Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term exposure to air pollution and prevalent nonalcoholic fatty liver disease

Background: Nonalcoholic fatty liver disease (NAFLD) is a disease characterized by lipid accumulation within hepatocytes, ranging from simple steatosis to steatohepatitis, in the absence of secondary causes of hepatic fat accumulation. Although air pollution (AP) has been associated with several conditions related to NAFLD (e.g., metabolic syndrome, type 2 diabetes mellitus), few studies have explored an association between AP and NAFLD. The aim of the study was to investigate whether exposure to AP is associated with NAFLD prevalence. Methods: We used baseline cross-sectional data (2000–2003) of the Heinz–Nixdorf–Recall cohort study in Germany (baseline n = 4,814), a prospective population-based cohort study in the urbanized Ruhr Area. Mean annual exposure to size-fractioned particulate matter (PM10, PM2.5, PMcoarse, and PM2.5abs), nitrogen dioxide, and particle number was assessed using two different exposure models: a chemistry transport dispersion model, which captures urban background AP exposure on a 1 km2 grid at participant’s residential addresses, and a land use regression model, which captures point-specific AP exposure at participant’s residential addresses. NAFLD was assessed with the fatty liver index (n = 4,065), with NAFLD defined as fatty liver index ≥60. We estimated ORs of NAFLD per interquartile range of exposure using logistic regression, adjusted for socio-demographic and lifestyle variables. Results: We observed a NAFLD prevalence of 31.7% (n = 1,288). All air pollutants were positively associated with NAFLD prevalence, with an OR per interquartile range for PM2.5 of 1.11 (95% confidence interval [CI] = 1.00, 1.24) using chemistry transport model, and 1.06 (95% CI = 0.94, 1.19) using the land use regression model, respectively. Conclusion: There was a positive association between long-term AP exposure and NAFLD.
Detection of living cells in stratospheric samples

Air samples collected aseptically over tropical India at various stratospheric altitudes ranging from 20 to 41 km using cryosampler assemblies carried on balloons flown from Hyderabad have shown evidence of living microbial cells. Unambiguous evidence of living cells came from examining micropore filters on which the samples were recovered with the use of voltage sensitive lipophilic dyes that could detect the presents of active cells. Clumps of viable cells were found at all altitudes using this technique, and this conclusion was found to be consistent with images obtained from electron microscopy. Since the 41 km sample was collected well above the local tropopause, a prima facie case for a space incidence of these microorganisms is established. Further work on culturing, PCR analysis and isotopic analysis is in progress.
DNA methylation 101: what is important to know about DNA methylation and its role in SLE risk and disease heterogeneity

SLE is a complex autoimmune disease that results from the interplay of genetics, epigenetics and environmental exposures. DNA methylation is an epigenetic mechanism that regulates gene expression and tissue differentiation. Among all the epigenetic modifications, DNA methylation perturbations have been the most widely studied in SLE. It mediates processes relevant to SLE, including lymphocyte development, X-chromosome inactivation and the suppression of endogenous retroviruses. The establishment of most DNA methylation marks occurs in utero; however, a small percentage of epigenetic marks are dynamic and can change throughout a person’s lifetime and in relation to exposures. In this review, we discuss the current understanding of the biology of DNA methylation and its regulators, the measurement and interpretation of methylation marks, the effects of genetics on DNA methylation and the role of environmental exposures with relevance to SLE. We also summarise research findings associated with SLE disease risk and heterogeneity. The robust finding of hypomethylation of interferon-responsive genes in patients with SLE and new associations beyond interferon-responsive genes such as cell-specific methylation abnormalities are described. We also discuss methylation changes associated with lupus nephritis, autoantibody status and disease activity. Lastly, we explore future research directions, emphasising the need for longitudinal studies, cell tissue and context-specific profiling, as well as integrative approaches. With new technologies, DNA methylation perturbations could be targeted and edited, offering novel therapeutic approaches.
Geomorphic control on the δ 15 N of mountain forests

