Miracle-dz/UniFAR-FTUs huggingface dataset:
Negative feedback increases information transmission, enabling bacteria to discriminate sublethal antibiotic concentrations

Bacteria have evolved 2-bit depth sensors able to evaluate antibiotic threats. In the cell, noise constrains information transmission through signaling pathways and regulatory networks. There is growing evidence that the channel capacity of cellular pathways is limited to a few bits, questioning whether cells quantify external stimuli or rely on threshold detection and binary on/off decisions. Here, using fluorescence microscopy and information theory, we analyzed the ability of the transcriptional regulator TetR to sense and quantify the antibiotic tetracycline. The results showed that noise filtering by negative feedback increased information transmission up to 2 bits, generating a graded response able to discriminate different antibiotic concentrations. This response matched the antibiotic subinhibitory selection window, suggesting that information transmission through TetR is optimized to quantify sublethal antibiotic levels. Noise filtering by negative feedback may thus boost the discriminative power of cellular sensors, enabling signal quantification.
Chronological Primacy of Oxidative-Induced Neuronal Damage in the Pathogenesis of Alzheimer's Disease

Alzheimer’s disease (AD) is associated with hallmark pathologies including extracellular Aβ protein deposition in extracellular senile plaques and vessels, and intraneuronal tau deposition as neurofibrillary tangles. The current study comprises the oxidative modifications associated with the pathological lesions of neuronal damage characterized AD. The repeated exposure to aluminum and heavy metals, mutations in a number of chromosomes and genes, diabetes, cardiovascular diseases, obesity and brain injury, are the major causes for these modifications. There is clearly a need for the identification and development of panels of biomarkers for accurate diagnosis and early detection of sporadic AD. Thus, a collection of the most globally manifested expeditious diagnostic tools for early detection of AD is outlined in this review. Also, a survey of the vast clinically approved therapeutic modalities for restricting and even treating the symptoms of AD is summarized. These arguments provide useful information in both understanding pathogenesis as well as accessing the novel treatment approaches for AD. Review Article International Journal of Biochemistry Research & Review, 3(2): 82-96, 2013 83
Foxp3 Serum Levels in Contrast Induced Nephrophaty Patients After the Administration of Contrast Media

Percutaneous Coronary Intervention (PCI) procedure increases the risk of inflammation risk and represents adverse effects to immune system in the human body. One of the functions in the human body in maintaining the balance of immune system is Foxp3 of regulatory T cells and the function of Foxp3 is seldom to be the subject of study in coronary patients from the administration of contrast agents after PCI. This study was conducted to analyze the comparison Foxp3 levels of regulatory T cells in blood serums in patients who experienced contrast induced nephrophaty (CIN) after PCI procedure for both the CIN group and the non-CIN group. The population of coronary patients after PCI. The sample size was 20 patients that consisted of 10 patients who experienced CIN and 10 patients who experienced the CIN group. Categorization of both the CIN and non-CIN group used Kidney Disease Improving Global Outcomes (KDIGO) and detection of Foxp3 levels in blood serums using Enzyme-linked immunosorbent assay (ELISA) technique. Result of this study indicated that the characteristics of patients between the CIN group and the non-CIN group did not reveal significant difference, except for the characteristic of age. Results of the analysis by using statistical pair and non-pair t-test showed that patients for both the CIN group and non-CIN group experienced significant reduction of Foxp3 levels of regulatory T cells in their blood serums. This indicated that the PCI procedure indeed led to inflammation and Foxp3 levels and it could not be used as the specific marker for CIN incidence, but it should be mediated by the inflammation marker.
Ecotype adaptation and acclimation of leaf traits to rainfall in 29 species of 16‐year‐old Eucalyptus at two common gardens

