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Aslı Demir

and 3 more

An incubation experiment was carried out to assess bone char application on the availability and distribution of phosphorus in agricultural alkaline sandy soils. Three alkaline agricultural sandy soils in Upper Egypt have been collected from Arab El-Awamer at Assiut governorate, West El-Minia at El-Minia governorate, and New Valley Governorate. 100 grams were taken from each soil under study and placed in a plastic jar. The bone char is applied at level 0.4 g jar-1 into these soils. This experiment was incubated at 23 ºC in the dark for periods of 7, 16, 35, 65, and 84 days and arranged in a completely randomized design with three replicates. The results revealed that bone char applications to the soils resulted in a significant positive increase in the availability of phosphorus affected by the soil type and incubation periods in Arab El-Awamer soil. The percentage of increase in available phosphorous after adding bone char compared to before incubation was as follows: Arab El-Awamer soil ˃New Valley soil ˃West El-Minia soil. The available phosphorous was negatively correlated with electrical conductivity (r=-0.288*), soluble calcium (r=-0.306*), and soluble sulfate (r=-0.413*). The concentrations of NH4Cl-Pi, NaHCO3-Pi, NaOH-Pi, HCl-Pi, residual-P fractions increased significantly in some soil types with applying bone char. The concentrations of available phosphorous in all soils under study were positively correlated with all phosphorus fractions. We conclude that bone char applications into P-poor soil are important to potentially enhance phosphorus availability. Bone char is considered a promising strategy in sustainable agriculture.

Antonis Ioannou

and 9 more

We present the case of a 44-year-old woman who suffered an out of hospital cardiorespiratory arrest. After six direct current shocks and 10 minutes of cardiopulmonary resuscitation she had return of spontaneous circulation and regained consciousness. Transthoracic echocardiography showed normal left ventricular ejection fraction and a mildly dilated left atrium. The mitral valve was thickened with myxomatous degeneration (Barlow’s disease) and moderate regurgitation secondary to bi-leaflet prolapse. Cardiac catheterization showed no coronary artery disease while left ventriculography revealed a mildly dilated left ventricle with preserved systolic function and high-end diastolic pressures. Cardiac MRI revealed an enlarged left ventricle with mitral valve (MV) prolapse and moderate to severe mitral regurgitation (MR). There were no features suggestive of a specific cardiomyopathy other than her valvular heart disease. The patient had an uneventful hospitalization, received an implantable cardioverter defibrillator (ICD), and eventually had MV repair surgery. A genetic investigation revealed two DNA variants, one each in the MYPN and TMPO gene, substitutions of highly conserved aminoacid residues. Family segregation could not establish unequivocally their pathogenicity although the MYPN variant represents the same residue that was shown previously to be substituted by another aminoacid. In this article we also review the literature regarding similar cases and record important data for the epidemiology of the disease and the important research that has been carried out in the identification of prognostic imaging factors and the genetic background of these patients.

Bastian Saez

and 2 more

The Norte Grande of Chile (17°S-29°S) features arid regions, where rainfall is generally convective with high spatial and temporal variability, which is the cause of floods with large amounts of sediments due to water erosion. The most relevant factor in erosive processes in arid regions is erosivity, which can be quantified by the RUSLE R-factor, but precipitation data are required every 30 minutes, however, these records are limited. The ones that are available are not enough to characterize it spatially. Consequently, the objective of this study is to evaluate regression models of the annual erosivity using rainfall aggressiveness indices as an explanatory variable, with the aim of analyzing the spatial behavior of erosion. Correlations were made between the maximum intensity in 30 minutes (I30) to the maximum intensity in one hour (I60), which were useful for calculating the R-factor for stations with hourly data by applying a correction factor to I60 determined by the correlations. Four regression models were established for each of the six aggressiveness indices and a relationship was selected through validation, using stations with few years of continuous recording. The selected equation allowed generating 103 spatially distributed erositivy-values, which served to make a subsequent co-kriging, in order to make a spatial analysis of rainfall erosivity. Results showed that there are under-estimations of I30, however, they are considered acceptable due to the efficiency obtained (Nash-Sutcliffe = 0.787). The calculated R-factor data-points allowed selection of the best-fit potential equation, which uses the mean annual rainfall as a predictor

