Miracle-dz/UniFAR-FTUs huggingface dataset:
Stratigraphy and Tectonics of the East Ketungau Basin, West Kalimantan during Palaeogene

DOI: 10.17014/ijog.v8i4. 170East Ketungau Basin is one of frontier basins in Indonesia. Some of these basins, especially those in eastern Indonesia, have been identified to possess potential of oil and gas. The existing publications of geological fieldworks and extensive exploration in the East Ketungau Basin are limited. The detailed sedimentological and biostratigraphical studies of the sedimentary succession will be used to reconstruct the tectonic and palaeogeographical history of the basin. The sedimentary Mandai Group consists of three facies such as mudstone facies, clean sand facies and alternation between thinly coal seam, coaly shale, and claystone facies. However, each facies characterizes depositional environment of barrier- island and associated strand-plain systems.
CARBON ACCUMULATION AND STRUCTURAL CHANGES IN SECONDARY FORESTS IN EASTERN ANTIOQUIA, COLOMBIA

We studied secondary forest succession of areas in eastern Antioquia, Colombia that were previously used for cattle ranching by analyzing tree density, basal area and aboveground biomass. Six forest patches in two age categories were investigated: Secondary forest (BS) that was 15 to 20 years old, and BS that was 25 to 30 years old. BS recovery was compared to secondary information from mature forest (BM). the BS and BM presented significant differences between the mean above ground biomass and basal area, but not in tree density as a function of years since abandonment. 25 to 30 year old secondary forests had recovered an estimated 85.2% of basal area and 52.7% of aboveground biomass with respect to those of BM. Over the entire area studied, mean annual accumulation of aboveground biomass in the forest patches in 2005 was 4.6 ± 0.3 t ha-1 per year, which represented a total of 323,469.8 ± 23,227.3 t, equivalent to 161,734.88 ± 11,613.65 t of carbon storage (C). These results confirm that management of natural regeneration is a viable, low cost strategy for the recovery of forest structure in this study area. Also, they demonstrate the high net primary productivity of this successional forest ecosystem and its contribution to the global carbon cycle.
Lichenometric ages of the little ice age moraines on king george island and of the last volcanic activity on penguin island (west antarctica)

Abstract The recently observed recession of glaciers on King George Island is associated with decades of climate warming in the Antarctic Peninsula region. However, with only 60 years of glaciological observations in the study area ages of the oldest moraines are still uncertain. The goal of the study was to estimate ages of lichen colonization on the oldest moraines of the Ecology and White Eagle Glaciers on King George Island and on the Principal Cone of Penguin Island volcano. The first lichenometric studies on these islands from the late 1970s used rates that had about four to five times slower Rhizocarpon growth rates. We re‐examined the sites and measured 996 thalli diameters to establish the surface ages. To estimate the age we used (1) long‐term Rhizocarpon lichen group growth rates established by authors using data from a previous lichenometric study on King George Island, and (2) previous data of lichen growth rates from other sub‐Antarctic islands. Our results suggest growth rates between 0.5 and 0.8 mmyr–1. According to these rates the ages of the oldest moraine ridges are of the Little Ice Age and were colonized at the beginning of the twentieth century. The mid‐twentieth century age of lichen colonization on the historically active Penguin Island volcano might support the date of the last eruption reported by whalers in the end of the nineteenth and the beginning of the twentieth century.
Decadal accumulation of anthropogenic CO2 in the Southern Ocean: A comparison of CFC‐age derived estimates to multiple‐linear regression estimates