Abstract. Mountain forests are subject to high rates of physical erosion which can export particulate nitrogen from ecosystems. However, the impact of geomorphic processes on nitrogen budgets remains poorly constrained. We have used the elemental and isotopic composition of soil and plant organic matter to investigate nitrogen cycling in the mountain forest of Taiwan, from 24 sites with distinct geomorphic (topographic slope) and climatic (precipitation, temperature) characteristics. The organic carbon to nitrogen ratio of soil organic matter decreased with soil 14C age, providing constraint on average rates of nitrogen loss using a mass balance model. Model predictions suggest that present day estimates of nitrogen deposition exceed contemporary and historic nitrogen losses. We found ∼6‰ variability in the stable isotopic composition (δ15N) of soil and plants which was not related to soil 14C age or climatic conditions. Instead, δ15N was significantly, negatively correlated with topographic slope. Using the mass balance model, we demonstrate that the correlation can be explained by an increase in nitrogen loss by non-fractioning pathways on steeper slopes, where physical erosion most effectively removes particulate nitrogen. Published data from forests on steep slopes are consistent with the correlation. Based on our dataset and these observations, we hypothesise that variable physical erosion rates can significantly influence soil δ15N, and suggest particulate nitrogen export is a major, yet underappreciated, loss term in the nitrogen budget of mountain forests.
Predictors of time to death among preterm neonates admitted to neonatal intensive care units at public hospitals in southern Ethiopia: A cohort study

Background Although the survival of preterm neonates has improved, thanks to advanced and specialized neonatal intensive care, it remains the main reason for neonatal admission, death, and risk of lifelong complication. In this study, we assessed time to death and its predictors among preterm neonates admitted to neonatal intensive care units (NICU) at public hospitals in southern Ethiopia. Methods A hospital based retrospective cohort was conducted among preterm neonates admitted to NICU at public hospitals in west Guji and Borena zones, Oromia National Regional State, southern Ethiopia. Simple random sampling technique was used to select records of preterm neonates admitted to both major hospitals in the study area. Data on neonatal condition, obstetric information, and status at discharge were collected from admission to discharge by trained research assistant through review of their medical records. Kaplan Meir curve and Log rank test were used to estimate the survival time and compare survival curves between variables. Cox-Proportional Hazards model was used to identify significant predictors of time to death at p<0.05. Result Of 510 neonates enrolled, 130(25.5%; 95% CI: 22–29) neonates died at discharge or 28days. The median survival time was 18 days with an interquartile range of (IQR = 6, 24). The overall incidence of neonatal mortality was 47.7 (95% CI: 40.2–56.7) per 1000 neonatal days. In the multivariable cox-proportional hazard analysis, lack of antenatal care (AHR: 7.1; 95%CI: 4–12.65), primipara (AHR: 2.3; 95% CI: 1.16–4.43), pregnancy complications (AHR: 3.4; 95% CI: 1.94–6.0), resuscitation at birth (AHR: 2.1, 95% CI: 0.28–0.77) and not receiving Kangaroo mother care (AHR: 9.3, 95% CI: 4.36–19.9) were predictors of preterm neonatal death. Conclusion Despite admission to NICU for advanced care and follow up, mortality of preterm neonates was found to be high in the study settings. Addressing major intrapartum complications is required to improve survival of neonates admitted to NICU.
Cinnamaldehyde alleviates doxorubicin-induced cardiotoxicity by decreasing oxidative stress and ferroptosis in cardiomyocytes

Although doxorubicin (DOX) is an efficient chemotherapeutic drug for human tumors, severe cardiotoxicity restricts its clinical use. Cinnamaldehyde (CA), a bioactive component isolated from Cinnamonum cassia, possesses potent anti-oxidative and anti-apoptotic potentials. The major aim of this study was to evaluate the protective role of CA against DOX-induced cardiotoxicity. To this end, cardiomyocyte injury models were developed using DOX-treated H9c2 cells and DOX-treated rats, respectively. Herein, we found that CA treatment increased cardiomyocyte viability and attenuated DOX-induced cardiomyocyte death in vitro. CA further protected rats against DOX-induced cardiotoxicity, as indicated by elevated creatine kinase (CK) and lactate dehydrogenase (LDH) levels, myocardium injury, and myocardial fibrosis. CA alleviated DOX-induced myocardial oxidative stress by regulating reactive oxygen species (ROS), malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione (GSH) levels. Mechanistically, CA markedly accelerated nuclear translocation of nuclear erythroid factor 2-related factor 2 (Nrf2) and increased heme oxygenase-1 (HO-1) expression. Consequently, CA decreased DOX-induced cardiomyocyte ferroptosis, while Erastin (a ferroptosis agonist) treatment destroyed the effect of CA on increasing cardiomyocyte viability. Taken together, the current results demonstrate that CA alleviates DOX-induced cardiotoxicity, providing a promising opportunity to increase the clinical application of DOX.
New evidence on the age of the Taklimakan Desert

