jimnoneill/paper-to-field-training huggingface dataset:
Lagrangian Coherent Data Assimilation for chaotic geophysical systems

This thesis develops a new method for estimating geophysical parameters based on Lagrangian&#13;\nCoherent Data Assimilation (LaCoDA), a nascent eld combining data assimilation&#13;\nand Lagrangian coherent structure techniques. Lagrangian coherent structure theory&#13;\ndeals with characterising and extracting &#13;\nuid structures which have a dominant impact on&#13;\nthe transport of key &#13;\now properties (Balasuriya et. al., Physica D, 2018:31-51). Data assimilation&#13;\n(DA) is a methodology for combining information from observational data with&#13;\nthat from a mathematical model to make predictions about dynamical systems (Lahoz &amp;&#13;\nSchneider, Front. Environ. Sci., Springer-Verlag, 2014). Lagrangian Coherent Data Assimilation&#13;\nattempts to combine these two areas to devise data assimilation schemes which&#13;\nexploit information from Lagrangian coherent structures to improve data assimilation in&#13;\nchaotic systems (Maclean et. al. Physica D, 2017:36-45).&#13;\nThe LaCoDA technique developed here combines the data assimilation algorithm&#13;\nknown as Approximate Bayesian Computation (ABC) with a Lagrangian coherent structure&#13;\nmethod, the Finite Time Lyaponov Exponent (FTLE). The new method, denoted&#13;\nFTLE-ABC, is tested on estimating the parameter from the Rossby wave model, a mathematical&#13;\nmodel which simulates an important type of atmospheric &#13;\now. FTLE-ABC is&#13;\nshown to outperform the benchmark methods, a standard particle lter and a standard&#13;\nABC scheme, for particular regimes of the true value of , the chaoticity of the &#13;\now and&#13;\nthe time step used in the DA scheme. In particular, the estimated chaotic timescale is&#13;\nfound to impact FTLE-ABC's performance, with the algorithm often performing better&#13;\nin parameter regimes for which the chaotic timescale is fairly constant with .

Topic: Geophysics and Gravity Measurements
Subfield: Oceanography
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Reference‐free discovery of nuclear SNPs permits accurate, sensitive identification of <i>Carya</i> (hickory) species and hybrids

Abstract Premise DNA‐based species identification is critical when morphological identification is restricted, but DNA‐based identification pipelines typically rely on the ability to compare homologous sequence data across species. Because many clades lack robust genomic resources, we present here a bioinformatics pipeline capable of generating genome‐wide single‐nucleotide polymorphism (SNP) data while circumventing the need for any reference genome or annotation data. Methods Using the SISRS bioinformatics pipeline, we generated de novo ortholog data for the genus Carya , isolating sites where genetic variation was restricted to a single Carya species (i.e., species‐informative SNPs). We leveraged these SNPs to identify both full‐species and hybrid Carya specimens, even at very low sequencing depths. Results We identified between 46,000 and 476,000 species‐identifying SNPs for each of eight diploid Carya species, and all species identifications were concordant with the species of record. For all putative F 1 hybrid specimens, both parental species were correctly identified in all cases, and more punctate patterns of introgression were detectable in more cryptic crosses. Discussion Bioinformatics pipelines that use only short‐read sequencing data provide vital new tools enabling rapid expansion of DNA identification assays for model and non‐model clades alike.

Topic: Genetic diversity and population structure
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Iodine-125 Seed Implantation as an Adjunct to Surgery in Advanced Recurrent Squamous Cell Cancer of the Head and Neck

Survival for extensive recurrent squamous cell carcinomas of the head and neck remains poor, with the major cause of death being local recurrence. Surgical implantation of iodine-125 interstitial seeds allows tumoricidal doses of radiation to be delivered to residual tumor while minimizing radiation doses to the surrounding tissues. From 1978 to 1988, 39 implantations were performed on 35 patients for extensive recurrent squamous cell carcinoma of the head and neck. The decision for implantation was based on positive margins or close to resection margins from frozen sections after salvage resection. The determinate 5-year disease-free survival was 41%, with both the overall and no evidence of disease 5-year survivals being 29%. Significant complications occurred in 36% of all cases. This figure increased to 56% when flap reconstruction was required. Possible reasons for this seemingly high complication rate are discussed. Considering the advanced nature of these recurrent carcinomas, surgical resection with iodine-125 seed implantation appears to be an effective method of managing disease that might otherwise be judged unresectable and treated for palliation only.