Summary 1Relationships of leaf traits with rainfall at the place of origin of seed (RPO) are a function of acclimation and adaptation. To disentangle these effects we studied 29 species of 16-year-old Eucalyptus at a productive and an unproductive common garden (mean annual increments of above-ground stem volume = 21 ± 11 and 8 ± 5 m3 ha−1 years−1, respectively). We tested three hypotheses: (i) leaf traits vary between sites, but relationships among them do not; (ii) relationships of leaf traits with RPO do not vary between sites; and (iii) ecotypes originating from low-rainfall areas allocate a small fraction of nitrogen to thylakoid proteins and Rubisco, and have small SLA, small and narrow leaves, and large water-use efficiency (WUE). 2Eleven leaf traits (leaf area, leaf thickness, leaf width/length, specific leaf area, fresh weight/dry weight, N, chlorophyll a/b, carotenoids/chlorophyll, thylakoid N%, Rubisco N%, WUE derived from 13C content) were measured in 1-year-old sun leaves. 3Site had a large effect on not only the absolute values of leaf traits, but also relationships between pairs of traits. There were 20 significant correlations between pairs of traits. Three of the correlations had different slopes between sites, while a further nine had different intercepts. Hence the majority of significant correlations were not independent of site. 4Leaf area and leaf width/length were the only traits related to RPO. There was no evidence that N allocation to Rubisco or thylakoid proteins was related to RPO, or that WUE was greater in ecotypes from dry areas. 5For Eucalyptus, and perhaps other genera, physiological leaf traits may play a minor role in adaptation to water availability. There is large phenotypic plasticity in many leaf traits affecting not only the absolute values of traits, but also relationships among them.
The Effect of Priming and Salinity on Physiological and Chemical Characteristics of Wheat ( Triticum aestivum L . )

In order to study of the effect of priming and salinity on physiological and chemical characteristics of wheat (Triticum aestivum L.), an experiment was carried out at the Experimental Farm of Shiraz University. Results showed that primed plants significantly reduced its gas exchanges by accelerating senescence under a series of salt stress, which became more serious along with the increasing of salt concentrations, especially at 21 d after anthesis. Under each level of salt stress, dry matter accumulation of primed plants was always higher than the non-primed plants. Primed plants had higher potassium selectivity against sodium than non-primed plants with the former could maintain relatively stable balance of ions, potassium/sodium was found not to be the limited factor for salt tolerant plants, but it was in salt-sensitive plants. Net photosynthesis (Pn) significantly positively correlated with leaf potassium/sodium (K/Na), relative water content (RWC), and leaf area duration (P < 0.01). So those four parameters might be ideal criterions of salt tolerance in wheat. In conclusion, salt stresses caused significant declines in growth period of wheat by accelerating leaf senescence at reproductive stage. Primed plants of wheat successfully preserved normal growth by maintaining Pn, K/Na, leaf area duration (LAD) and dry matter accumulation (DMA), while non-primed plants decreased considerably in those parameters. The improvement of photosynthesis and related traits in reproductive stage was a key to the growth of wheat under saline conditions.
Synchrony and copying in conversational interactions

Proceedings of the 3rd Nordic Symposium on Multimodal Communication. Editors: Patrizia Paggio, Elisabeth Ahlsen, Jens Allwood, Kristiina Jokinen, Costanza Navarretta. NEALT Proceedings Series, Vol. 15 (2011), 18–24. © 2011 The editors and contributors. Published by Northern European Association for Language Technology (NEALT) http://omilia.uio. no/nealt . Electronically published at Tartu University Library (Estonia) http://hdl.handle. net/10062/22532 .
Population Genetics of Borrelia burgdorferi in the Eastern and Midwestern United States

Changes in climate and land-use are influencing the spatial distributions and population structure of species throughout the world. Among those species predicted to be affected by changes in climate and land-use are the hosts and vectors of many zoonotic pathogens, including the hosts and vectors of the Lyme borreliosis pathogen, Borrelia burgdorferi. In this study, we investigate the population structure of B. burgdorferi at the interface of two expanding vector populations using a population genetic and phylogeographic approach. We then examine the influence of recombination between major B. burgdorferi lineages on the population structure of B. burgdorferi within and between geographic regions. We found that B. burgdorferi lineages were heterogeneously distributed between the Northeast and Southeast United States, suggesting that gene flow between geographic regions is limited for some lineages while other lineages showed evidence of long distance dispersal. We identified at least two clonal B. burgdorferi lineages present in both competent vector species found in southern Virginia, suggesting that vector species is not a barrier to dispersal between regions. Population genetic and phylogeographic analyses of B. burgdorferi reveal a complicated pattern of population structure within and between geographic regions. Population genomic analyses show recombination between lineages despite evidence of strong linkage disequilibrium and a lack of genetic variation within B. burgdorferi lineages, suggesting a small effective population size. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biology First Advisor Dustin Brisson Second Advisor Paul S. Schmidt
Moral hazard in a voluntary deposit insurance system: Revisited

