Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Genetic Biodiversity and Molecular Approach

Biodiversity is given by the variety of species on Earth resulting from billions of years of evolution. Molecular-phylogenetic studies have revealed that the main diversity of life is microbial and it is distributed among three domains: Achaea, Bacteria, and Eukarya. The functioning of whole biosphere depends absolutely on the activities of the microbial world. Due to their versatility microbes are the major natural providers of ecological services as well play major role in semi-artificial systems such as sewage treatment plants, landfills, and in toxic waste bioremediation. As for other organisms many pressures and drivers are causing decrease of microbial biodiversity. Several publications document the effect of chemical pollutants e.g. Polycyclic Aromatic Hydrocarbons (PAHs), of atmospheric pollution, of temperature change and of fertilization on microbial community structure. These studies are now possible because sequencing technologies are in ongoing revolution allowing massive de novo sequencing producing millions of bases in a single day. Metagenomics, metatranscriptomics, metaproteomics and single-cell sequencing are approaches providing a view not only of the community structure (species phylogeny, richness, and distribution) but also of the functional (metabolic) potential of a community because virtually about all genes are captured and sequenced.
Using distance transform based algorithms for extracting measures of the fiber network in volume images of paper

Nowadays volume images are frequently used in many applications. Volume images of paper can be analyzed to increase the understanding of the complexity of the fiber network in paper and its effect on the optical and mechanical properties of paper. We show how curve and surface representations of the fiber, the fiber wall, and the fiber lumen can be computed using distance transform based algorithms. These representations are used for easy computation of wall thickness, degree of collapse, fiber length, slenderness ratio, fiber curl, and torsional resistance for the fibers. Free-fiber segments are identified, again using a distance transform based algorithm. Finally, we show tools for qualitative visual inspection of the fibers. The methods are evaluated and illustrated using both sets of synthetic and of real data. In addition to the analysis of the fiber network in paper, they can be used in many other applications where shape analysis of elongated objects is to be performed.
Multifaceted Assessment of Chronic Gastritis: A Study of Correlations between Serological, Endoscopic, and Histological Diagnostics

Aim. Chronic gastritis was assessed serologically, endoscopically and histologically to identify correlations between these methods. Methods. Subjects comprised 319 patients who had provided informed consent. Serological assessment of chronic gastritis was based on the pepsinogen test method. Endoscopic gastritis and histological gastritis were assessed and scored according to the Kimura-Takemoto classification system and the updated Sydney classification system respectively, and correlations between these three methods were studied. Results. Pepsinogen I/II ratio showed a significant correlation to the extent of mononuclear cell infiltration of the gastric corpus. When histological gastritis was divided, on the basis of the distribution of mononuclear cell infiltration, into gastritis limited to the antrum and corpus gastritis, these types were distinguished with high accuracy using a pepsinogen I/II ratio of 3 as the cutoff. A good correlation was also seen between pepsinogen I/II ratio and development of atrophy in endoscopic gastritis, where groups with and without advanced atrophy were also distinguished with high accuracy using a cutoff value of 3. Conclusion. Significant correlations exist between serum pepsinogen levels, endoscopic gastritis, and histological gastritis. Pepsinogen I/II ratio allows prediction of the existence of endoscopic gastritis and histological gastritis, or the extent of their development, with high accuracy.
Persuasive political argument

In this paper we discuss how a computational version of argumentation involving practical reasoning can be applied to the domain of e-democracy. We discuss our previous work which proposed an argument scheme and associated critical questions to make use of presumptive reasoning in order to justify a proposal for action. We explain how this proposal can be made computational for use by BDI agents and we illustrate the approach with an example application of a recent political debate involving the Government’s justification of a proposed action. We then go on to discuss some interesting issues arising from the example regarding the strength of the arguments and how they can be accrued to put forward a more convincing case for justifying the action. We also examine how this application compares with a previously implemented system which makes use of the same underlying theory.
A Relevance Rule Organizing Responsive Behavior During Projectably Multi-Unit Tellings

