Miracle-dz/UniFAR-FTUs huggingface dataset:
New challenges in integrated water quality modelling

There is an increasing pressure for development of integrated water quality models that effectively couple catchment and in‐stream biogeochemical processes. This need stems from increasing legislative requirements and emerging demands related to contemporary climate and land use changes. Modelling water quality and nutrient transport is challenging due a number of serious constraints associated with the input data as well as existing knowledge gaps related to the mathematical description of landscape and in‐stream biogeochemical processes. The present paper summarizes the discussions held during the workshop on ‘Integrated water quality modelling: future demands and perspectives’ (Magdeburg, Germany, 23–24 June 2008). Our primary focus is placed on the current limitations and future challenges in water quality modelling. In particular, we evaluate the current state of integrated water quality modelling, we highlight major research needs to assess and reduce model uncertainties, and we examine opportunities to enhance model predictive capacity. To better account for the need of upscaling process knowledge, we advocate the adoption of combined process‐oriented field and modelling studies at representative sites. In‐stream nutrient metabolism investigations at the entire range of stream and river scales will enable the improvement of the mathematical representation of these processes and therefore the articulation level of coupled watershed‐receiving waterbody models. Keeping the complexity of integrated water quality models in mind, the development of novel uncertainty analysis techniques for rigorous assessing parameter identification and model credibility is essential. In this regard, we recommend the use of Bayesian calibration frameworks that explicitly accommodate measurement errors, parameter uncertainties, and model structure errors. The Bayesian inference can be used to quantify the information the data contain about model inputs, to offer insights into the covariance structure among parameter estimates, to obtain predictions along with credible intervals for model outputs, and to effectively address the ‘change of support’ problems. Copyright © 2010 John Wiley & Sons, Ltd.
Pharmacists Views and Practices in Regard to Sales of Antibiotics Without a Prescription in Madinah, Saudi Arabia

Objective The aim of this study was to investigate pharmacists views and practices in Madinah, Saudi Arabia, through conducting direct interviews including direct questions and hypothetical scenarios. Methods A purposeful sample of 150 community pharmacists of different ethnic and educational backgrounds were approached to participate in the study. Semistructured interviews including general questions and 5 hypothetical scenarios were used for the investigation. Complete transcripts of the interviews were prepared. All transcripts were coded and categorized into main themes using a computer software. Results Fifty-four pharmacists agreed to participate (response rate, 36%). Sale of antibiotics without prescription is commonly practiced in Saudi Arabia. Lack of legislation enforcement has exacerbated this practice. Economic hardship, patient’s age, emotional factors, and pharmacists’ self confidence in diagnosing and prescribing medications in general and antibiotics in particular were the themes included in the interviews and influenced pharmacists’ decision to sell antibiotics without a prescription. Many pharmacists did not see the practice as a problem and felt capable of continuing to dispense antibiotics without a prescription. Pharmacists who saw the practice as a problem sees legislation enforcement to be the solution of the problem. Conclusions Pharmacist views and practices are alarming. The results of this study show that this practice will continue to spread unless strict enforcement is put in place, Lack of clear understanding of the limitations of pharmacist’s scope of practice. Results of these studies can be extrapolated to other countries in the region and other countries of the similar social and professional development status.
Regeneration of a phosphate-polluted field site: Implications of arbuscular mycorrhiza

This work aimed to investigate the structure and function of arbuscular mycorrhiza (AM) in a phosphate-polluted field site. Despite exceedingly high phosphorus (P)-availability, plants were strongly mycorrhizal, although the fungi should not play an essential role in the P-nutrition of hosts, usually their main function. Molecular analyses revealed that fungal diversity was reduced; however, no species were exclusive – and thus, maybe adapted – to this site. Instead, enriching the nitrogen (N)-level in the N-poor area led to reduced mycorrhization intensities of roots, implying that plants are mycorrhizal due to N-deficiency. Reduced mycorrhization following fungicide treatments led to as well reduced N-concentrations in some plant species, indicating that in fact, AM is able to improve N-nutrition of its hosts at this field site. However, not all species benefited from this mycorrhiza-mediated N-uptake and accordingly, -distribution: even negative mycorrhizal effects could be detected. This is discussed with regard to mycorrhizal responsiveness of different plant species and possible implications of mycorrhizal networks.
Histopathological Correlations between Mediastinal Fat-Associated Lymphoid Clusters and the Development of Lung Inflammation and Fibrosis following Bleomycin Administration in Mice

