jimnoneill/paper-to-field-training huggingface dataset:
Extremal quantile regression: an overview

Extremal quantile regression, i.e. quantile regression applied to the tails of the conditional distribution, counts with an increasing number of economic and financial applications such as value-at-risk, production frontiers, determinants of low infant birth weights, and auction models. This chapter provides an overview of recent developments in the theory and empirics of extremal quantile regression. The advances in the theory have relied on the use of extreme value approximations to the law of the Koenker and Bassett (1978) quantile regression estimator. Extreme value laws not only have been shown to provide more accurate approximations than Gaussian laws at the tails, but also have served as the basis to develop bias corrected estimators and inference methods using simulation and suitable variations of bootstrap and subsampling. The applicability of these methods is illustrated with two empirical examples on conditional value-at-risk and financial contagion.

Topic: Market Dynamics and Volatility
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
The Gaboye of Somaliland: Legacies of Marginality, Trajectories of Emancipation

A partire da una ricerca etnografica condotta tra il 2014 ed il 2015 nella città di Hargeisa, capitale della Repubblica del Somaliland (Somalia), la tesi illustra la traiettoria storica di trasformazione di una forma di marginalizzazione socio-politico-economica di cui sono oggetto i Gaboye, un agglomerato di gruppi minoritari locali. Tale marginalizzazione veniva descritta da autori di epoca coloniale (viaggiatori, studiosi, funzionari coloniali) come segregazione di “casta”. L’oggetto in questione apre squarci analitici sia su importanti snodi storici di mutamento sociale che hanno interessato l’area – quali i processi migratori che determinarono l’espansione urbana nell’area ed altre trasformazioni del tessuto economico occorse a partire dall’epoca coloniale – sia su temi e strumenti concettuali su cui antropologi e storici si interrogano in relazione ad altri contesti africani (e non solo), quali la relazione tra status ascritti, segregazione professionale, esclusione dagli scambi matrimoniali e stratificazione sociale.

Topic: African history and culture studies
Subfield: Anthropology
Field: Social Sciences
Domain: Social Sciences
Additional file 2: Table S1. of UGT74S1 is the key player in controlling secoisolariciresinol diglucoside (SDG) formation in flax

Primers used for PCR mediated splicing, cloning and real-time gene expression of Lus10006353 and Lus10014148. (DOCX 16Â kb)

Topic: Phytoestrogen effects and research
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
Long-term effects of nocturnal continuous positive airway pressure therapy in patients with resistant hypertension and obstructive sleep apnea.

Obstructive sleep apnea (OSA) is often linked to high blood pressure and has a particularly high prevalence in patients with resistant hypertension. The effect of continuous positive airway pressure (CPAP) therapy on blood pressure (BP) values has been evaluated in several short-term clinical trials with conflicting results. Our aim was to investigate the role of long-term CPAP treatment in achieving BP control in patients who associate OSA and resistant hypertension. We have included in the study 33 patients with resistant hypertension, diagnosed with OSA in our sleep lab. Data was collected initially and after a mean follow-up period of 4 years. Patients were divided into 2 groups according to the use of CPAP therapy. Patients under CPAP therapy (n = 12) exhibited a higher reduction in both systolic and diastolic pressure and BP control was achieved in 75% of cases, while patients without CPAP treatment (n = 21) remained with refractory hypertension in proportion of 90.5%. A de-escalation of antihypertensive drug regimen by discontinuation of 1 or more drugs was observed in 41.6% (n = 5) of patients from CPAP group and in the other 33.4% (n = 4) the medication remained unchanged, but BP control was reached. Using a direct logistic regression model for examining the impact of different confounders on the probability of diagnosis of resistant hypertension at follow-up, the only statistically significant predictor found was the lack of CPAP usage.

Topic: Obstructive Sleep Apnea Research
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
Steps to an Ecology of Psychotherapy: The Legacy of Gregory Bateson

The article addresses the relevance of the work of Gregory Bateson for psychotherapy today. Despite being quite eclipsed by other mental health paradigms, the author's ecological epistemology still seems to be topical for a proper framing of complex features such as psychological well‐being. Indeed, many approaches to psychotherapy, not only systemic‐relational approaches, affirm the crucial importance of context and the centrality of relationships in defining psychosocial functioning and making psychotherapies actually effective. This article recalls the most relevant contributions of Gregory Bateson for the understanding of communication and the functioning of the mind, from the original formulation of the double bind theory to the parallels between thought and biological processes. In this light, Bateson's view of mind and learning still appears to be a valuable framework for thinking about some of the more relevant aspects of psychotherapy, not least the issue of research and the social context in which psychotherapy itself takes place. © 2018 John Wiley &amp; Sons, Ltd.