The decadal accumulation of anthropogenic CO2 from 1968 to 1996 was estimated from CFC‐ages along three WOCE sections (SR3, P14, P15) in the Southern Ocean. We explore the validity of the method in the Southern Ocean by directly comparing the CFC‐age derived estimates to values obtained using a multiparametric linear regression method over the same period. The agreement in anthropogenic CO2 accumulation between the two independent methods was very good (less than ±8%) for waters younger than 30 years. We found waters older than 30 years to significantly overestimate the decadal accumulation when using the CFC‐age method. This is mainly due to significant mixing biases when using CFCs to infer ages for these older waters [ Sonnerup, 2001 ]. The CFC‐age method assumes a steady state circulation. CFC‐11 variations on interannual timescales have been found to be relatively large [ Doney et al., 1998 ]. To test the biases from interannual variations, we compare CFC data on the SR3 section for two different years (1991 and 1994). Although we found large differences in the estimated CFC‐11 ages (∼8 years) from the two cruises, these differences had little impact on the decadal accumulation of anthropogenic CO2 estimated by the CFC‐age method. We found the CFC‐age method to be insensitive to interannual variations or non‐ideal “age” biases [ Sonnerup, 2001 ; Haine and Hall, 2002 ] because of the similar atmospheric histories of CFC‐11 and CO2 from about 1965 to 1993. Our study validates the use of transient tracer ages to infer decadal anthropogenic CO2 accumulations in the Southern Ocean during the 1970s, 1980s, and 1990s. The application of other transient tracers to determine ages will be needed to improve the estimates of anthropogenic CO2 accumulation and uptake by the Southern Ocean for both now and into the future.
’ s Choice Series on the Next Generation of Biotech Crops Planning Environmental Risk Assessment for Genetically Modified Crops : Problem Formulation for Stress-Tolerant Crops

A scientifically sound environmental risk assessment is required for crops derived from modern biotechnology (also referred to as genetically modified [GM]) prior to unrestricted release into the environment. The scientific principles underlying the environmental risk assessments completed for herbicide-tolerant and insect-protected GM crops commercialized to date are now being applied to crops currently under development that are modified for improved tolerance to abiotic stresses. These principles, and the processes built upon them, have been shown to be sufficiently robust to provide the appropriate information for regulatory decision making and to ensure an adequate level of environmental protection. This article describes the initial steps in the environmental risk assessment process and illustrates an approach that could be taken for GM crops tolerant to an abiotic stress (e.g. water, salt, cold, and heat). The discussion below begins with an overview of the initial steps in an environmental risk assessment, known as problem formulation (US EPA, 1998). A general overview describing how problem formulation has been applied for the first GM crops is presented next. Finally, the approach is applied to a hypothetical drought-tolerant maize (Zea mays) product as an example of how problem formulation can guide the environmental risk assessment for a specific abiotic stress tolerant crop. Recent advances in functional genomics have led to the discovery of genes associated with tolerance to abiotic stresses such as cold, heat, water, and salt (Vij and Tyagi, 2007). Some of these genes show promise in major crops like maize (Nelson et al., 2007) and rice (Oryza sativa; Hu et al., 2006). As such, a discussion on planning an environmental risk assessment of GM abiotic stress-tolerant crops is timely. Regulators are now confronting the challenges involved in evaluating data from these new and potentially beneficial products. Products expressing stress tolerance phenotypes are now being widely tested in field trials around the world. Very soon, technology providers will submit data and information on GM crops with stress-tolerant phenotypes to regulatory authorities for review that will include an environmental risk assessment as part of a request for commercial release.
3D Geostatistical Modeling and Uncertainty Analysis in a Carbonate Reservoir, SW Iran

The aim of geostatistical reservoir characterization is to utilize wide variety of data, in different scales and accuracies, to construct reservoir models which are able to represent geological heterogeneities and also quantifying uncertainties by producing numbers of equiprobable models. Since all geostatistical methods used in estimation of reservoir parameters are inaccurate, modeling of “estimation error” in form of uncertainty analysis is very important. In this paper, the definition of Sequential Gaussian Simulation has been reviewed and construction of stochastic models based on it has been discussed. Subsequently ranking and uncertainty quantification of those stochastically populated equiprobable models and sensitivity study of modeled properties have been presented. Consequently, the application of sensitivity analysis on stochastic models of reservoir horizons, petrophysical properties, and stochastic oil-water contacts, also their effect on reserve, clearly shows any alteration in the reservoir geometry has significant effect on the oil in place. The studied reservoir is located at carbonate sequences of Sarvak Formation, Zagros, Iran; it comprises three layers. The first one which is located beneath the cap rock contains the largest portion of the reserve and other layers just hold little oil. Simulations show that average porosity and water saturation of the reservoir is about 20% and 52%, respectively.
Increased cardiovascular mortality associated with gout: a systematic review and meta-analysis