Bleomycin (BLM) has been reported to induce lung inflammation and fibrosis in human and mice and showed genetic susceptibility. Interestingly, the C57BL/6 (B6) mice had prominent mediastinal fat-associated lymphoid cluster (MFALCs) under healthy condition, and showed susceptibility to development of lung fibrosis following BLM administration. However, the pathogenesis of lung lesion progression, and their correlation with MFALC morphologies, remain to be clarified. To investigate the correlations between MFALC structures and lung injuries in B6 mice, histopathological examination of mediastinal fat tissues and lungs was examined at 7 and 21 days (d) following a single 50 μL intranasal (i.n.) instillation of either BLM sulfate (5 mg/kg) (BLM group) or phosphate-buffered saline (control group). The lung fibrosis was examined by Masson’s trichrome (MT) stain of paraffin sections and mRNA expression levels of Col1a1, Col3a1, and Acta2 in different frozen lung samples. Furthermore, immunohistochemistry for CD3, B220, Iba1, Gr1, BrdU, LYVE-1, and peripheral node addressin (PNAd) was performed to detect T- and B-cells, macrophages, granulocytes, proliferating cells, lymph vessels (LVs), and high endothelial venules (HEVs). We found that MFALCs were more abundant in the BLM group as compared to the control group. The lung of BLM group developed pneumonitis with severe cellular infiltrations at 7 days and significant collagen deposition (MT) and higher expression of Col1a1, and Col3a1 at 21 days post-administration. Numerous immune cells, proliferating cells, HEVs, and LVs were observed in both MFALCs and lungs of the BLM group. Interestingly, PNAd + HEVs were observed in the lungs of the BLM group, but not the control group. Moreover, numerous Gr1 + polymorphonuclear and mononuclear-like ring cells were found in the MFALCs and lungs of the BLM group. Interestingly, flow cytometric analysis revealed a significant increase of B-cell populations within the MFALCs of BLM group suggesting a potential proliferative induction of B-cells following inflammation. Furthermore, significant positive correlations were observed between quantitative parameters of these immune cells in both the lungs and MFALCs. Thus, we suggest a potentially important role for MFALCs and HEVs in the progression of lung disease, especially in inflammatory lung disease.
Edge effects enhance carbon uptake and its vulnerability to climate change in temperate broadleaf forests

Significance A large proportion of the world’s forest is highly fragmented, but our understanding of forest carbon dynamics and their response to climate largely comes from unfragmented forests, which presents an important mismatch between landscapes that we study and those that we aim to characterize. We find that temperate broadleaf forest growth and biomass in southern New England increase substantially from forest interior to edge. However, forest growth reductions with climate stress increase with proximity to the edge, pointing to important interactions between forest fragmentation and climate change. We show that, by not accounting for edge effects, current approaches to quantifying regional and global carbon balance may underestimate carbon sequestration and not accurately represent forest growth response to future climate change. Forest fragmentation is a ubiquitous, ongoing global phenomenon with profound impacts on the growing conditions of the world’s remaining forest. The temperate broadleaf forest makes a large contribution to the global terrestrial carbon sink but is also the most heavily fragmented forest biome in the world. We use field measurements and geospatial analyses to characterize carbon dynamics in temperate broadleaf forest fragments. We show that forest growth and biomass increase by 89 ± 17% and 64 ± 12%, respectively, from the forest interior to edge, but ecosystem edge enhancements are not currently captured by models or approaches to quantifying regional C balance. To the extent that the findings from our research represent the forest of southern New England in the United States, we provide a preliminary estimate that edge growth enhancement could increase estimates of the region’s carbon uptake and storage by 13 ± 3% and 10 ± 1%, respectively. However, we also find that forest growth near the edge declines three times faster than that in the interior in response to heat stress during the growing season. Using climate projections, we show that future heat stress could reduce the forest edge growth enhancement by one-third by the end of the century. These findings contrast studies of edge effects in the world’s other major forest biomes and indicate that the strength of the temperate broadleaf forest carbon sink and its capacity to mitigate anthropogenic carbon emissions may be stronger, but also more sensitive to climate change than previous estimates suggest.
The Assessment and Treatment of Precursor Behavior Evoked by Aversive Noise in a Residential Setting