Dan Hu

and 7 more

Objective: To evaluate the impact of elevated body mass index (BMI) on short- and long-term outcomes of in-vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) treatments. Design: Retrospective cohort study. Setting: Teaching hospital. Population: Overall, 7229 patients undergoing IVF/ICSI fresh cycles and subsequent frozen embryo transfer cycles during 2014-2020. Methods: The patients were divided into normal (18.5–24.9 kg/m2) and high BMI (≥ 25 kg/m2) groups. Subgroup analyses were performed based on the boundary of 38 years old. Multivariate analysis was used to determine whether BMI was associated with live birth rate (LBR) or cumulative live birth rate (CLBR). Main Outcome Measure: Ovarian response, pregnancy outcomes, and safety for both mother and fetus. Results: For younger women (< 38y), CLBR was significantly reduced in the high BMI subgroup compared to the normal BMI control (73.7% vs 76.8%, p = 0.008) and was accompanied by fewer retrieved oocytes and available embryos. Meanwhile, the incidences of cesarean section (92.9% vs 87.1%, p < 0.001), hypertensive disorders of pregnancy (6.7% vs 3.1%, p < 0.001), fetal macrosomia (4.7% vs 2.8%, p = 0.002) and birth defects involving cleft lip and palate (0.4% vs 0.1%, p = 0.030) were significantly higher than the normal BMI group. However, no such differences were observed among older women (≥ 38y). Multivariate analysis revealed that high BMI was a risk factor for CLBR (OR = 0.837, 95% CI: 0.729–0.96). Conclusions: Elevated BMI has a greater adverse impact on younger women.
Background: The aim of the current investigation was to explore predisposing factors for food protein induced allergic proctocolitis (FPIAP) in Greek infants relevant in the maternal diet, during pregnancy and breastfeeding, as relevant knowledge is limited. Methods: A multicenter retrospective case-control study was conducted in 6 regions in Greece, with 96 mothers of infants with and 141 mothers of infants without a history of FPIAP. Maternal dietary habits during pregnancy and breastfeeding were evaluated with validated questionnaires: a) The Mediterranean Diet (MedDiet) Score, and b) The Mediterranean Oriented Culture Specific Semi-Quantitative Food Frequency Questionnaire. Statistical tests, modeling and exploration of the FPIAP risk in relation to the maternal diet using elastic net regression models were performed with R software and Studio. Results: FPIAP was associated with cow’s milk (83.6%), egg (7.3 %), and wheat, beef (6.4%) in the maternal diet. Adherence to MedDiet was similar among the mothers, but mothers of FPIAP infants consumed more vegetables (p=0.018) and olive oil (p=0.003). Elastic net prediction models showed that, in this Mediterranean population, increased consumption during pregnancy and lactation of common allergens, whole grain products, homemade food, fish and shellfish, fruit offered protection; conversely, high intake of vegetables, sugar and total fat, and non-stick/grilled cooking, increased the risk of FPIAP, as did high intake of salt and white flour during lactation. Conclusions: Components of a maternal Mediterranean diet can protect against FPIAP when traditional cooking methods are adopted and fish, fruit and whole wheat products are consumed frequently.