Background Hyperuricaemia, the biochemical precursor to gout, has been shown to be an independent risk factor for mortality from cardiovascular disease (CVD), although studies examining the clinical phenomenon of gout and risk of CVD mortality report conflicting results. This study aimed to produce a pooled estimate of risk of mortality from cardiovascular disease in patients with gout. Design Systematic review and meta-analysis. Methods Electronic bibliographic databases were searched from inception to November 2012, with results reviewed by two independent reviewers. Studies were included if they reported data on CVD mortality in adults with gout who were free of CVD at time of entry into the study. Pooled hazard ratios (HRs) for this association were calculated both unadjusted and adjusted for traditional vascular risk factors. Results Six papers, including 223,448 patients, were eligible for inclusion (all (CVD) mortality n = 4, coronary heart disease (CHD) mortality n = 3, and myocardial infarction mortality n = 3). Gout was associated with an excess risk of CVD mortality (unadjusted HR 1.51 (95% confidence interval, CI, 1.17–1.84)) and CHD mortality (unadjusted HR 1.59, 95% CI 1.25–1.94)). After adjusting for traditional vascular risk factors, the pooled HR for both CVD mortality (HR 1.29, 95% CI 1.14–1.44) and CHD mortality (HR 1.42, 95% CI 1.22–1.63) remained statistically significant, but none of the studies reported a significant association with myocardial infarction. Conclusions Gout increases the risk of mortality from CVD and CHD, but not myocardial infarction, independently of vascular risk factors.
Constraints on the Presence or Absence of Post‐Perovskite in the Lowermost Mantle from Long‐Period Seismology

In this study, the ability to detect post-perovskite is examined using three long-period seismology approaches; normal modes, arrival time variations, and seismic tomography. Although normal modes provide robust integral constraints on 1D velocity and density profiles of the Earth, their ability to resolve variations in shear velocity and density decreases near the core-mantle boundary (CMB). Therefore, it is possible for post-perovskite to exist globally within 200 km of the CMB without resolution by normal modes. Deep-turning long-period S wave arrival times are examined in regions of dense ray coverage and a shift representing an increase in velocity consistent with presence of post-perovskite is observed in localized areas approximately 100 km above the CMB. Therefore, post-perovskite is not a ubiquitous feature but may be locally stable within both tomographically slow and fast regions near the CMB. To globally determine if regions are cold or iron-enriched enough for post-perovskite to be stable, recent thermo-chemical models are applied to a suite of geotherms and phase transition depths. The results suggest that variations in iron content are too small to control the stability of post-perovskite. It is demonstrated that only a narrow range of temperatures and phase transition depths can allow post-perovskite to exist in anomalously fast (cold) regions in the lowermost mantle. Furthermore, if post-perovskite is a major constituent of fast regions, then the temperature at 2780 km depth ranges from 2400 K - 2700 K, and post-peorvskite does not explain the observed anti-correlation of shear velocity and bulk sound speed near the CMB.
Broadening the spectrum of treatment options for SNHL.

Kubo T. Effects of intratympanic injection of steroids on changes in rat inner ear aquaporin expression. Acta Otolaryngol. 2002;122:600606. 8. Parnes LS, Sun AH, Freeman DJ. Corticosteroid pharmacokinetics in the inner ear fluids: an animal study followed by clinical application. Laryngoscope. 1999;109:1-17. 9. Alzamil KS, Linthicum FH Jr. Extraneous round window membranes and plugs: possible effect on intratympanic therapy. Ann Otol Rhinol Laryngol. 2000;109:30-32. 10. Silverstein H, Arruda J, Rosenberg SI, Deems D, Hester TO. Direct round window membrane application of gentamicin in the treatment of Meniere’s disease. Otolaryngol Head Neck Surg. 1999; 120:649-655.
Role of BAFF in pulmonary autoantibody responses induced by chronic cigarette smoke exposure in mice