Topic: Psychotherapy Techniques and Applications
Subfield: Clinical Psychology
Field: Psychology
Domain: Social Sciences
Balance optimization method of energy shipping based on Hopfield neural network

It is of great significance for the optimization of transportation strategy to study the methods of energy shipping scheduling. Based on the Hopfield neural network (HNN) theory, this paper proposes Hopfield neural network energy transportation path optimization algorithm with improved activation function, which solves the problems of poor mapping ability, low flexibility and high sensitivity of neurons near zero to input of traditional activation function. The improved activation function can reduce the derivative value of the activation function and the sensitivity of neurons near zero to the input value by flexibly adjusting the steepness, positioning and mapping range of energy sea transportation at the same time. The experimental results show that: under the same initial conditions, the model proposed in this paper shows better error code performance, and the data length of the required transmission sequence is shorter. When sending 8PSK (Phase Shift Keying) signal with a data length of N = 40, the error rate of the 2-path synthesized random channel is less than 0.112. The error code performance and convergence speed of the energy shipping path planning algorithm are improved effectively.

Topic: Neural Networks and Applications
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES

Electronic health records (EHR) provide a comprehensive resource for discovery, allowing unprecedented exploration of the impact of genetic architecture on health and disease. The data of EHRs also allow for exploration of the complex interactions between health measures across health and disease. The discoveries arising from EHR based research provide important information for the identification of genetic variation for clinical decision-making. Due to the breadth of information collected within the EHR, a challenge for discovery using EHR based data is the development of high-throughput tools that expose important areas of further research, from genetic variants to phenotypes. Phenome-Wide Association studies (PheWAS) provide a way to explore the association between genetic variants and comprehensive phenotypic measurements, generating new hypotheses and also exposing the complex relationships between genetic architecture and outcomes, including pleiotropy. EHR based PheWAS have mainly evaluated associations with case/control status from International Classification of Disease, Ninth Edition (ICD-9) codes. While these studies have highlighted discovery through PheWAS, the rich resource of clinical lab measures collected within the EHR can be better utilized for high-throughput PheWAS analyses and discovery. To better use these resources and enrich PheWAS association results we have developed a sound methodology for extracting a wide range of clinical lab measures from EHR data. We have extracted a first set of 21 clinical lab measures from the de-identified EHR of participants of the Geisinger MyCodeTM biorepository, and calculated the median of these lab measures for 12,039 subjects. Next we evaluated the association between these 21 clinical lab median values and 635,525 genetic variants, performing a genome-wide association study (GWAS) for each of 21 clinical lab measures. We then calculated the association between SNPs from these GWAS passing our Bonferroni defined p-value cutoff and 165 ICD-9 codes. Through the GWAS we found a series of results replicating known associations, and also some potentially novel associations with less studied clinical lab measures. We found the majority of the PheWAS ICD-9 diagnoses highly related to the clinical lab measures associated with same SNPs. Moving forward, we will be evaluating further phenotypes and expanding the methodology for successful extraction of clinical lab measurements for research and PheWAS use. These developments are important for expanding the PheWAS approach for improved EHR based discovery.

Topic: Genetic Associations and Epidemiology
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Real-time Parameter Estimation of Dynamic Power Systems using Multiple Observers

In this paper we describe a method suitable for real-time estimation of parameters of differential algebraic equation (DAE) dynamical models, generally used to model power systems. The method uses multiple observers that run in parallel, processing the same measured data from the process under consideration. The outputs from these observers are then used in a secondary least-squares estimation (LSE) process in order to identify the unknown parameters. We will demonstrate this parameter estimation using multiple observers (PEMO) on a single machine infinite bus (SMIB) example (where the generator inertia, prime mover torque and damping of the generator are unknown). This method can also be used as a fault detection, isolation and identification (FDI) filter that tracks parameter changes that can be indicative of such events as line outages, load and generation changes in a power system. We illustrate this concept on a nine-bus example.

Topic: Power System Optimization and Stability
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
The Impact of Obesity on Postoperative Outcomes in Adults with Congenital Heart Disease Undergoing Pulmonary Valve Replacement

Obesity is associated with increased morbidity in adults with congenital heart disease undergoing pulmonary valve replacement, including longer hospitalization and higher risk for postoperative arrhythmias.