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Sangjun Yoo

and 7 more

Introduction: We assessed the effects of preoperative bladder compliance on the long-term functional outcomes, especially focused on postoperative storage symptom changes, after laser prostatectomy. Materials and Methods: From January 2008 to March 2014, 1608 men who underwent laser prostatectomy, including holmium laser enucleation or photo-vaporization of the prostate, were included in the analysis. We divided patients into 3 groups according to bladder compliance on a baseline urodynamic study: < 12.5; 12.5–25.0; ≥25 mL/cm H2O. A multivariable analysis was performed to determine the impact of bladder compliance on long-term functional outcomes after laser prostatectomy. Results: Bladder compliance was less than 12.5 ml/cm H2O in 50 (3.1%), 12.5-25 ml/cm H2O in 232 (14.4%) patients. As bladder compliance decreased, the baseline International Prostate Symptom (I-PSS) total score and storage sub-score were increased; the voiding sub-score remain unchanged. At postoperative 36 months, improvements in the I-PSS total score and storage sub-score were significantly higher in < 12.5 mL/cm H2O group compared to other groups, although those were equivalent at postoperative 1 and 12 months. On the multivariable analysis, decreased bladder compliance < 12.5 mL/cm H2O was significantly associated with superior improvement in storage sub-score at postoperative 36 months, although it was not associated with voiding sub-score. Conclusion: In patients with preoperative bladder compliance < 12.5 mL/cm H2O, storage symptoms could be further improved at 36 months after laser prostatectomy compared to others. Thus, laser prostatectomy could be a considerable treatment option for patients with severely decreased bladder compliance

Colum Keohane

and 6 more

Abstract Objective To determine whether the introduction of a one-stop see and treat clinic offering early reflux ablation for Venous Leg Ulcer (VLU) patients in July 2016 has affected rates of unplanned inpatient admissions due to venous ulceration. Design Review of inpatient admission data and analysis of related costs. Materials The Hospital Inpatient Enquiry collects data from acute public hospitals in Ireland on admissions and discharges, coded by diagnosis and acuity. This was the primary source of all data relating to admissions and length of stay. Costs were calculated from data published by the Health Service Executive in Ireland on average costs per inpatient stay for given diagnosis codes. Methods Data were collected on admission rates, length of stay, overall bed day usage, and costs across a four-year period; the two years since the introduction of the rapid access clinic, and the two years immediately prior as a control. Results 218 patients admitted with VLUs accounted for a total of 2,529 inpatient bed-days, with 4.5(2-6) unplanned admissions, and a median hospital stay of 7(4-13) days per month. Median unplanned admissions per month decreased from 6(2.5-8.5) in the control period, to 3.5(2-5) after introduction of the clinic p=.040. Bed-day usage was significantly reduced from median 62.5(27-92.5), to 36.5(21-44) bed-days per month (p=.035), though length of stay remained unchanged (p=.57). Cost of unplanned inpatient admissions fell from median \euro33,336.25(\euro14,401.26-\euro49,337.65) per month to \euro19,468.37(\euro11,200.98-\euro22,401.96) (p=.03). Conclusions Admissions for inpatient management of VLUs have fallen after beginning aggressive endovenous treatment of venous reflux in a dedicated one-stop see-and-treat clinic for these patients. As a result, bed-day usage has also fallen, leading to cost savings.

Mürşide Zengin

and 2 more

Aim: The aim of this study was to determine the anxiety levels of parents with children aged 3-6 years due to the Coronavirus Disease-2019 (COVID-19) pandemic and to examine the effects of Solution-Focused Support Program (SFSP) applied to parents with high level of anxiety. Methods: The study was conducted as a parallel-group, randomized controlled design. The sample of the study consisted of 77 parents who were randomly assigned to the experimental and control groups (control group n = 40; intervention group n = 37). One session of online SFSP was applied to the intervention group each week and 4 sessions were applied in total. No intervention was applied to the control group. The data were collected using introductory information form and State-Trait Anxiety Inventory (STAI). Statistical Package for the Social Sciences (SPSS) programme and Analysis of Moment Structures (AMOS) 23 application were used in the analysis of the data.  Structural Equation Modeling (SEM) was used to examine a hypothesized model that SFSP has both direct and indirect effects on anxiety levels of parents.Results: The state and trait anxiety mean scores of the intervention group decreased compared to the pre-intervention mean scores after the implemented programme. While this difference between state anxiety scores was statistically significant (p≤ .001), the difference between trait anxiety scores was not statistically significant (p> .05). There was no statistically significant difference between the pre-test and post-test STAI total scores of the control group.Conclusions: In the study, it has been found that SFSP applied to parents with high level of anxiety is an effective method in reducing the state anxiety levels of parents. Clinical trial number: NCT04609722 (Registration date: 30.10.2020)