Emerging evidence suggests that autoimmune processes are implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). In this study, we assessed the expression of B‐cell activating factor (BAFF) in smokers, and investigated the functional importance of BAFF in the induction and maintenance of cigarette smoke‐induced pulmonary antinuclear antibodies (ANA) and tertiary lymphoid tissues (TLTs) using a preclinical mouse model. We observed that BAFF levels were elevated in smokers and mice exposed to cigarette smoke. In mice, BAFF expression was rapidly induced in the lungs following 4 days of cigarette smoke exposure and remained elevated following 8 and 24 weeks of exposure. Alveolar macrophages were the major source of BAFF. Blockade of BAFF using a BAFF receptor‐Fc (BAFFR‐Fc) construct prevented pulmonary ANA and TLT formation when delivered concurrent with cigarette smoke exposure. Under these conditions, no impact on lung inflammation was observed. However, administration of BAFFR‐Fc following smoking cessation markedly reduced the number of TLTs and ANA levels and, of note, reduced pulmonary neutrophilia. Altogether, this study shows for the first time a central role of BAFF in the induction and maintenance of cigarette smoke‐induced pulmonary ANA and suggests that BAFF blockade following smoking cessation could have beneficial effects on persistent inflammatory processes.
Combining a Two-step Conditional Random Field Model and a Joint Source Channel Model for Machine Transliteration

This paper describes our system for "NEWS 2009 Machine Transliteration Shared Task" (NEWS 2009). We only participated in the standard run, which is a direct orthographical mapping (DOP) between two languages without using any intermediate phonemic mapping. We propose a new two-step conditional random field (CRF) model for DOP machine transliteration, in which the first CRF segments a source word into chunks and the second CRF maps the chunks to a word in the target language. The two-step CRF model obtains a slightly lower top-1 accuracy when compared to a state-of-the-art n-gram joint source-channel model. The combination of the CRF model with the joint source-channel leads to improvements in all the tasks. The official result of our system in the NEWS 2009 shared task confirms the effectiveness of our system; where we achieved 0.627 top-1 accuracy for Japanese transliterated to Japanese Kanji(JJ), 0.713 for English-to-Chinese(E2C) and 0.510 for English-to-Japanese Katakana(E2J).
Transcriptional changes induced by the tumor dormancy-associated microRNA-190

Tumor dormancy is a highly prevalent stage in cancer progression. We have previously generated and characterized in vivo experimental models of human tumor dormancy in which micro-tumors remain occult until they spontaneously shift into rapid tumor growth. We showed that the dormant micro-tumors undergo a stable microRNA (miRNA) switch during their transition from dormancy to a fast-growing phenotype and reported the identification of a consensus signature of human tumor dormancy-associated miRNAs (DmiRs). miRNA-190 (miR-190) is among the most upregulated DmiRs in all dormant tumors analyzed. Upregulation of miR-190 led to prolonged tumor dormancy in otherwise fast-growing glioblastomas and osteosarcomas. Here we investigate the transcriptional changes induced by miR-190 expression in cancer cells and show similar patterns of miR-190 mediated transcriptional reprogramming in both glioblastoma and osteosarcoma cells. The data suggests that miR-190 mediated effects rely on an extensive network of molecular changes in tumor cells and that miR-190 affects several transcriptional factors, tumor suppressor genes and interferon response pathways. The molecular mechanisms governing tumor dormancy described in this work may provide promising targets for early prevention of cancer and may lead to novel treatments to convert the malignant tumor phenotype into an asymptomatic dormant state.
LA PRÉVENTION DES RISQUES D'INONDATION EN FRANCE : ENTRE APPROCHE NORMATIVE DE L'ÉTAT ET EXPÉRIENCES LOCALES DES COURS D'EAU

This article addresses two approaches to flood risk prevention in France: the first is institutional in nature and government managed; the other is local in nature and under the authority of territorial communities. Great emphasis is placed on risk in institutionalized government prevention. This normative approach defines one type of risk for all territories. Managed locally, risk is defined in terms of everyday perceptions. Risk at this level is territorially-based, and prevention must therefore consider other kinds of logic. Both approaches do not draw on the same criteria of rationalization and knowledge of risks. The first approach argues that major risks are entirely unacceptable, but when experienced at the local level, they involve making difficult compromises between the presence of risk and the need for land-use planning. Flood-risk prevention in France is chiefly founded on an institutional, government managed approach that does not embrace local knowledge of risk. As a result, the implementation of flood prevention policy is characterized by dissonance.
Acquisition of meiotic competence in growing pig oocytes correlates with their ability to activate Cdc2 kinase and MAP kinase

