Miracle-dz/UniFAR-FTUs huggingface dataset:
The chemistry of episodic accretion in embedded objects. 2D radiation thermo-chemical models of the post-burst phase

Context. Episodic accretion is an important process in the evolution of young stars and their environment. The observed strong luminosity bursts of young stellar objects likely have a long lasting (I.e. longer than the burst duration) impact on the chemical evolution of the disk and envelope of young stars. Aims: We aim to investigate the observational signatures of the chemical evolution in the post-burst phase for embedded sources. With such signatures it is possible to identify targets that experienced a recent luminosity burst. Methods: We present a new model for the chemistry of episodic accretion based on the two dimensional, radiation thermo-chemical disk code PRODIMO (PROtoplanetary DIsk MOdel). We have extended PRODIMO with a proper treatment for envelope structures. For a representative Class I model, we calculated the chemical abundances in the post-burst phase and produced synthetic observables such as intensity maps and radial intensity profiles. Results: During a burst, many chemical species, such as CO, sublimate from the dust surfaces. As the burst ends they freeze out again (post-burst phase). This freeze-out happens from inside-out due to the radial density gradient in the disk and envelope structure. This inside-out freeze-out produces clear observational signatures in spectral line emission, such as rings and distinct features in the slope of radial intensity profiles. We fitted synthetic C18O J = 2-1 observations with single and two component fits and find that post-burst images are much better matched by the latter. Comparing the quality of such fits therefore allows identification of post-burst targets in a model-independent way. Conclusions: Our models confirm that it is possible to identify post-burst objects from spatially resolved CO observations. However, to derive proper statistics, such as the strength and frequencies of bursts, from observations it is important to consider the inclination and structure of the target and dust properties, as these have a significant impact on the freeze-out timescale.
Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development

Global microarray gene expression analyses previously demonstrated differences in female and male embryos during neurodevelopment. In particular, before sexual maturation of the gonads, the differences seem to concentrate on the expression of genes encoded on the X- and Y-chromosomes. To investigate genome-wide differences in expression during this early developmental window, we combined high-resolution RNA sequencing with qPCR to analyze brain samples from human embryos during the first trimester of development. Our analysis was tailored for maximum sensitivity to discover Y-chromosome gene expression, but at the same time, it was underpowered to detect X-inactivation escapees. Using this approach, we found that 5 out of 13 expressed gametolog pairs showed unbalanced gene dosage, and as a consequence, a male-biased expression. In addition, we found six novel non-annotated long non-coding RNAs on the Y-chromosome with conserved expression patterns in newborn chimpanzee. The tissue specific and time-restricted expression of these long non-coding RNAs strongly suggests important functions during central nervous system development in human males.
Pathogenicity and phylogenetic analysis of Fusarium oxysporum f. sp. capsici isolates from pepper in Turkey

Abstract The pathogenic Fusarium oxysporum species complex (FOSC) causes significant yield losses in the family Solanaceae including on tomato, eggplant and pepper in the Aegean and Mediterranean regions of Turkey. Fusarium wilt of pepper, caused by Fusarium oxysporum f. sp. capsici (Foc), has emerged recently in Turkey, where its significance has not been investigated thoroughly. In the present study, disease prevalence was determined with surveys conducted in 67 pepper-growing greenhouses and 56 pepper fields in the Aegean and Mediterranean regions in 2015 and 2016. In both years, about 32% of the greenhouses and 55% of the fields were found to be infested with the wilting disease. It was observed in a pathogenicity experiment that 64 isolates were pathogenic to pepper. In cross-inoculation experiments, these isolates did not cause wilting symptoms on tomato and eggplant and therefore were designated as Foc. Phylogenetic analyses were carried out with TEF-1α and actA DNA regions of a selected subset of 40 Foc isolates, along with non-host formae of F. oxysporum and outgroup Fusarium species. Sequence data for the TEF-1α and actA DNA regions displayed limited variation among Foc isolates and failed to distinguish reliably several formae speciales of F. oxysporum. The phylogenetic tree successfully separated the outgroup isolates. All Foc isolates were placed in the same branch, suggesting a single monophyletic group in the dendrogram. This is the first comprehensive study for pathogenic and phylogenetic analysis of Foc isolates from peppers in Turkey.
Primitive and modern swimmers solve the challenges of turning similarly to achieve high maneuverability