Mohammed Al-Sadawi

and 7 more

Abstract: Background: This meta-analysis assessed the relationship between Obstructive Sleep Apnea (OSA) and echocardiographic parameters of diastolic dysfunction (DD), which are used in the assessment of Heart Failure with Preserved Ejection Fraction (HFpEF). Methods: We searched the databases including Ovid MEDLINE, Ovid Embase Scopus, Web of Science, Google Scholar, and EBSCO CINAHL from inception up to December 26th, 2020. The search was not restricted to time, publication status or language. Comparisons were made between patients with OSA, diagnosed in-laboratory polysomnography (PSG) or home sleep apnea testing (HSAT), and patients without OSA in relation to established markers of diastolic dysfunction. Results: Primary search identified 2512 studies. A total of 18 studies including 2509 participants were included. The two groups were free of conventional cardiovascular risk factors. Significant structural changes were observed between the two groups. Patients with OSA exhibited greater LAVI (3.94 CI [0.8, 7.07]; p=0.000) and left ventricular mass index (11.10 CI [2.56,19.65]; p=0.000) as compared to control group. The presence of OSA was also associated with more prolonged DT (10.44 ms CI [0.71,20.16]; p=0.04), IVRT (7.85 ms CI[4.48, 11.22]; p=0.000), and lower E/A ratio (-0.62 CI [-1,-0.24]; p=0.001) suggestive of early DD. The E/e’ ratio (0.94 CI[0.44, 1.45]; p=0.000) was increased. Conclusion: An association between OSA and echocardiographic parameters of DD was detected that was independent of conventional cardiovascular risk factors. OSA may be independently associated with DD perhaps due to higher LV mass. Investigating the role of CPAP therapy in reversing or ameliorating diastolic dysfunction is recommended.