Topic: Cardiac Valve Diseases and Treatments
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
Effect of Education on Choosing Delivery Mode among Pregnant Women Referred to Health Centers of Minoodasht City: An Application of BASNEF Model

Aim: Caesarean section is dramatically increasing across the world. Pregnant women have an increasing tendency for caesarean section without acceptable medical indications. In general, 50 to 60% of childbirths in Iran are cesarean section. Despite the high complications of cesarean section, they are not caused by medical problems. Therefore, the current survey aims to screen the effect of education on choosing delivery mode based on BASNEF model.Methods: A quasi-experimental study was done on 160 nulliparous women in the third trimester of pregnancy who were assigned randomly to the intervention (80 subjects) and control (80 samples) groups. A researcher-made questionnaire was utilized to collect the required data. Education and its content were developed according to the BASNEF model and the pregnant women's educational requirements. Numerous education methods were implemented in all target groups of intervention including pregnant women, their family and the health staffs. To analyze the data, paired and McNemar tests through SPSS version 18 were utilized. Significant level was also considered &lt;0.05.Findings: The majority of women were in the age range of 24-20 years. Only 1.2% of the women were illiterate in both groups. Knowledge, attitude, enabling factors, subjective norms and intention were significantly different between the two arms before and 2 months after the intervention (p=0.001) except for intention. In addition, in the intervention group, they get information significantly from friends, families, printed materials, educational films, educational sessions in the Health Centers, and the health personnel after the intervention (p=0.001).Conclusion: Designing educational programs about delivery mode based on BASNEF model appeared to be beneficial due to the model‟s emphasis on subjective norms and enabling factors; therefore, educational programs based on change behavior model can notably decrease the unnecessary cesarean section in the country.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

&lt;div&gt; &lt;div&gt; &lt;div&gt; &lt;p&gt;Alchemical free energy calculations are an increasingly important modern simulation technique. Contemporary molecular simulation software such as AMBER, CHARMM, GROMACS and SOMD include support for the method. Implementation details vary among those codes but users expect reliability and reproducibility, i.e. for a given molec- ular model and set of forcefield parameters, comparable free energy should be obtained within statistical bounds regardless of the code used. Relative alchemical free energy (RAFE) simulation is increasingly used to support molecule discovery projects, yet the reproducibility of the methodology has been less well tested than its absolute counter- part. Here we present RAFE calculations of hydration free energies for a set of small organic molecules and demonstrate that free energies can be reproduced to within about 0.2 kcal/mol with aforementioned codes. Achieving this level of reproducibility requires considerable attention to detail and package–specific simulation protocols, and no uni- versally applicable protocol emerges. The benchmarks and protocols reported here should be useful for the community to validate new and future versions of software for free energy calculations.&lt;/p&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt;

Topic: Protein Structure and Dynamics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules

Abstract We developed VariantBam, a C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations of rules, defined by any number of genomic intervals or variant sites. We have implemented filters based on alignment data, sequence motifs, regional coverage and base quality. For example, VariantBam achieved a median size reduction ratio of 3.1:1 when applied to 10 lung cancer whole genome BAMs by removing large tags and selecting for only high-quality variant-supporting reads and reads matching a large dictionary of sequence motifs. Thus VariantBam enables efficient storage of sequencing data while preserving the most relevant information for downstream analysis. Availability and implementation: VariantBam and full documentation are available at github.com/jwalabroad/VariantBam. Contact: rameen@broadinstitute.org Supplementary information: Supplementary data are available at Bioinformatics online.

Topic: Genomics and Phylogenetic Studies
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Optimization of an industrial heat exchanger by the minimalization of entropy

Práce pojednává o analýze tří různých druhů tepelných výměníků pomocí druhého termodynamického zákona. Generace entropie, jako kvantitativní míra nevratnosti (nedokonalosti) vztažené k přenosu tepla a tekutinového tření při provozu, slouží jako přímá míra ztracené schopnosti přenést teplo. Dále byl vytvořen matematický model, který využívá metodu efektivnosti-NTU společně s citlivostní analýzou a minimalizace čísla generace entropie, které je funkcí optimální proudové cesty a bezrozměrové hmotnostní rychlosti.

Topic: Greenhouse Technology and Climate Control
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
TEST BEAM LINE FOR PULSED BEAM GENERATION AT CIAE'S CRM CYCLOTRON

A test beam line for pulsed beam generation for 10 MeV Central Region Model (CRM) compact cyclotron is being constructed at China Institute of Atomic Energy (CIAE). About 10 mA H- beam from a multicusp source is injected into the central region of CRM cyclotron. To provide the pulse beam from the CRM cyclotron, a new beam line with pulsed system for the injection is needed. A 70MHz buncher and a 2.2MHz chopper are designed for the beam pulsed system. A pulsed proton beam with 4.4MHz repetition rate and pulse length of less than 10ns is expected to be provided by CRM cyclotron. The energy spread produced by buncher and chopper are calculated and the emittance growth due to the chopper is considered.