Animal swimmers alter trajectories – or turn - for a variety of critical life functions such as feeding, mating and avoiding predation. Yet turning represents a fundamental dilemma based in rotational dynamics: the torque powering a turn is favored by an expanded body configuration, yet minimizing the resistance to a turn (the moment of inertia) is favored by a contracted body configuration. How do animals balance these opposing demands to achieve high maneuverability? By noninvasively measuring fluid and body motions, we found that both jellyfish (Aurelia aurita) and fish (Danio rerio) initially maximized torque using previously undescribed, rapid body movements. Both species then minimized resistance to turning by bending their bodies to reduce their moment of inertia. Use of this sequential solution by such distantly related animals as an invertebrate and a vertebrate suggests strong selection for these turning dynamics that may extend to other swimmers and inform future vehicle designs.
Passive Approximation and Optimization Using B-splines

A passive approximation problem is formulated where the target function is an arbitrary complex valued continuous function defined on an approximation domain consisting of a finite union of closed and bounded intervals on the real axis. The norm used is a weighted $\text{L}^p$-norm where $1\leq p\leq\infty$. The approximating functions are Herglotz functions generated by a measure with H\"{o}lder continuous density in an arbitrary neighborhood of the approximation domain. Hence, the imaginary and the real parts of the approximating functions are H\"{o}lder continuous functions given by the density of the measure and its Hilbert transform, respectively. In practice, it is useful to employ finite B-spline expansions to represent the generating measure. The corresponding approximation problem can then be posed as a finite-dimensional convex optimization problem which is amenable for numerical solution. A constructive proof is given here showing that the convex cone of approximating functions generated by finite uniform B-spline expansions of fixed arbitrary order (linear, quadratic, cubic, etc) is dense in the convex cone of Herglotz functions which are locally H\"{o}lder continuous in a neighborhood of the approximation domain, as mentioned above. As an illustration, a typical physical application example is included regarding the passive approximation and optimization of a linear system having metamaterial characteristics.
Effectiveness of differentiated physical activity for the therapy of depression: a review

In various forms, depressive disorders may affect over 300 million people worldwide. Physical activity has been studied as a form of therapy for depression for many decades, with generally promising results as either a cost-effective therapy for mild to moderate depression or as an addition to conventional therapies for MDD (major depressive disorder). However, the mechanisms of how regular exercise may alleviate the symptoms of depression are poorly understood. Because structured and regular physical activity is already recommended to professionals as a useful tool of extending typical therapies, there is a growing need for data about what kinds of exercise would be of most benefit to individuals suffering from depression. The current state of knowledge remains inconclusive about many characteristics of the exercise therapy. Proposed therapies lack clear evidence that would suggest the effectiveness of a particular training regimen for remission of depressive symptoms. Among the main problems are differences among used therapies, diverse types of control groups, and variability of applied measures of the symptoms of depressive disorders. However, there is growing evidence suggesting that not the type nor the mode of exercise, but its caloric expenditure measured weekly in kcal and maintaining workout regularity may be the most important factors that should be taken into account when planning a structured antidepressant exercise therapy.
Genomic characterization of mithun (Bos frontalis) populations using
high density SNP array