This paper extends Wheelock and Kumbhakar’s (1995) test for moral hazard in the Kansas deposit insurance system (1910-1920). This paper tests and finds evidence of omitted bank-specific effects. Estimates in Wheelock and Kumbhakar (1995), as a result, are biased. This paper introduces unobserved individual heterogeneity to the test for moral hazard, corrects their estimates, and finds more evidence of moral hazard in the Kansas deposit insurance system.
OMEN-SED 1.0: a novel, numerically efficient organic matter sediment diagenesis module for coupling to Earth system models

Abstract. We present the first version of OMEN-SED (Organic Matter ENabled SEDiment model), a new, one-dimensional analytical early diagenetic model resolving organic matter cycling and the associated biogeochemical dynamics in marine sediments designed to be coupled to Earth system models. OMEN-SED explicitly describes organic matter (OM) cycling and the associated dynamics of the most important terminal electron acceptors (i.e. O2 , NO3, SO4) and methane (CH4), related reduced substances (NH4, H2S), macronutrients (PO4) and associated pore water quantities (ALK, DIC). Its reaction network accounts for the most important primary and secondary redox reactions, equilibrium reactions, mineral dissolution and precipitation, as well as adsorption and desorption processes associated with OM dynamics that affect the dissolved and solid species explicitly resolved in the model. To represent a redox-dependent sedimentary P cycle we also include a representation of the formation and burial of Fe-bound P and authigenic Ca–P minerals. Thus, OMEN-SED is able to capture the main features of diagenetic dynamics in marine sediments and therefore offers similar predictive abilities as a complex, numerical diagenetic model. Yet, its computational efficiency allows for its coupling to global Earth system models and therefore the investigation of coupled global biogeochemical dynamics over a wide range of climate-relevant timescales. This paper provides a detailed description of the new sediment model, an extensive sensitivity analysis and an evaluation of OMEN-SED's performance through comprehensive comparisons with observations and results from a more complex numerical model. We find that solid-phase and dissolved pore water profiles for different ocean depths are reproduced with good accuracy and simulated terminal electron acceptor fluxes fall well within the range of globally observed fluxes. Finally, we illustrate its application in an Earth system model framework by coupling OMEN-SED to the Earth system model cGENIE and tune the OM degradation rate constants to optimise the fit of simulated benthic OM contents to global observations. We find that the simulated sediment characteristics of the coupled model framework, such as OM degradation rates, oxygen penetration depths and sediment–water interface fluxes, are generally in good agreement with observations and in line with what one would expect on a global scale. Coupled to an Earth system model, OMEN-SED is thus a powerful tool that will not only help elucidate the role of benthic–pelagic exchange processes in the evolution and the termination of a wide range of climate events, but will also allow for a direct comparison of model output with the sedimentary record – the most important climate archive on Earth.
Serial Case: Colorectal Malignancy in Young Age

Colorectal cancer was the third most common cancer found worldwide. In 2002, colorectal cancer was the 2 nd most common cancer in men, while it ranked third among women. Based on Indonesian Ministry of Health data, its prevalence was 1.8 per 100.000 population. We report four cases of colorectal cancer in this case series, and all cases was occured among person aged 28-32 years old. Age was the main relevant risk factors for colorectal cancer in most population. Only 3% of colorectal cancer found in individual aged less than 40 years old. This case series also aimed to show that risk factors was various and changing by the time, but its determinant factors could not be explained yet.
CHAPTER 1 Awakening Giants , Feet of Clay A Comparative Assessment of the Rise of China and India