The Taklimakan Desert is the world's second-largest shifting sand desert, located in the rain shadow of the Tibetan Plateau. The initiation of desert formation in the Asian interior is one of the most prominent climate changes in the Northern Hemisphere during the Cenozoic Era. Dating the earliest formation of this desert is important for understanding the climatic effects of the uplifted Tibetan Plateau. Here we report 1071-m-thick Neogene deposits with inter calated eolian dune sands from the only outcrop in the central Taklimakan Desert. Based on paleo- magnetic measurements, biostratigraphic age control, and previous electron spin resonance dating results, the oldest in situ eolian dune sands were confi rmed to be ca. 7 Ma, much older than the previous reported wind-blown siltstone from the southern edge of the Taklimakan Desert. This new result indicates that desert conditions initiated ca. 7 Ma in the center of the Tarim Basin. We attribute this event to the late Cenozoic climatic deterioration and/or to the rain-shadow effect caused by late Miocene uplift of the northern Tibetan margin.
Characteristics of positive horizontal margins in patients who underwent colorectal endoscopic submucosal dissection

Abstract Objectives Endoscopic submucosal dissection (ESD) enables en bloc resection of colorectal neoplasms, but occasionally results in positive horizontal margins (HMs). However, the site of the resected specimen that tends to be positive for HM has not been investigated. We aimed to clarify the characteristics associated with HMs in lesions resected en bloc with ESD. Methods Patients with colorectal neoplasms who underwent en bloc resection with ESD were included in this study. The patients were divided into negative HMs (HM0) and positive or indeterminate HMs (HM1) groups. The characteristics associated with HM1 resection were investigated. In addition, the local recurrence rate during endoscopic follow‐up for >6 months after ESD was observed. Results In total, 201 lesions were analyzed in 189 patients (HM0, 189 lesions; HM1, 12 lesions). The HM1 group had a significantly larger median lesion diameter (25 vs. 55 mm; p < 0.001) and more lesions with >50% circumference than did the HM0 group (p < 0.001). Furthermore, the prevalence of severe fibrosis was significantly higher in the HM1 group than in the HM0 group (p < 0.001). Positive horizontal sites of the resected specimens were more frequent at the oral and anal sites than at the lateral sites. No local recurrences were observed in either group. Conclusions The characteristics associated with HM1 depended on lesion size, particularly lesions with >50% circumference, and submucosal fibrosis.
Microbial-Activated Sediment Traps Associated with Oncolite Formation Along a Peritidal Beach, Northern Arabian (Persian) Gulf, Kuwait

Identification of microbial communities within shoreline sediments and sediment precipitates from the Tigris-Euphrates delta (northern Kuwait) were determined by microscopic/nanoscopic studies, and by molecular analysis. Oncolites are syn-diagenetic carbonate precipitates that are surviving in a shallow subtidal to intertidal siliciclastic environment with periodically excessive hydraulic energy, extreme salinity (up to 47 per mil), and high concentrations of organic matter. X-ray diffraction techniques reveal that oncolite cortices are predominantly composed of calcite, quartz, halite and dolomite, associated with minor fractions of clay minerals. Quantitative analysis of the Corey Shape Factor reveals distinct morphological populations but with local overlap. A plot of the Equivalent Diameter vs. Corey Shape Factor provided the best indicator of the morphological relationships within the total oncolite population, indicating a hydrodynamically controlled morphological distribution defining intertidal and subtidal oncolite classes. Direct microscopic examination of the samples indicates that diatoms are the most abundant eukaryotic algae in subtidal sediments and within actively precipitating carbonate cements, especially the genus Navicula. In contrast, filamentous cyanobacteria from the genus Anabaena are most abundant in the intertidal zone sediments. The PCR-DGGE of the 16SrRNA gene of the cyanobacteria shows a higher diversity for this genus of bacteria in all sediment samples and that the cyanobacterial population in the diagenetically precipitating oncolites are closely related to the population found in the subtidal sediments. Dunaliella viridis dominates the culturable algae obtained from the four tidal zones. Our results indicate that a range of microbial populations are actively contributing to the formation of microbially-induced sedimentary structures in the extreme conditions of the southern Tigris-Euphrates delta.
Atmospheric deposition and forest nutrient cycling. A synthesis of the Integrated Forest Study.