Mithun (Bos frontalis) is a bovine species found in the four North-Eastern Hilly States of India viz., Nagaland, Arunachal, Manipur and Mizoram. The 770k BovineHDBeadChip (Illumina, CA), which is basically a highdensity SNP array was utilized for genomic characterization of four mithun populations and to study genetic diversity present in the populations. SNP genotyping of a total 24 samples representing four mithun populations as per their geographic locations were carried out. The results indicated that the majority of polymorphic SNPs were found to be in HWE. Observed heterozygosity ranged between 0.263±0.040 (Nagaland) to 0.299±0.044 (Arunachal). Inbreeding coefficient ranged from 0.087±0.139 for Nagaland to 0.186±0.053 for Manipur mithun. The result of the Principal Component Analysis (PCA) indicated all the mithuns were distributed together in close proximity and no clear separation of the four populations was observed.The first and second principal components (PC1 and PC2) explained 9.59% and 88.0% of the total variation, respectively. The results of the STRUCTURE analysis also showed no population substructure as inferred from an increasing plot of cross validation error, similar to PCA. In our knowledge, this is the first study on genomic characterization of any Indian livestock species, through analysis of population structure and genetic diversity using high density SNP array. The baseline information generated in our study will help in developing proper strategies for implementing genomic selection and conservation of mithun.
A General Equilibrium Evaluation of the Employment Service

This paper provides a general equilibrium evaluation of the Employment Service, also known as the Public Labor Exchange (PLX), a national program that facilitates meetings between job seekers and vacancies. The paper departs from the standard partial equilibrium framework of program evaluation by constructing a dynamic general equilibrium matching model with the PLX as a directed search channel and all other search methods as the other channel. In the calibrated model, the general equilibrium impacts of the PLX are different from the standard partial equilibrium ones, mainly because employers post more high-skill vacancies when both search channels operate.
Uncertainty and Volatility in MENA Stock Markets During the Arab Spring

This paper sheds light on the economic impacts of political uncertainty caused by the civil uprisings that swept across the Arab World and have been collectively known as the Arab Spring. Measuring documented effects of political uncertainty on regional stock market indices, we examine the impact of the Arab Spring on the volatility of stock markets in eight countries in the Middle East and North Africa (MENA) region: Egypt, Lebanon, Jordon, United Arab Emirate, Qatar, Bahrain, Oman and Kuwait. This analysis also permits testing the existence of financial contagion among equity markets in the MENA region during the Arab Spring. To capture the time-varying and multi-horizon nature of the evidence of volatility and contagion in the eight MENA stock markets, we apply two robust methodologies on data from November 2008 to March 2014: MGARCH-DCC, Continuous Wavelet Transforms (CWT). Our results tend to indicate two key findings. First, the discrepancies between the volatile stock markets of countries directly impacted by the Arab Spring and the countries that were not directly impacted indicate that international investors may still enjoy portfolio diversification and investment in MENA markets. Second, the lack of financial contagion during the Arab Spring suggests that there is little evidence of cointegration among MENA markets implying the opportunities of portfolio diversification. Providing a general analysis of the economic situation and the investment climate in the MENA region during and after the Arab Spring, this study bears significant importance for the policy makers, local and international investors, and market regulators.
Pricing Vulnerable Options with Market Prices of Common Jump Risks under Regime-Switching Models

This paper investigates the valuation of vulnerable European options considering the market prices of common systematic jump risks under regime-switching jump-diffusion models. The way of regime-switching Esscher transform is adopted to identify an equivalent martingale measure for pricing vulnerable European options. Explicit analytical pricing formulae for vulnerable European options are derived by risk-neutral pricing theory. For comparison, the other two cases are also considered separately. The first case considers all jump risks as unsystematic risks while the second one assumes all jumps risks to be systematic risks. Numerical examples for the valuation of vulnerable European options are provided to illustrate our results and indicate the influence of the market prices of jump risks on the valuation of vulnerable European options.
Approach to the Integration of Management Systems in a Pharmaceutical Organization