2 Introduction 3 General Method 12 Participants and Setting 12 Response Measurement and Reliability 13 Phase One: Preference Assessments 15 Procedure 15 Results 16 Phase Two: Functional Analysis 17 Procedure 17 Results 18 Phase Three: Treatment Evaluation 19 Baseline 19 Extinction plus Stimulus Fading 19 Design 20 Results 20 Discussion 22 References 28 Tables 30 Figure Captions 32 Figures 33 PRECURSOR EVOKED BY NOISE 2 Abstract Previous research has demonstrated both an effective methodology of assessment and treatment of problem behavior evoked by aversive noises. The current study extended previous research by conducting both the assessment and treatment of precursor behavior evoked by a peer’s noises within a residential setting. During the first phase, a modified functional analysis (McCord, Iwata, Galensky, Elligson, & Thomson, 2001) was conducted for three participants with autism. Precursor behavior occurred during only the escape from noise condition of the functional analysis suggesting that all three individual’s tantrum behavior was evoked by a specific peer’s noises and maintained by escape from these noises. An intervention consisting of extinction combined with stimulus fading, during which the duration of the aversive noise was systematically increased, was then implemented. Near zero levels of precursor behavior in the presence of the loud noise was observed across all three participants during the final three 10 minute sessions.
Does mRNA structure contain genetic information for regulating co-translational protein folding?

Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model with supports of genomic data is still lacking. Recent technological advances have enabled much needed genome-wide experiments. While putting the effect of codon optimality on debate, these studies have supplied mounting evidence suggesting a role of mRNA structure in the regulation of protein folding by modulating translational elongation rate. In conjunctions with previous theories, this mechanistic model of protein folding guided by mRNA structure shall expand our understandings of genetic information and offer new insights into various biomedical puzzles.
Basic and Clinical Evidence of an Alternative Method to Produce Vivo Nanofat

Background: Fat grafting technologies are popularly used in plastic and reconstructive surgery. Due to its size limitation, it is hard to directly inject untreated fat tissue into the dermal layer. Nanofat, which was introduced by Tonnard, solves this problem by mechanically emulsifying fat tissue. However, the viability of the cells was greatly destroyed. In this study, we reported a new method by “gently” digesting the fat tissue to produce viable adipocytes, progenitors, and stromal stem cells using collagenase I digestion and centrifugation. This was named “Vivo nanofat”. Methods: Human liposuction aspirates were obtained from five healthy female donors with mean age of 28.7 ± 5.6 years. Colony-forming assay, flow cytometry analysis, and adipogenic and osteogenic induction of the adherent cells from the Vivo nanofat were used to characterize the adipose mesenchymal stem cells (MSCs). To investigate in vivo survival, we respectively injected Vivo nanofat and nanofat subcutaneously to the back of 8-week-old male BALB/c nude mice. Samples were harvested 2 days, 2 weeks, and 4 weeks postinjection for measurement, hematoxylin and eosin staining, and immunostaining. Results: Our results showed that the Vivo nanofat contained a large number of colony-forming cells. These cells expressed MSC markers and had multi-differentiative potential. In vivo transplantation showed that the Vivo nanofat had lower resorption ratio than that of nanofat. The size of the transplanted nanofat was obviously smaller than that of Vivo nanofat 4 weeks postinjection (0.50 ± 0.17 cm vs. 0.81 ± 0.07 cm, t = −5783, P = 0.01). Conclusion: Vivo nanofat may serve as a cell fraction injectable through a fine needle; this could be used for cosmetic applications.
Visualizations for genetic assignment analyses using the saddlepoint approximation method