Over the past decade there has been considerable interest in the effects of atmospheric deposition on forest ecosystems. This volume summarizes the results of the Integrated Forest Study (IFS), one of the most comprehensive research programs conducted. It involved intensive measurements of deposition and nutrient cycling at seventeen diverse forested sites in the United States, Canada, and Norway. The IFS is unique as an applied research project in its complete, ecosystem-level evaluation of nutrient budgets, including significant inputs, outputs, and internal fluxes. It is also noteworthy as a more basic investigation of ecosystem nutrient cycling because of its incorporation of state-of-the-art methods, such as quantifying dry and cloud water deposition. Most significantly, the IFS data was used to test several general hypotheses regarding atmospheric deposition and its effects. The data sets also allow for far-reaching conclusions because all sites were monitored over the same period using comparable instruments and standardized protocols.
Modeled deposition of nitrogen and sulfur in Europe estimated by 14 air quality model systems: evaluation, effects of changes in emissions and implications for habitat protection

The evaluation and intercomparison of air quality models is key to reducing model errors and uncertainty. The projects AQMEII3 and EURODELTA-Trends, in the framework of the Task Force on Hemispheric Transport of Air Pollutants and the Task Force on Measurements and Modelling, respectively (both task forces under the UNECE Convention on the Long Range Transport of Air Pollution, LTRAP), have brought together various regional air quality models to analyze their performance in terms of air concentrations and wet deposition, as well as to address other specific objectives. This paper jointly examines the results from both project communities by intercomparing and evaluating the deposition estimates of reduced and oxidized nitrogen (N) and sulfur (S) in Europe simulated by 14 air quality model systems for the year 2010. An accurate estimate of deposition is key to an accurate simulation of atmospheric concentrations. In addition, deposition fluxes are increasingly being used to estimate ecological impacts. It is therefore important to know by how much model results differ and how well they agree with observed values, at least when comparison with observations is possible, such as in the case of wet deposition. This study reveals a large variability between the wet deposition estimates of the models, with some performing acceptably (according to previously defined criteria) and others underestimating wet deposition rates. For dry deposition, there are also considerable differences between the model estimates. An ensemble of the models with the best performance for N wet deposition was made and used to explore the implications of N deposition in the conservation of protected European habitats. Exceedances of empirical critical loads were calculated for the most common habitats at a resolution of 100 × 100 m2 within the Natura 2000 network, and the habitats with the largest areas showing exceedances are determined. Moreover, simulations with reduced emissions in selected source areas indicated a fairly linear relationship between reductions in emissions and changes in the deposition rates of N and S. An approximate 20 % reduction in N and S deposition in Europe is found when emissions at a global scale are reduced by the same amount. European emissions are by far the main contributor to deposition in Europe, whereas the reduction in deposition due to a decrease in emissions in North America is very small and confined to the western part of the domain. Reductions in European emissions led to substantial decreases in the protected habitat areas with critical load exceedances (halving the exceeded area for certain habitats), whereas no change was found, on average, when reducing North American emissions in terms of average values per habitat.
Longitudinal modulation of the O/N2 column density retrieved from TIMED/GUVI measurement