i Dedication . ii Acknowledgements . iii List of Tables . vi List of Figures . vii Chapter 1: Introduction and Literature Review . 1 International Students Studying at Colleges and Universities in the United States . 2 Culture Shock and Adaptation . 3 Individualism and Collectivism . 4 Cross-Cultural Misunderstandings.5 Advising International Students . 6 Projectably Extended Tellings and Understanding . 7 Chapter 2: Data and Method . 13 Data-Collection Site and Rationale . 13 Qualitative Research: Conversation Analytic Approach . 14 Participants . 15 Data Collection Procedure . 16 Room Layout and Participant Orientation . 17 Transcription and Analysis. 17 The Activity Context and Foci of Analysis . 18 Chapter 3: Analysis . 22 The Nature of a Possible-Completion Place . 22 Syntactic Completion . 23 Intonational Completion . 24 Pragmatic Completion . 24 Specifying the Focal Engagement Framework . 26 The Frequency and Type of Advisors’ Responses . 27 Vocal Continuers . 28 Stand-Alone Head Nods . 29 Okay . 30 Yeah . 30 Positive Assessments . 31 Right . 31 The Positioning of Advisors’ Responses . 34 ‘Early’ Responses . 35 ‘Precisely-On-Time’ Responses . 36 v ‘Late’ Responses . 36 No Response at All . 38 The Nature of Student Progression from Unit to Unit . 38 Self Repairs . 39 Understanding Checks . 40 Increments . 41 Answers to Advisors’ Initiations of Repair . 44 The Relationship Between Position of Advisor Response and Student Progression. 45 Deviant-Case Analysis . 48 Chapter 4: Discussion and Conclusion . 54 Limitations . 56 References . 60 Appendices . 74 A: HSRRC Approval . 74 B: HSRRC Approval for Continuation of Project . 76 C: Informed Consent Form for Advisor.77 D: Informed Consent Form for International Student.79 E: Survey for Advisor . 81 F: Survey for International Student.83
Interseismic coupling on the main Himalayan thrust

We determine the slip rate and pattern of interseismic coupling on the Main Himalayan Thrust along the entire Himalayan arc based on a compilation of geodetic, interferometric synthetic aperture radar, and microseismicity data. We show that convergence is perpendicular to the arc and increases eastwards from 13.3 ± 1.7 mm/yr to 21.2 ± 2.0 mm/yr. These rates are comparable to geological and geomorphic estimates, indicating an essentially elastic geodetic surface strain. The interseismic uplift rate predicted from the coupling model closely mimics the topography, suggesting that a small percentage of the interseismic strain is permanent. We find that the fault is fully locked along its complete length over about 100 km width. We don't find any resolvable aseismic barrier that could affect the seismic segmentation of the arc and limit the along‐strike propagation of seismic ruptures. The moment deficit builds up at a rate of 15.1 ± 1 × 1019 N m/yr for the entire length of the Himalaya.
Associations of Plasma C-Peptide and IGFBP-1 Levels with Risk of Colorectal Adenoma in a Multiethnic Population

Background: Circulating levels of insulin and insulin-like growth factor (IGF) hormones have been associated with colorectal cancer risk, but few studies have examined their associations with colorectal adenoma. Methods: We measured plasma C-peptide, a marker of insulin secretion, and IGF hormones in a case-control study of 554 pathologically confirmed, first-time adenoma cases and 786 controls with normal endoscopy among Caucasians, Japanese, and Native Hawaiians in Hawaii. Results: High plasma levels of C-peptide were statistically significantly associated with risk of colorectal adenoma [multivariate odds ratio (95% confidence interval) for increasing quartiles: 1.0, 0.91 (0.65-1.27), 1.21 (0.86-1.71), and 1.79 (1.23-2.60); Ptrend = 0.0002]. We also observed a statistically significant inverse association between levels of plasma IGF binding protein-1 (IGFBP-1) and adenoma risk [1.0, 0.97 (0.70-1.34), 0.82 (0.58-1.15), and 0.47 (0.32-0.70); Ptrend <0.0001]. These associations remain significant after adjusting for each other and were not confounded by known risk factors. IGF-I, IGFBP-3, body mass index, and waist or hip circumference were not independently associated with adenoma risk. Conclusion: These results provide evidence for an association of insulin and IGFBP-1 levels with colorectal adenoma. Impact: This study suggests that hyperinsulinemia and IGF hormones may act as etiologic factors in colorectal carcinogenesis, as early as during adenoma formation. Cancer Epidemiol Biomarkers Prev; 19(6); 1471–7. ©2010 AACR.
New non-interactive key agreement and progression (NIKAP) protocols and their applications to security in ad hoc networks