China and India are the economic superstars of the last quarter century, with China in particular showing remarkable annual economic growth. At the same time, both struggle with entrenched structural problems that could hobble their continued growth. This article compares the two economies and the development indicators of each. Then it looks at deeper social and historical issues as well as ongoing political problems that continue to limit each country.
FERMI OBSERVATIONS OF GRB 090510: A SHORT–HARD GAMMA-RAY BURST WITH AN ADDITIONAL, HARD POWER-LAW COMPONENT FROM 10 keV TO GeV ENERGIES

We present detailed observations of the bright short–hard gamma-ray burst GRB 090510 made with the Gamma-ray Burst Monitor (GBM) and Large Area Telescope (LAT) on board the Fermi observatory. GRB 090510 is the first burst detected by the LAT that shows strong evidence for a deviation from a Band spectral fitting function during the prompt emission phase. The time-integrated spectrum is fit by the sum of a Band function with Epeak = 3.9 ± 0.3 MeV, which is the highest yet measured, and a hard power-law component with photon index −1.62 ± 0.03 that dominates the emission below ≈20 keV and above ≈100 MeV. The onset of the high-energy spectral component appears to be delayed by ∼0.1 s with respect to the onset of a component well fit with a single Band function. A faint GBM pulse and a LAT photon are detected 0.5 s before the main pulse. During the prompt phase, the LAT detected a photon with energy 30.5+5.8−2.6 GeV, the highest ever measured from a short GRB. Observation of this photon sets a minimum bulk outflow Lorentz factor, Γ≳ 1200, using simple γγ opacity arguments for this GRB at redshift z = 0.903 and a variability timescale on the order of tens of ms for the ≈100 keV–few MeV flux. Stricter high confidence estimates imply Γ ≳ 1000 and still require that the outflows powering short GRBs are at least as highly relativistic as those of long-duration GRBs. Implications of the temporal behavior and power-law shape of the additional component on synchrotron/synchrotron self-Compton, external-shock synchrotron, and hadronic models are considered.
Spirituelle Ressourcen für eine islamische Seelsorge

Auch wenn der Begriff der Seelsorge oftmals mit der christlichen Tradition assoziiert wird, ist die Sorge um die Seele auch dem Islam nicht fremd. Sich um Kranke und Notleidende zu kümmern, ist für Muslime ein religiöser Auftrag, zu dem sie in diversen Koranversen und Aussprüchen des Propheten aufgefordert werden. So verlangt der Koran beispielsweise von den Gläubigen an vielen Stellen, die Armen zu speisen (Koran, 22:28 & 22:36, zit. nach Paret 2012), sich um dieWaisen zu kümmern (Koran, 2:220 & 4:2, zit. nach Paret 2012) den Bittenden nicht abzuweisen (Koran, 93:10), in finanzieller Not Beistand zu leisten (Koran, 2:280, zit. nach Paret 2012) und verspricht, dass Gutes mit Gutem vergoltenwird (Koran, 27:89 & 55:60, zit. nach Paret 2012). Daneben gibt es viele Aussprüche des Propheten, die den Muslimen nahelegen, dass sie sich um Kranke und Leidende kümmern sollten. Ein in diesem Kontext häufig erwähnter Ausspruch ist, dass Gott am Jüngsten Tag seine Diener fragen wird: „Oh Kind Adams, ich war krank und du hast mich nicht besucht. “ Daraufhin wird die Person antworten: „Oh Herr, wie könnte ich dich besuchen, wo du doch der Herr der Welten bist. “ Gott wird hierauf sagen: „Wusstest du nicht, dass die Person Soundso krank war. Wusstest du nicht, dass wenn du sie besucht hättest, dann hättest du mich bei ihr gefunden. “ Dieser Dialog geht weiter und analog dazu fragt Gott seine Diener, warum sie ihm nicht zu Essen und zu Trinken gaben (Muslim, Buch VI, Nr. 6556). Der Prophet Muḥammad besuchte regelmäßig kranke Leute und sprach ihnen Hoffnung und Mut zu. Dabei machte er bei seinen Besuchen keinen Unterschied zwischen Muslimen oder Nicht-Muslimen (AlBuḫārī, Buch VII, Nr. 5657). Bisher lief eine Sorge um Notleidende in der islamischen Tradition oft innerhalb beziehungsweise im Rahmen der Familie, der Nachbarschaft oder muslimischen Gemeinde ab. Durch den Wandel der Gesellschaftsund Familienstrukturen drängt sich immer stärker die Notwendigkeit und Anfrage auf, eine islamische Seelsorge zu professionalisieren und einen institutionellen Rahmen für die Ausund Fortbildung von muslimischen Seelsorgern zu schaffen. Erste Ausbildungen der islamischen Seelsorge, oftmals in Zusammenarbeit mit den christlichen Vereinen in Deutschland, sind bereits vorhanden, jedoch mangelt es an einem islamisch-theologischen Konzept für eine Seelsorge, welche das Menschenbild, die Beziehung zwischen Gott und Mensch und mögliche Techniken für seelsorgliche Aktivitäten beinhaltet. Dabei sollten die islamischen Hauptquellen als Grundlage genutzt und fruchtbar gemacht werden. In diesem Beitrag möchte ich kurz auf das Menschenbild im Islam und die Beziehung zwischen dem Individuum und Gott eingehen, welches die Grundlage für eine islamische Seelsorge legt. Anschließend möchte ich daraus ableitend einige mögliche spirituelle Interventionstechniken aufzeigen.
Cow-Calf Producer Preferences for Voluntary Traceability Systems