Hans Fangohr

and 2 more

Guest Editors’ IntroductionNotebook interfaces – documents combining executable code with output and notes – first became popular as part of computational mathematics software such as Mathematica and Maple. The Jupyter Notebook, which began as part of the IPython project in 2012, is an open source notebook that can be used with a wide range of general-purpose programming languages.Before notebooks, a scientist working with Python code, for instance, might have used a mixture of script files and code typed into an interactive shell. The shell is good for rapid experimentation, but the code and results are typically transient, and a linear record of everything that was tried would be long and not very clear. The notebook interface combines the convenience of the shell with some of the benefits of saving and editing code in a file, while also incorporating results, including rich output such as plots, in a document that can be shared with others.The Jupyter Notebook is used through a web browser. Although it is often run locally, on a desktop or a laptop, this design means that it can also be used remotely, so the computation occurs, and the notebook files are saved, on an institutional server, a high performance computing facility or in the cloud. This simplifies access to data and computational power, while also allowing researchers to work without installing any special software on their own computer: specialized research software environments can be provided on the server, and the researcher can access those with a standard web browser from their computer.These advantages have led to the rapid uptake of Jupyter notebooks in many kinds of research. The articles in this special issue highlight this breadth, with the authors representing various scientific fields. But more importantly, they describe different aspects of using notebooks in practice, in ways that are applicable beyond a single field.We open this special issue with an invited article by Brian Granger and Fernando Perez – two of the co-founders and leaders of Project Jupyter. Starting from the origins of the project, they introduce the main ideas behind Jupyter notebooks, and explore the question of why Jupyter notebooks have been so useful to such a wide range of users. They have three key messages. The first is that Notebooks are centered around the humans using them and building knowledge with them. Next, notebooks provide a write-eval-think loop that lets the user have a conversation with the computer and the system under study, which can be turned into a persistent narrative of computational exploration. The third idea is that Project Jupyter is more than software: it is a community that is nourished deliberately by its members and leaders.The following five articles in this special issue illustrate the key features of Project Jupyter effectively. They show us a small sample of where researchers can go when empowered by the tool, and represent a range of scientific domains.Stephanie Juneau et al. describe how Jupyter has been used to ‘bring the compute to the data’ in astrophysics, allowing geographically distributed teams to work efficiently on large datasets. Their platform is also used for education & training, including giving school students a realistic taste of modern science.Ryan Abernathey et al. , of the Pangeo project, present a similar scenario with a focus on data from the geosciences. They have enabled analysis of big datasets on public cloud platforms, facilitating a more widely accessible ‘pay as you go’ style of analysis without the high fixed costs of buying and setting up powerful computing and storage hardware. Their discussion of best practices includes details of the different data formats required for efficient access to data in cloud object stores rather than local filesystems.Marijan Beg et al. describe features of Jupyter notebooks and Project Jupyter that help scientists make their research reproducible. In particular, the work focuses on the use of computer simulation and mathematical experiments for research. The self-documenting qualities of the notebook—where the response to a code cell can be archived in the notebook—is an important aspect. The paper addresses wider questions, including use of legacy computational tools, exploitation of HPC resources, and creation of executable notebooks to accompany publications.Blaine Mooers describes the use of a snippet library in the context of molecular structure visualization. Using a Python interface, the PyMOL visualization application can be driven through commands to visualize molecular structures such as proteins and nucleic acids. By using those commands from the Jupyter notebook, a reproducible record of analysis and visualizations can be created. The paper focuses on making this process more user-friendly and efficient by developing a snippet library, which provides a wide selection of pre-composed and commonly used PyMOL commands, as a JupyterLab extension. These commands can be selected via hierarchical pull-down menus rather than having to be typed from memory. The article discusses the benefits of this approach more generally.Aaron Watters describes a widget that can display 3D objects using webGL, while the back-end processes the scene using a data visualization pipeline. In this case, the front-end takes advantage of the client GPU for visualization of the widget, while the back-end takes advantage of whatever computing resources are accessible to Python.The articles for this special issue were all invited submissions, in most cases from selected presentations given at JupyterCon in October 2020. Each article was reviewed by three independent reviewers. The guest editors are grateful to Ryan Abernathey, Luca de Alfaro, Hannah Bruce MacDonald, Christopher Cave-Ayland, Mike Croucher, Marco Della Vedova, Michael Donahue, Vidar Fauske, Jeremy Frey, Konrad Hinsen, Alistair Miles, Arik Mitschang, Blaine Mooers, Samual Munday, Chelsea Parlett, Prabhu Ramachandran, John Readey, Petr Škoda and James Tocknell for their work as reviewers, along with other reviewers who preferred not to be named. The article by Brian Granger and Fernando Perez was invited by the editor in chief, and reviewed by the editors of this special issue.Hans Fangohr is currently heading the Computational Science group at the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg, Germany, and is a Professor of Computational Modelling at the University of Southampton, UK. A physicist by training, he received his PhD in Computer Science in 2002. He authored more than 150 scientific articles in computational science and materials modelling, several open source software projects, and a text book on Python for Computational Science and Engineering. Contact him at hans.fangohr@mpsd.mpg.deThomas Kluyver is currently a software engineer at European XFEL. Since gaining a PhD in plant sciences from the University of Sheffield in 2013, he has been involved in various parts of the open source & scientific computing ecosystems, including the Jupyter & IPython projects. Contact him at thomas.kluyver@xfel.euMassimo Di Pierro is a Professor of Computer Science at DePaul University. He has a PhD in Theoretical Physics from the University of Southampton and is an expert in Numerical Algorithms, High Performance Computing, and Machine Learning. Massimo is the lead developer of many open source projects including web2py, py4web, and pydal. He has authored more than 70 articles in Physics, Computer Science, and Finance and has published three books. Contact him at