Meiotic maturation of mammalian oocytes is under the control of cell cycle molecules Cdc2 kinase and MAP kinase (mitogen-activated protein kinase). In the present study, we investigated the relationship between the ability to activate Cdc2 kinase and MAP kinase and the acquisition of meiotic competence during pig oocyte growth. Growing and fully grown pig oocytes were collected from four groups of antral follicles of various diameters (A, 0.5-0.7 mm; B, 1.0-1.5 mm; C, 2.0-2.5 mm; D, 4.0-6.0 mm) and cultured in vitro. Fully grown oocytes from class D follicles, which have full competence to mature to metaphase II, had the ability to activate both Cdc2 kinase and MAP kinase. In contrast, growing oocytes from class A follicles, which have limited competence to resume meiosis, had no such ability. Cyclin B1 molecules did accumulate, however, with phosphorylated 35 and 36 kDa bands of p34cdc2 appearing in the cultured oocytes. Of the growing oocytes from class B follicles, 60% resumed meiosis but arrested at metaphase I. Some of the oocytes in this class were capable of activating Cdc2 kinase, although they did not appear to have established a MAP kinase-activating pathway or the ability to activate MEK. These results suggest that limited meiotic competence in growing oocytes from class A follicles is due to their inability to activate Cdc2 kinase and their incomplete MEK-MAP-kinase pathway, although the oocytes are capable of accumulating cyclin B1 molecules. During the final growth phase, pig oocytes acquire the ability to activate Cdc2 kinase and then establish the MEK-MAP-kinase pathway for full meiotic competence.
Effects of different nitrogen forms, ammonia gas and wet deposited ammonium and nitrate, on methane and nitrous oxide emissions from an ombrotrophic bog, Whim Moss, in the Scottish Borders

Enhanced reactive nitrogen deposition may compromise the sustainability and functioning of bogs, with respect to carbon sequestration and greenhouse gas production. Since 2002, three N forms have been applied to an ombrotrophic bog growing Calluna, Sphagnum capillifolium and Eriophorum vaginatum in order to test this. Significant changes in species cover and soil chemistry, especially in response to elevated ammonia concentrations, have been recorded. Ammonia deposition has also increased nitrous oxide emissions, while the same N dose as ammonium or nitrate had a far smaller effect. Methane emissions were increased by nitrate additions, although fluxes were equally responsive to water table and temperature. The significance of N form, and ’natural’ drivers, is discussed.
Genome-Scale Approaches to Identify Genes Essential for Haemophilus influenzae Pathogenesis

Haemophilus influenzae is a Gram-negative bacterium that has no identified natural niche outside of the human host. It primarily colonizes the nasopharyngeal mucosa in an asymptomatic mode, but has the ability to disseminate to other anatomical sites to cause otitis media, upper, and lower respiratory tract infections, septicemia, and meningitis. To persist in diverse environments the bacterium must exploit and utilize the nutrients and other resources available in these sites for optimal growth/survival. Recent evidence suggests that regulatory factors that direct such adaptations also control virulence determinants required to resist and evade immune clearance mechanisms. In this review, we describe the recent application of whole-genome approaches that together provide insight into distinct survival mechanisms of H. influenzae in the context of different sites of pathogenesis.
Circulating biomarkers : the platelet releasate and the platelet sheddome

The most convincing evidence for the participation of platelets in arterial thrombosis in humans comes from studies of platelet activation in patients with acute coronary syndromes (ACS) and from trials of antiplatelet drugs. Both strongly support the concept that repeated episodes of platelet activation over the thrombogenic surface of a vulnerable plaque may contribute to the risk of death from coronary causes. However, the relation of in vivo platelet activation and adverse clinical events to results of platelet function tests remains largely unknown. A valuable marker of in vivo platelet activation should be specific, unal-