This paper discusses how a system approach to management can be used for the development and implementation of an integrated management system (IMS) in a company producing medicinal products. It is argued in the paper that approaches to the solutions of how to integrate management systems all require two elements: a conceptual model and a supporting methodology. Although a large number of models has been developed that could provide the basis for integration, development of methodologies to achieve fully integrated systems is still stagnating. This paper presents the IMS model that can be used to integrate the requirements of existing and upcoming standards in the pharmaceutical industry, followed by a discussion on the issue of the IMS methodology.
Coronary-Heart-Disease-Associated Genetic Variant at the COL 4 A 1 / COL 4 A 2 Locus Affects COL 4 A 1 / COL 4 A 2 Expression , Vascular Cell Survival , Atherosclerotic Plaque Stability and Risk of Myocardial Infarction

Genome-wide association studies have revealed an association between coronary heart disease (CHD) and genetic variation on chromosome 13q34, with the lead single nucleotide polymorphism rs4773144 residing in the COL4A2 gene in this genomic region. We investigated the functional effects of this genetic variant. Analyses of primary cultures of vascular smooth muscle cells (SMCs) and endothelial cells (ECs) from different individuals showed a difference between rs4773144 genotypes in COL4A2 and COL4A1 expression levels, being lowest in the G/G genotype, intermediate in A/G and highest in A/A. Chromatin immunoprecipitation followed by allelic imbalance assays of primary cultures of SMCs and ECs that were of the A/G genotype revealed that the G allele had lower transcriptional activity than the A allele. Electrophoretic mobility shift assays and luciferase reporter gene assays showed that a short DNA sequence encompassing the rs4773144 site interacted with a nuclear protein, with lower efficiency for the G allele, and that the G allele sequence had lower activity in driving reporter gene expression. Analyses of cultured SMCs from different individuals demonstrated that cells of the G/G genotype had higher apoptosis rates. Immunohistochemical and histological examinations of ex vivo atherosclerotic coronary arteries from different individuals disclosed that atherosclerotic plaques with the G/G genotype had lower collagen IV abundance and thinner fibrous cap, a hallmark of unstable, rupture-prone plaques. A study of a cohort of patients with angiographically documented coronary artery disease showed that patients of the G/G genotype had higher rates of myocardial infarction, PLOS Genetics | DOI:10.1371/journal.pgen. 1006127 July 7, 2016 1 / 15 a11111
The Acquisition of Disjunction and Positive Polarity in Japanese

The fact that English or yields the conjunctive interpretation within the scope of negation suggests that this lexical item corresponds to Boolean inclusive disjunction. In positive contexts, the Boolean operator continues to supply the basic meaning of or, but a derived exclusive-or interpretation is computed, due to a conversational implicature (e.g., Grice 1975). In contrast to English, Japanese appears to be less faithful to the laws of logic. The Japanese counterpart of (1), with the disjunction operator ka, does not require the conjunctive interpretation of disjunction in negative
Depressive disorder and its associated factors among prisoners in Debre Berhan Town, North Showa, Ethiopia

Background Depression is a commonest mental disorder among prisoners characterized by an intense mood involving a feeling of sadness, lack of interest or hopelessness that lasts for weeks, months, or even longer. In addition to imprisonment, depression is the primary factor leading to suicidal attempt. Therefore, this study revealed the magnitude of depressive disorder and its associated factors among prisoners of Debre Berhan Town. Methods We conducted an institution based cross-sectional quantitative study. We collected the data from 336 randomly selected prisoners by using interviewer-administered Patient Health Questioner-9 (PHQ-9). Multiple logistic regression was performed to identify independent predictors. Result Out of the total of 336 prisoners 330 (98%) were males. Using PHQ-9 at the cut of point >5 for caseness, the prevalence of depression found to be 44% (n=148). Widowed (AOR=6.30 CI: 1.09-36.67), those who are educated at college or university level (AOR=5.34 CI:1.59-17.94), a history of suicidal attempt (AOR=2.76 CI: 1.04-7.31), Previously facing severe stressful life event (AOR=2.57 CI: 1.41-4.67), 5-10 years of sentence (AOR=2.51 CI:1.32-4.79) and having chronic medical illness (AOR= 3.32 CI: 1.26-8.75) are found to be independently associated with depression. Conclusion In general, there is a high prevalence of depression among prisoners in of Debre Berhan town. Therefore, designing strategies for early screening and treatment of depression at prisons is very crucial.
Scenario Analysis on Greenhouse Gas Emission for Waste-to-Energy Alternatives in Japan