Jumpei Ogura

and 9 more

Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) infection has a significant clinical impact on both pregnant women and neonates. The aim of this study was to accurately assess the vertical transmission rate of MRSA and its clinical impacts on both pregnant mothers and neonates.Material and Methods: We conducted a prospective observational cohort study of 898 pregnant women who were admitted to our department and 905 neonates from August 2016 to December 2017. MRSA was cultured from  nasal and vaginal samples taken from the mothers at enrollment and from nasal and umbilical surface swabs taken from neonates at the time of delivery. We examined the vertical transmission rate of MRSA in mother-neonate pairs. We used multivariable logistic regression to identify risk factors for maternal MRSA colonization and maternal/neonatal adverse outcomes associated with maternal MRSA colonization.Results: The prevalence of maternal MRSA colonization was 6.1% (55 out of 898) at enrollment. The independent risk factors were multiparity and occupation (healthcare provider) (OR: 2.35, 95% CI: 1.25-4.42, OR: 2.58, 95% CI: 1.39-4.79, respectively). The prevalence of neonatal MRSA colonization at birth was 12.7% (7 out of 55 mother-neonate pairs) in the maternal MRSA-positive group, whereas it was only 0.12% (one out of 843 pairs) in the maternal MRSA-negative group (OR: 121, 95% CI: 14.6-1000). When maternal vaginal samples were MRSA positive, vertical transmission was observed in four out of nine cases (44.4%) in this study. Skin and soft tissue infections (SSTIs) developed more frequently in neonates in the maternal MRSA-positive group than in the MRSA-negative group (OR: 7.47, 95% CI: 2.50-22.3).Conclusions: The prevalence of MRSA in pregnant women was approximately 6%. Vertical transmission caused by maternal vaginal MRSA colonization was observed in four out of nine cases (44.4%). Although our study includes limited number of maternal MRSA positive cases, the vertical transmission of MRSA may occur in up to 44% of neonates of mothers with vaginal MRSA colonization. Maternal MRSA colonization may associate with increased development of SSTIs in neonates via vertical transmission.
Many societal opportunities and challenges, both current and future, are either inter- or transdisciplinary in nature. Focus and action to cut across traditional academic boundaries has increased in research and, to a less extent, teaching. One successful collaboration has been the augmentation of fields within the Humanities, Social Sciences, and Arts by integrating complementary tools and methods originated from STEM. This trend is gradually materializing in formal undergraduate and secondary education.The proven effectiveness of Jupyter notebooks for teaching and learning STEM practices gives rise to a nascent case for education seeking to replicate this interdisciplinary design to adopt notebook technology as the best pedagogical tool for this job. This article presents two sets of data to help argue this case.The first set of data demonstrates the art of the possible. A sample of undergraduate and secondary level courses showcases existing or recent work of educational stakeholders in the US and UK who are already pioneering instruction where computational and data practices are integrated into the study of the Humanities, Social Sciences, and Arts, with Jupyter notebooks chosen as a central pedagogical tool. Supplementary data providing an overview of the types of technical material covered by each course syllabi further evidences what interdisciplinary education is perceived to be or is already feasible using this Jupyter technology with student audiences of these levels.The second set of data provides more granular, concrete insight derived from user experiences of a handful of the courses from the sample. Four instructors and one student describe a range of pedagogical benefits and value they attribute to the use of Jupyter notebooks in their course(s).In presenting this nascent case, the article aims to stimulate the development of Jupyter notebook-enabled, computational data-driven interdisciplinary education within undergraduate and secondary school programs.

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