Symmetric cryptographic primitives are preferable in designing security protocols for mobile ad hoc networks (MANETs) because they are computationally affordable for resource-constrained mobile devices forming a MANET. Most proposed key-distribution and key-agreement schemes for symmetric cryptosystem assume services from on-line centralized authorities, or require the interaction between communicating parties. However, the presence of a centralized authority violates the ad hoc definition of MANETs, and interactive schemes require the routing of the ad hoc network to be established before the key agreement, which is difficult to ensure in a mobile ad hoc network (MANET). We propose a new non-interactive key agreement and progression (NIKAP) scheme for MANETs, which does not require an on-line centralized authority, can establish and update pairwise shared keys between any two nodes in a non-interactive manner, is configurable to operate synchronously (S-NIKAP) or asynchronously (A-NIKAP), and is able to provide differentiated security services w.r. t. specified security policies. As the name implies, NIKAP is especially valuable to scenarios in which shared secret keys are desired to be computed without negotiation between nodes over insecure channels, and need to be updated frequently
Asymmetric Binding to NS5A by Daclatasvir (BMS-790052) and Analogs Suggests Two Novel Modes of HCV Inhibition

Symmetric, dimeric daclatasvir (BMS-790052) is the clinical lead for a class of picomolar inhibitors of HCV replication. While specific, resistance-bearing mutations at positions 31 and 93 of domain I strongly suggest the viral NS5A as target, structural mechanism(s) for the drugs’ activities and resistance remains unclear. Several previous models suggested symmetric binding modes relative to the homodimeric target; however, none can fully explain SAR details for this class. We present semiautomated workflows to model potential receptor conformations for docking. Surprisingly, ranking docked hits with our library-derived 3D-pharmacophore revealed two distinct asymmetric binding modes, at a conserved poly-proline region between 31 and 93, consistent with SAR. Interfering with protein–protein interactions at this membrane interface can explain potent inhibition of replication–complex formation, resistance, effects on lipid droplet distribution, and virion release. These detailed interaction models and proposed mechanisms of action will allow structure-based design of new NS5A directed compounds with higher barriers to HCV resistance.
Neuroadaptations to chronic exposure to drugs of abuse: Relevance to depressive symptomatology seen across psychiatric diagnostic categories

Depressive symptomatology is expressed across a wide spectrum of psychiatric disorders including major depression and schizophrenia. Further, depressive symptomatology is also observed in individuals undergoing withdrawal from chronic exposure to various drugs of abuse including cocaine, amphetamine and nicotine. The negative affective state associated with drug withdrawal is phenomenonologically similar to that observed in depressed and schizophrenia patients suggesting that common underlying pathophysiological deficits may be involved in the depressive symptomatology seen across these different psychiatric disorders. The aim of the present review is to examine clinical and preclinical evidence in support of common neurobiological substrates mediating the negative affect associated with different psychiatric illnesses. First, clinical and epidemiological data are presented demonstrating the high comorbidity between nicotine and psychostimulant dependence, and depression or schizophrenia. It is hypothesized that drug use may represent an attempt to self-medicate an underlying negative affective state present in depressed and schizophrenia patients. Second, preclinical findings are presented that demonstrate common neurochemical deficits in drug withdrawal and depression. Taken together, these clinical and preclinical data support the hypothesis that common neurobiological substrates may mediate the depressive state observed across psychiatric diagnostic categories. Therefore, it is proposed that the study of drug-induced depressions in laboratory animals may have heuristic value in identifying the mechanisms underlying the depressive symptomatology associated not only with drug withdrawal but also major depression and schizophrenia.
Detection of the Intrinsic Size of Sagittarius A* Through Closure Amplitude Imaging

We have detected the intrinsic size of Sagittarius A*, the Galactic center radio source associated with a supermassive black hole, showing that the short-wavelength radio emission arises from very near the event horizon of the black hole. Radio observations with the Very Long Baseline Array show that the source has a size of 24 ± 2 Schwarzschild radii at 7-millimeter wavelength. In one of eight 7-millimeter epochs, we also detected an increase in the intrinsic size of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(60_{-17}^{+25}\%\) \end{document}. These observations place a lower limit to the mass density of Sagittarius A* of 1.4 × 104 solar masses per cubic astronomical unit.
Polyamines: mysterious modulators of cellular functions.