This article identifies preferences of US cow-calf producers for voluntary traceability systems to better identify the potential success of alternative voluntary traceability systems. Results suggest that notable heterogeneity exists between cow-calf producers in their preferences and the welfare effects of mandating traceability adoption. Producers are sensitive to price, managing entity and information requirements. We provide forecasts of voluntary participation rates under different price premium and discount scenarios that producers may face. This analysis has policy implications as success of voluntary traceability systems hinges critically upon cow-calf producer preferences.
Regionalization of meso-scale physically based nitrogen modeling outputs to the macro-scale by the use of regression trees

Abstract. In this paper, a method is presented to estimate excess nitrogen on large scales considering single field processes. The approach was implemented by using the physically based model J2000-S to simulate the nitrogen balance as well as the hydrological dynamics within meso-scale test catchments. The model input data, the parameterization, the results and a detailed system understanding were used to generate the regression tree models with GUIDE (Loh, 2002). For each landscape type in the federal state of Thuringia a regression tree was calibrated and validated using the model data and results of excess nitrogen from the test catchments. Hydrological parameters such as precipitation and evapotranspiration were also used to predict excess nitrogen by the regression tree model. Hence they had to be calculated and regionalized as well for the state of Thuringia. Here the model J2000g was used to simulate the water balance on the macro scale. With the regression trees the excess nitrogen was regionalized for each landscape type of Thuringia. The approach allows calculating the potential nitrogen input into the streams of the drainage area. The results show that the applied methodology was able to transfer the detailed model results of the meso-scale catchments to the entire state of Thuringia by low computing time without losing the detailed knowledge from the nitrogen transport modeling. This was validated with modeling results from Fink (2004) in a catchment lying in the regionalization area. The regionalized and modeled excess nitrogen correspond with 94%. The study was conducted within the framework of a project in collaboration with the Thuringian Environmental Ministry, whose overall aim was to assess the effect of agro-environmental measures regarding load reduction in the water bodies of Thuringia to fulfill the requirements of the European Water Framework Directive (Base et al., 2007; Fink, 2006; Fink et al., 2007).
MERMAID : Production-level Knowledge Base Construction System

Knowledge bases play crucial roles in a wide variety of information systems, such as search engines and intelligent personal assistants. For responding constantly fluctuating user information demands, we aim to construct a large-scale and well-structured global knowledge base from the world’s evolving data. In this paper, we discuss enterprise-specific issues with knowledge base construction and present how to deal with these issues in our construction system called “MERMAID”. To maintain the quality of our knowledge base at the production-level, MERMAID is carefully designed to incorporate various automatic and manual validation methods. We partly leverage manual validation methods to deal with business requirements and user feedback quickly since it is difficult to filter out all incorrect facts automatically in practice. Moreover, we propose a novel information extraction method that obtains reliable factual information from Web-crawled data on the basis of distant supervision. Our constructed knowledge base is already utilized in real-world Japanese Web services, and the number of entities in it keeps growing steadily.