous cell types, consistent with our blood versus adipose results as well as results of previous studies in lymphoblastoid cell lines. Finally, we obtained similar estimates of the cis components of heritability using IBD between unrelated individuals, indicating that transgenerational epigenetic inheritance does not contribute substantially to the “missing heritability” of gene expression in these tissue types.
Symptomatology under storm conditions in the North Atlantic in control subjects and in persons with bilateral labyrinthine defects.

Ten labyrinthine defective (L-D) and twenty normal subjects were exposed to extremely severe weather conditions during a sea voyage. The effects of such a stress were complicated by a feeling of fear in all of the normal and in some of the L-D subjects. None of the latter manifested typical symptoms of motion sickness whereas all of the normal subjects did. The fact that the L-D subjects did not become sick suggests that, even in instances where motion sickness symptoms appear to be triggered by anxiety, the vestibular organs play an essential etiological role.