Topic: Particle accelerators and beam dynamics
Subfield: Aerospace Engineering
Field: Engineering
Domain: Physical Sciences
&lt;title&gt;Mammographic Image Quality And Exposure Levels Using Conventional Generators And Type M Film&lt;/title&gt;

With the four technical factors of controlled motion, long target-film distance, exquisite collimation and good processing meticulously cared for, conventional generators and type M film mammography can be done with skin dose less than or comparable to other contemporary mammographic techniques with far superior image quality.

Topic: Digital Radiography and Breast Imaging
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Additional file 5 of Darwinian Selection Discriminates Young Athletes: the Relative Age Effect in Relation to Sporting Performance

Additional file 5. The Supplement file 5 can be accessed via the DOI: https://doi.org/10.6084/m9.figshare.12191898 .

Topic: Sports Analytics and Performance
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Chemical properties of Zarafshon lower and middle flow soils

The article describes the chemical composition of newly irrigated, newly developed sandy-desert, old-irrigated alluvial-meadow, newly-irrigated gray-brown-meadow, gray-earth-meadow soils, common in the lower and middle reaches of the Zarafshan River, describes the decrease in the amount of nutrients in the soil under the influence of anthropogenic factors. In arable and subarable layers of old irrigated meadow-alluvial soils, the amount of humus is 0.859-0.971% and 0.715-0.894%, while in newly irrigated gray brown-meadow soils it is 0.891-0.750%. In irrigated and newly developed desert sandy areas, the total amount of nitrogen is 0.052-0.082%, phosphorus - 0.075-0.15%, potassium content - 66-0.916%.

Topic: Engineering and Agricultural Innovations
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures

The accurate prediction of an RNA’s three-dimensional structure from its “primary structure” will have a tremendous influence on the experimental design and its interpretation and ultimately our understanding of the many functions of RNA. This paper presents a general coarse-grained (CG) potential for modeling RNA 3-D structures. Each nucleotide is represented by five pseudo atoms, two for the backbone (one for the phosphate and another for the sugar) and three for the base to represent base-stacking interactions. The CG potential has been parametrized from statistical analysis of 688 RNA experimental structures. Molecular dynamic simulations of 15 RNA molecules with the length of 12−27 nucleotides have been performed using the CG potential, with performance comparable to that from all-atom simulations. For ∼75% of systems tested, simulated annealing led to native-like structures at least once out of multiple repeated runs. Furthermore, with weak distance restraints based on the knowledge of three to five canonical Watson−Crick pairs, all 15 RNAs tested are successfully folded to within 6.5 Å of native structures using the CG potential and simulated annealing. The results reveal that with a limited secondary structure model the current CG potential can reliably predict the 3-D structures for small RNA molecules. We also explored an all-atom force field to construct atomic structures from the CG simulations.

Topic: RNA and protein synthesis mechanisms
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
An Efficient Method of Eliminating the Range Ambiguity for a Low-Cost FMCW Radar Using VCO Tuning Characteristics

This paper describes a simple method of eliminating the range ambiguity and the design approach for low-cost and small-size homodyne frequency-modulated continuous-wave (FMCW) radars. The range measurement accuracy could be efficiently improved by proper time gating of the beat signal without any closed-loop linearity compensation circuitry for typical varactor-tuned voltage-controlled oscillators (VCOs). The presented selectively gated fast Fourier transformation method is immune to the frequency shift of the VCOs. A W-band FMCW radar using a raw varactor-tuned VCO having the percent linearity of 7.16% was implemented, and achieved less than 2% ranging error of the target lying at 200 m. Owing to the simple structure and fast processing speed, this method is applicable to the various low-cost radar sensors for ranging and detection

Topic: Radar Systems and Signal Processing
Subfield: Aerospace Engineering
Field: Engineering
Domain: Physical Sciences
Newcomers' Biographical Explanations: The Self As An Adjustment Process*

The newcomers' situation necessarily involves change and a variety of adjustment processes. In this situation the self may come into question and become an object of conscious reflection and definition. This paper focuses on the processes of change and continuity in the newcomer's self‐concept during the first year after moving to a new locale. Data are drawn from a broader longitudinal study of 30 newcomer families in an Australian city and are interpreted from a symbolic interactionist perspective.

Topic: Education Systems and Policy
Subfield: Education
Field: Social Sciences
Domain: Social Sciences