In recent years the functions of polyamines (putrescine, spermidine, and spermine) have been studied at the molecular level. Polyamines can modulate the functions of RNA, DNA, nucleotide triphosphates, proteins, and other acidic substances. A major part of the cellular functions of polyamines can be explained through a structural change of RNA which occurs at physiological concentrations of Mg(2+) and K(+) because most polyamines exist in a polyamine-RNA complex within cells. Polyamines were found to modulate protein synthesis at several different levels including stimulation of special kinds of protein synthesis, stimulation of the assembly of 30 S ribosomal subunits and stimulation of Ile-tRNA formation. Effects of polyamines on ion channels have also been reported and are gradually being clarified at the molecular level.
Enteric Flora Expands Gut Lamina Propria CX3CR1+ Dendritic Cells Supporting Inflammatory Immune Responses under Normal and Inflammatory Conditions

CD103 or CX3CR1 surface expression defines distinct dendritic cells (DCs) and macrophages in the murine lamina propria of the colon (cLP). We investigated the surface marker and functional phenotype of CD103+ and CX3CR1+ cLP DCs and their role in transfer colitis. cLP CD11c+ cells were isolated from specific pathogen-free or germ-free mice to elucidate the role of the commensal flora in their development. The cLP CD11c+ cells are a heterogeneous cell population that includes 16% CX3CR1+, 34% CD103+, 30% CD103−CX3CR1− DCs, and 17% CD68+/F4/80+CX3CR1+CD11c+ macrophages. All DCs expressed high levels of MHC II but low levels of costimulatory (CD40, CD86, and CD80) and coinhibitory (programmed death ligand-1) molecules. Ex vivo confocal microscopy demonstrated that CX3CR1+CD11c+ cells, but not CD103+ DCs, were reduced in the cLP of germ-free (CX3CR1-GFP) mice. The absence of the enteric flora prevents the formation of transepithelial processes by the CX3CR1+ DCs. CX3CR1+ DCs preferentially supported Th1/Th17 CD4 T cell differentiation. CD103+ DCs preferentially induced the differentiation of Foxp3-expressing regulatory T cells. The stimulation of cLP DCs with fractalkine/CX3CL1 increased the release of IL-6 and TNF-α. In the absence of CX3CR1, the CD45RBhigh CD4 transfer colitis was suppressed and associated with reduced numbers of DCs in the mesenteric lymph nodes and a reduction in serum IFN-γ and IL-17. The local bacteria-driven accumulation of CX3CR1+ DCs seems to support inflammatory immune responses.
Monoclonal antibodies against the free subunits of human chorionic gonadotrophin.

Discordant results on body fluid levels of human chorionic gonadotrophin (hCG) free alpha- and beta-subunits under physiological and pathophysiological conditions, prompted us to raise a total of 260 monoclonal antibodies (MCA) against free hCG-alpha, free hCG-beta, holo-hCG, human follicle-stimulating hormone and bovine luteinizing hormone; 153 MCA recognizing the human alpha-subunit and 28 reacting with hCG-beta were extensively analysed for their intra- and inter-species cross-reactivity with homologous hormones, and for the compatibility of epitopes recognized by them. The immunological topography of free hCG-alpha and free hCG-beta was resolved by these MCA, and epitope maps were designed. Six antigenic determinants on the free alpha-chain (alpha 1-alpha 6), clustered in three spatially distinct domains, and seven epitopes on the surface of free hCG-beta (beta 1-beta 7), could be distinguished. Strikingly, three alpha-chain epitopes (alpha 4, alpha 5 and alpha 6) were shared between various species, which is in contradiction to the concept of immunological species-specificity of alpha-subunits. Three determinants were found to be present only on the free subunits but not on holo-hCG (alpha 6, beta 6 and beta 7), and only two determinants (beta 1 and beta 7) were hormone-specific for hCG. Based on this information, an immunoenzymometric assay for the free alpha-subunit of human glycoprotein hormones was established, with a sensitivity of 1.3 pg/well and a cross-reactivity with holo-hCG of less than 0.005%. (ABSTRACT TRUNCATED AT 250 WORDS)
Relative Validity of Three Food Frequency Questionnaires for Assessing Dietary Intakes of Guatemalan Schoolchildren