Topic: Head and Neck Surgical Oncology
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Numerical Solution of Sobolev Partial Differential Equations

Finite difference techniques can be applied to the numerical solution of the initial-boundary value problem in S for the semilinear Sobolev or pseudo-parabolic equation \[ \sum\limits_{i = 1}^n {\left[ {\frac{\partial } {{\partial x_i }}\left( {a_i \frac{\partial } {{\partial x_i }}u_t } \right) + \frac{\partial } {{\partial x_i }}\left( {b_i \frac{\partial } {{\partial x_i }}u} \right)} \right]} - q = ru_t , \] where $a_i $, $b_i $, q and r are functions of space and time variables, q is a boundedly differentiable function of u, and S is an open, connected domain in $\mathbb{R}^n $. Under suitable smoothness conditions, the solution of a Crank–Nicolson type of difference equation is shown to converge to u in the discrete $L^2 $-norm with an $O((\Delta x)^2 + (\Delta t)^2 )$ discretization error. The numerical problem is reduced to the inversion of a certain matrix at each time level. For the problem with constant coefficients in a two- or three-dimensional cube, a two-level iteration scheme with a Picard-type outer iteration and an alternating direction inner iteration is presented. For more general operators and more general regions in $\mathbb{R}^n $ for arbitrary n the same two-level scheme with a successive overrelaxation inner iteration is discussed.

Topic: Numerical methods in engineering
Subfield: Mechanics of Materials
Field: Engineering
Domain: Physical Sciences
Zastosowanie alteplazy w nebulizacji u pacjenta z plastycznym zapaleniem oskrzeli po operacji sposobem Fontana – opis przypadku

Plastic bronchitis (PB) is a rare disorder in children but a known complication of Fontan palliation. It is characterised by the formation of muco-cellular casts inside the tracheobronchial tree, which can cause recurrent life-threatening airway obstruction. Common presentation of PB includes atelectasis and dyspnea with potentially fatal outcome. The pathogenesis of this condition is not thoroughly understood. However, the abnormalities of lymphatic vessels may play a role. Various treatment strategies have been anecdotally reported but only few treatment options have been shown to be effective. Authors present a case of a five-year-old girl with Fontan physiology who developed plastic bronchitis. Symptoms occurred 15 months after third stage of correction. Treatment with mucoactive agents and inhaled bronchodilatators had no beneficial effect. A trial of inhaled alteplase was administered and resulted in a full symptomatic recovery. This kind of treatment is unregistered in Poland. The pathophysiology, clinical manifestation and therapeutic opportunities for PB in patients after cardiac surgeries have been reviewed.

Topic: Lymphatic Disorders and Treatments
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Heritability of fetal hemoglobin, white cell count, and other clinical traits from a sickle cell disease family cohort

Sickle cell disease (SCD) is the most common monogenic disorder in the world. Notably, there is extensive clinical heterogeneity in SCD that cannot be fully accounted for by known factors, and in particular, the extent to which the phenotypic diversity of SCD can be explained by genetic variation has not been reliably quantified. Here, in a family‐based cohort of 449 patients with SCD and 755 relatives, we first show that 5 known modifiers affect 11 adverse outcomes in SCD to varying degrees. We then utilize a restricted maximum likelihood procedure to estimate the heritability of 20 hematologic traits, including fetal hemoglobin (HbF) and white blood cell count (WBC), in the clinically relevant context of inheritance from healthy carriers to SCD patients. We report novel estimations of heritability for HbF at 31.6% (±5.4%) and WBC at 41.2% (±6.8%) in our cohort. Finally, we demonstrate shared genetic bases between HbF, WBC, and other hematologic traits, but surprisingly little overlap between HbF and WBC themselves. In total, our analyses show that HbF and WBC have significant heritable components among individuals with SCD and their relatives, demonstrating the value of using family‐based studies to better understand modifiers of SCD.