We propose a method for visualizing genetic assignment data by characterizing the distribution of genetic profiles for each candidate source population. This method enhances the assignment method of Rannala and Mountain (1997) by calculating appropriate graph positions for individuals for which some genetic data are missing. An individual with missing data is positioned in the distributions of genetic profiles for a population according to its estimated quantile based on its available data. The quantiles of the genetic profile distribution for each population are calculated by approximating the cumulative distribution function (CDF) using the saddlepoint method, and then inverting the CDF to get the quantile function. The saddlepoint method also provides a way to visualize assignment results calculated using the leave‐one‐out procedure. This new method offers an advance upon assignment software such as geneclass2, which provides no visualization method, and is biologically more interpretable than the bar charts provided by the software structure. We show results from simulated data and apply the methods to microsatellite genotype data from ship rats (Rattus rattus) captured on the Great Barrier Island archipelago, New Zealand. The visualization method makes it straightforward to detect features of population structure and to judge the discriminative power of the genetic data for assigning individuals to source populations.
The association between expression of IFIT1 in podocytes of MRL/lpr mice and the renal pathological changes it causes: An animal study

Renal damage is the major cause of SLE associated mortality, and IFIT1expression was elevated in SLE cases in accordance of previous studies. Therefore, we conducted an animal study to identify the role of IFIT1 expression in renal pathological changes.18 female MRL/lpr mice and same number of female BALB/c mice were enrolled in present study. Quantitative analysis of urine protein, Complement C3 and C4, and anti-ds DNA antibody were conducted. HE and PAS staining and TEM analysis were employed to observe the pathological changes in renal tissue. Significant elevation on urine protein and anti-dsDNA and reduction on Complement C3 and C4 were observed in MRL/lpr mice when comparing the controls in same age. Staining and TEM analysis observed several pathological changes in glomerulus among MRL/lpr mice, including cellular enlargement, basement membrane thickening, and increased cellularcasts. The linear regression analysis found the optical density of IFIT1 was inversely associated with F-actin, Nephrin, and Podocin, but not Synatopodin. In summary, IFIT1 expression is associated with podocytes damage, and capable of suppressing some proteins essential to glomerular filtration.
Adverse drug reactions in Colombian patients, 2007-2013: Analysis of population databases.

INTRODUCTION Recognizing adverse drug reactions (ADRs) is becoming more important in clinical practice. OBJECTIVE To determine the frequency of adverse drug reactions and ADR suspicions among the population affiliated to the Colombian health system and to describe the drugs, reactions and associated variables. MATERIALS AND METHODS We revised ADRs and ADRs suspicion databases from drugs dispensed by Audifarma, S.A. , both for inpatient and outpatient care from 2007 to 2013. Variables included ADR report date, city, drug, drug's Anatomical Therapeutic Classification (ATC), ADR severity, ADR type, ADR classification and ADR probability according to the World Health Organization's definitions. RESULTS We obtained 5,342 reports for 468 different drugs. The ATC groups with the most reports were anti-infectives for systemic use (25.5%), nervous system agents (17.1%) and cardiovascular system drugs (15.0%). The drugs with the highest number of reports were metamizole (4.2%), enalapril (3.8%), clarithromycin (2.8%), warfarin (2.5%) and ciprofloxacin (2.4%). The most common ADR, classified following the World Health Organization adverse reaction terminology, were: skin and appendages disorders (35.3%), general disorders (14.2%) and gastrointestinal system disorders (11.8%). Overall, 49.4% of the ADRs were classified as "moderate" and 45.1% as "mild". CONCLUSION An increasing number of ADR reports were found coinciding with a worldwide tendency. Differences between inpatient and outpatient ADR reports were found when compared to scientific publications. The information on ADR reports, mainly gathered by the Instituto Nacional de Vigilancia de Medicamentos y Alimentos - Invima, should be made public for academic and institutional use.
Categorization in infancy: labeling induces a persisting focus on commonalities