Objective To determine the relative validity of three food frequency questionnaires (FFQs) compared with results from 24-hour dietary recalls for measuring dietary intakes in Guatemalan schoolchildren. Design A cross-sectional study of primary caregivers (mothers or grandmothers) of 6–11 year-old children. Caregivers completed one of three constructed FFQs to measure the child’s dietary consumption in the last week: FFQ1 did not incorporate portion sizes; FFQ2 provided portion sizes; and FFQ3 incorporated pictures of median portion sizes. During the same week, each caregiver also completed three 24-hour dietary recalls. Results from the FFQ were compared with corresponding results from the 24-hour dietary recalls. Setting Santa Catarina Pinula, peri-urban Guatemala City. Subjects Caregivers (n = 145) of 6–11 year-old children: 46 completed FFQ1, 49 completed FFQ2, and 50 completed FFQ3. Results The mean values for all nutrients obtained from the 24-hour dietary recall were lower than for those obtained from the FFQs, excluding folic acid in FFQ3, cholesterol and zinc in FFQ2, and cholesterol, folic acid, magnesium, potassium, sodium, and zinc in FFQ1. Energy-adjusted Pearson correlation coefficients ranged from 0.07 (protein) to 0.54 (cholesterol) for FFQ1 and from 0.05 to 0.74 for FFQ2 and FFQ3. Agreement by both methods (FFQ and 24-hour dietary recalls) of classifying children into the same or adjacent quartiles of energy-adjusted nutrient consumption ranged from 62.0% for cholesterol to 95.9% for vitamin B12 across all three FFQs. Conclusions Our FFQs had moderate to good relative validity in measuring energy and nutrient intakes for 6–11 year-old Guatemalan children. More evidence is needed to evaluate their reproducibility and applicability in similar populations.
Architecture and Systems for Monitoring Hospital Acquired Infections inside Hospital Information Workflows

This paper describes the latest developments in the design of a tool to monitor Patient Discharge Summaries to detected pieces of evidences related to Hospital Acquired Infections. Anonymization, Named Entity detection, Temporal Expressions analysis and Causality detection methods have been developed and evaluated. They are embedded in a tool designed to work in a Hospital Information Workflow.
Use of social media across the trip experience: An application of latent transition analysis

ABSTRACT Recent advanced technologies have enabled travelers to communicate, interact, and form relationships with destinations, businesses, and other travelers through social media. However, the nature/patterns of use of social media by travelers varies substantially between travelers and across the trip experience (e.g. pre-, during, and post-trip); consequently, travelers develop their own idiosyncratic strategies (i.e. media repertoires) for information searching, communicating, and storing memories. There are four distinct and dominant repertoires of social media use across the three stages of the trip experience. As such, the findings clearly indicate that destination marketers should target the respective groups very differently.
Characteristics of Agrobacterium tumefaciens Auxotrophic Mutant Infectivity

Lippincott, Barbara B. (Northwestern University, Evanston, Ill.), and James A. Lippincott. Characteristics of Agrobacterium tumefaciens auxotrophic mutant infectivity. J. Bacteriol. 92:937–945. 166. —Mutants of Agrobacterium tumefaciens auxotrophic for adenine, methionine, or asparagine are less infectious than the wild-type strain B6 from which they were derived and show increased infectivity on pinto bean leaves when the specific compounds required for growth of the mutants are added to the infected leaf. Reversion to a prototrophic form of nutrition is accompanied by increased infectivity. Tumors initiated by these auxotrophic mutants are shown to arise only at large wound sites where nutritional conditions may be less restricting. The data indicate that, after inoculation, the bacteria pass through a phase in which host-supplied nutrients are utilized for the production of one or more factors necessary for successful tumor initiation.