This study focuses on G reenhouse G as (GHG) emissions and reductions of M unicipal S olid W aste (MSW) incineration. The authors aim to estimate the detailed composition of GHG emissions and reductions from the waste incineration facility and their influence factors using two Japanese databases on the operation of incinerators from Japan Ministry of the Environment (1,243 facilities) and Japan Waste Research Foundation (814 facilities). The databases cover detailed data on MSW amount and characteristics, specifications of the facility, annual utility consumption, and annual energy/material recovery. The authors analyze the correlations among them and develop predictive models for the detailed components of GHG emissions and reductions. Japan Ministry of the Environment intended to group small municipalities for replacing small-scale incinerators to large-scale W aste-to- E nergy (WtE) facilities with a higher energy recovery efficiency. Based on the abovementioned data and models, the authors estimate the expected effects of the block formation and major technological alternatives for GHG mitigation by the national level. The current net GHG emission rate from 1,243 operating waste incineration plants in Japan in 2009 was estimated to be 653 kgCO 2 e/t. In the block formation, 1,007 plants were assumed to be closed; 236 kept operating; and 286 facilities would be newly built. The net GHG emission rate could be cut off to 454 kgCO 2 e/t by applying the block formation and technological alternatives with a higher energy recovery efficiency (stalker furnace with power generation by extraction condensing turbine providing steam higher than 3MPa and 300 C). Ash melting caused a larger GHG emission by the increase in energy consumption. The GHG reduction by slag recycling was limited. Furthermore, the net GHG emission rate could be reduced to 242 kgCO 2 e/t by applying the Best Available Technique (BAT) for combined heat and power plants. When compared with the current status, BAT can reduce 185 kgCO 2 e/t by improving the power generation efficiency and 187 kgCO 2 e/t by expanding heat utilization. At present, heat utilization is very limited in Japan, but heat utilization should be more focused and promoted for GHG mitigation decisions.
Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems

The use of proximity-dependent biotin labelling (PDL) approaches coupled with mass spectrometry recently greatly advanced the identification of protein-protein interactions and study of protein complexation. PDL is based on the expression of a promiscuous biotin ligase (PBL), e.g. BirA* or a peroxidase fused to a bait protein of interest. In the presence of biotin as substrate, PBL enables covalent biotin labelling of proteins in the vicinity of the PBL-fused bait in vivo, allowing the subsequent capture and identification of interacting and neighbouring proteins without the need for the protein complex to remain intact during purification. To date, PDL has not been extensively used in plants. Here we present the results of a systematic multi-lab study applying a variety of PDL approaches in several plant systems under various conditions and bait proteins. We show that TurboID is the most promiscuous variant for PDL in plants and establish protocols for its efficient application. We demonstrate the applicability of TurboID in capturing membrane protein interactomes using the Lotus japonicus symbiotically active receptor kinases RLKs NOD FACTOR RECEPTOR 5 (NFR5) and LRR-RLK SYMBIOTIC RECEPTOR-KINASE (SYMRK) as test-cases. Furthermore, we benchmark the efficiency of various PBLs using the octameric endocytic TPLATE complex and compare PDL with one-step AP-MS approaches. Our results indicate that different PDL approaches in plants may differ in signal-to-noise ratio and robustness. We present a straightforward strategy to identify both non-biotinylated as well as biotinylated proteins in plants in a single experimental setup. Finally, we provide initial evidence that this technique has potential to infer structural information of protein complexes. Our methods, tools and adjustable pipelines provide a useful resource for the plant research community.