Abstract Recent studies with infants and adults demonstrate a facilitative role of labels in object categorization. A common interpretation is that labels highlight commonalities between objects. However, direct evidence for such a mechanism is lacking. Using a novel object category with spatially separate features that are either of low or high variability across the stimulus set, we tracked 12‐month‐olds’ attention to object features during learning and at test. Learning occurred in both conditions, but what was learned depended on whether or not labels were heard. A detailed analysis of eye movements revealed that infants in the two conditions employed different object processing strategies. In the silent condition, looking patterns were governed exclusively by the variability of object parts. In the label condition, infants’ categorization performance was linked to their relative attention to commonalities. Moreover, the commonality focus persisted after learning even in the absence of labels. These findings constitute the first experimental evidence that labels induce a persistent focus on commonalities.
Parametric Studies on the Moderation Ratio of a 2-zone 1-fluid Molten Salt Reactor

In this thesis a numerical model to simulate the burnup and neutronics in a MSR (Molten Salt Reactor) has been used. Both a 1-zone core as well as a 2-zone core for improved breeding have been investigated. Simulation is done with the SCALE code system in combination with a burnup code LOWFAT. Aim of this study is to find a core that can operate at the highest power density within certain constraints. Different constraints are set, with respect to sustainability, safety and feasibility. This led to constraints for breeding (at least a self-breeder) graphite lifetime (>10 y), temperature feedback (<-1 pcm/K) initial fissile load and radiotoxicity of the TRUs (Trans-Uranic Elements) in the used salt. First a 1-zone core is compared to a PWR (Pressurised Water Reactor) in terms of radiotoxicity of TRUs. Results show a much cleaner energy production for the thorium fuel cycle used in a MSR compared to the uranium fuel cycle in a PWR. Also different self-breeder 1-zone MSRs are run for four cycles of 50 years, cleaning the salt from FP (Fission Products) in between cycles, to investigate effects on the breeding gain (BG) and radiotoxicity. The buildup of actinides in the salt during the cycles causes the BG to drop over time. A parametric study dividing a MSR into two zones radially with different graphite to salt volume ratios to improve breeding is done. The 2-zone MSR uses the same salt composition and chemical reprocessing scheme as the 1-zone MSR. Results show that due to a large increase in BG the 2-zone MSR is capable of operating at higher power densities while staying a selfbreeder compared to a 1-zone MSR. As a drawback graphite lifetime is shortened, as power production is concentrated mostly in one zone. MSc. Thesis Frederik de Vogel
Elevated Serum Uric Acid Level Predicts Rapid Decline in Kidney Function

Background: While elevated serum uric acid level (SUA) is a recognized risk factor for chronic kidney disease, it remains unclear whether change in SUA is independently associated with change in estimated glomerular filtration rate (eGFR) over time. Accordingly, we examined the longitudinal associations between change in SUA and change in eGFR over 5 years in a general Japanese population. Methods: This was a large, single-center, retrospective 5-year cohort study at St. Luke's International Hospital, Tokyo, Japan, between 2004 and 2009. We included 13,070 subjects (30-85 years) in our analyses whose data were available between 2004 and 2009. Of those, we excluded 492 subjects with eGFR <60 mL/min/1.73 m2 at baseline. In addition to examining the entire cohort (n = 12,578), we stratified our analyses by baseline eGFR groups: 60-90, 90-120, and ≥120 mL/min/1.73 m2. Linear and logistic regressions models were applied to examine the relationships between baseline and change in SUA, change in eGFR, and rapid eGFR decline (defined as the highest quartile of change in eGFR), adjusted for age, gender, body mass index, abdominal circumference, hypertension, dyslipidemia, and diabetes mellitus. Results: After multivariable adjustments including baseline eGFR, 1 mg/dL increase in baseline SUA was associated with greater odds of developing rapid eGFR decline (OR 1.27, 95% CI 1.17-1.38), and 1 mg/dL increase in SUA over 5 years was associated with 3.77-fold greater odds of rapid eGFR decline (OR 3.77, 95% CI 3.35-4.26). Conclusions: Elevated baseline SUA and increasing SUA over time were independent risk factors for rapid eGFR decline over 5 years.