The longitudinal variation of thermospheric O/N2 column density ratio is studied, based on the TIMED/GUVI measurements collected during 2002‐2007. In October, a four‐peaked longitudinal fluctuation in O/N2 is found. The wavenumber‐4 fluctuation in equatorial O/N2 is generally stronger at lower solar activity, and maximizes in the morning of boreal summer and autumn. In boreal winter, the wavenumber‐4 component gives way to the wavenumber‐3. Such seasonal variation and solar activity dependence are consistent with those of the diurnal eastward‐propagating mode with wavenumber‐3, but the local time dependence is not. The daytime wavenumber‐4 pattern in O/N2 does not shift eastward in local time as expected if it is directly connected to the DE3. No definite explanation is found for this structure, but a consideration of various mechanisms suggests that the vertical wind effect may be the most potential candidate.
Retention of Greenland runoff by refreezing: Implications for projected future sea level change

Melting produced at the surface of subfreezing permeable firn does not freely percolate but instead refreezes near its point of origin, raising the firn temperature and decreasing the pore space. If sufficient meltwater is introduced, the firn will warm to 0°C, and subsequent water will fill the remaining pore space without freezing. Only after the residual water content of the firn is exceeded will water flow through the firn and possibly escape as runoff. This process prevents summer melt on high Arctic glaciers and ice caps from escaping in its entirety, and it must be accounted for in modeling glacier runoff on the basis of surface energy balance. A model is presented here which describes in a simple way the transient process of infiltration, refreezing, and runoff in a future warming climate. The model is applied to Greenland, for which predictions of runoff-induced sea level rise that do not consider the refreezing process could be as much as 5.0 cm too high over 150 years.
Dynamics of phosphorus compounds in a lowland river system: Importance of retention and non‐point sources

Intensive measurements of the fluxes of phosphorus (P) and of P retention were carried out in a Danish lowland watershed (Gjern A) during two hydrological years (June 1987 to May 1989). Seasonal and short-term variations of P concentrations were measured by intensive automatic sampling covering P fluxes from the entire Gjern A watershed and two subcatchments: the Gelbaek and Lake Sobygard. Moreover, infrequent sampling was performed in all major tributaries of the river system. Transport of P compounds (dissolved and particulate P) exposed a seasonal pattern which was highly affected by flow conditions, instream processes, as well as point and non-point sources. Stormflow P transport during the two study years (1987-8 and 1988-9) constituted 56 and 61% in the Gelbaek, respectively, compared with 25 and 23% in the Gjern A, respectively. Particulate P transport in the Gelbaek constituted 56 and 75% of annual total P transport during the two years compared with 77 and 75% in the Gjern A. The magnitude of monthly baseflow and stormflow total P loads was significantly correlated with the mean monthly discharge during baseflow and stormflow in the Gelbaek, whereas only stormflow loads were correlated to discharge in the Gjern A. In situ measurements of retention showed that the maximum amount of P stored in the Gelbaek during summer (June to August) was 22gPm−2 (1988) compared with 27gPm−2 (1987) in the Gjern A. Lake Sobygard was a P source during summer but a P sink during winter and on an annual basis the net P released was 810 and 1420 kg, which corresponded to 7 and 20% of the annual P export from the watershed, respectively. Retention constituted about 30% of gross P transport in the Gelbaek during summer compared with 20% in the Gjern A. Resuspension of retained P during stormflows in September 1987 constituted 94% of the stormflow P transport and 54% of the total P transport. Monthly total P and dissolved reactive P (DRP) mass balances for the main channel of the Gjern A revealed a significant DRP retention over 17 months (p < 0.05) caused by P adsorption on sediments and biological uptake. On an annual basis the main channel was a sink of DRP (1220 and 1660 kg P) but a source of total P (3440 and 1000 kg P). implying that the channel is an important source of particulate P. Bank erosion proved to be a significant P source in the main channel of Gjern A, whereas P delivery from soil erosion was possibly of minor importance. The annual non-point P export from two intensively sampled catchments was significantly higher (0.89 and 0.45 kg Pha−1 yr−1) than from the five extensively sampled subbasins (0.43 and 0.17 kg Pha−1 yr−1). No significant relationship could be established between non-point P export and the proportion of arable land and soil type. Only for the wet year of 1987-8 was a significant relationship established between non-point P export and the P load from scattered dwellings outside sewage areas in five subbasins.