Topic: Hemoglobinopathies and Related Disorders
Subfield: Genetics
Field: Medicine
Domain: Health Sciences
Characterization of the effect of the menstrual cycle, estradiol and Fads2 transcript variants on fatty acid composition and enzyme expression

Estrogen is believed to regulate fatty acid composition based on observations of differences between men and women, and changes associated with altered estrogen levels in women during pregnancy, menopause and hormone treatment. Estrogen is consistently associated with increased levels of 18:0, 16:1n-7 and elongase 6, an enzyme in monounsaturated fatty acids (MUFA) biosynthesis. In some, but not all studies, estrogen has also been associated with increased 22:6n-3 and FADS2 expression. FADS2 is responsible for delta-6 desaturase activity, the rate-limiting step in polyunsaturated fatty acid (PUFA) biosynthesis and is necessary for the synthesis of 22:6n-3, which is critical for cardiovascular health and neural development. In this thesis, the effects of subtle changes in estrogen levels during the menstrual cycle in humans, and the estrous cycle in rats, on fatty acid metabolism was examined. In addition, the response of FADS2 to estrogen was examined using MCF7 cells. The presence of multiple FADS2 transcript variants in MCF7 cells was determined, and the role of two variants in PUFA biosynthesis was examined by transfecting them into HEK 293 cells. During the menstrual cycle in women and estrous cycle in rats, increased blood levels of 16:1n-7 and 22:6n-3, and decreased levels of 22:5n-3 were observed when blood estrogen levels were high. The increased 22:6n-3 and decreased 22:5n-3 suggests an effect of estrogen on FADS2 expression and/or activity. In the rat hepatic expression of FADS2 mRNA varied over the cycle, but protein levels did not. However, in estrogen sensitive MCF7 cells, FADS2 mRNA was induced by estrogen. Changes in 22:6n-3 and 22:5n-3 were not observed in the MCF7 cells. Further examination identified multiple transcript variants of FADS2 in MCF7 cells, and demonstrated that the expression of an alternatively spliced transcript variant (FADS2_v2) was considerably higher. Notably, this variant lacked the N-terminal cytochrome-binding domain that is critical for activity, suggesting that it may not be functional. In transfected HEK 293 cells, indirect evidence of delta-6 desaturase activity was observed for the full length wild type variant (FADS2_v0/1) but not for FADS2_v2. When the variants were co-transfected, FADS2_v2 interacted with and inhibited FADS2_v0/1. This work helps further understanding of the relationship between estrogen, lipid biosynthetic enzymes and fatty acid status that is important for determination of dietary requirements of 22:6n-3 for women throughout the lifespan.

Topic: Fatty Acid Research and Health
Subfield: Nutrition and Dietetics
Field: Nursing
Domain: Health Sciences
Structural and magnetic properties and tunnel magnetoresistance for Co<sub>2</sub>(Cr,Fe)Al and Co<sub>2</sub>FeSi full-Heusler alloys

We have investigated the structure and magnetization of Co2(Cr1−xFex)Al (0 ≤ x ≤ 1) and Co2FeSi full-Heusler alloy films deposited on thermally oxidized Si (SiO2) and MgO (001) single crystal substrates by ultra-high vacuum sputtering at various temperatures. The films were also post-annealed after deposition at room temperature (RT). Magnetic tunnel junctions with a full-Huesler alloy electrode were fabricated with a stacking structure of Co2YZ (20 nm)/Al (1.2 nm)-oxide/Co75Fe25 (3 nm)/IrMn (15 nm)/Ta (60 nm) and microfabricated using electron beam lithography and Ar ion etching with a 102 µm2 junction area, where Co2YZ stands for Co2(Cr1−xFex)Al or Co2FeSi. The tunnel barriers were formed by the deposition of 1.2 nm Al, followed by plasma oxidization in the chamber. The x-ray diffraction revealed the A2 or B2 structure depending on heat treatment conditions and the substrate, but not L21 structure for the Co2(Cr1−xFex)Al (0 ≤ x ≤ 1) films. The L21 structure, however, was obtained for the Co2FeSi films when deposited on a MgO (001) substrate at elevated temperatures above 473 K. The maximum tunnelling magnetoresistance (TMR) was obtained with 52% at RT and 83% at 5 K for a junction using a Co2(Cr0.4Fe0.6)Al electrode. While the junction using a Co2FeSi electrode with the L21 structure exhibited the TMR of 41% at RT and 60% at 5 K, which may be improved by using a buffer layer for reducing the lattice misfit between the Co2FeSi and MgO (001) substrate.

Topic: Heusler alloys: electronic and magnetic properties
Subfield: Electronic, Optical and Magnetic Materials
Field: Materials Science
Domain: Physical Sciences
STIMULUS COMPLEXITY, EEG ABUNDANCE GRADIENTS, AND DETECTION EFFICIENCY IN A VISUAL RECOGNITION TASK

Occipital EEG was monitored while subjects inspected 27 projected patterns. The number ( N ) and variety ( V ) of elements in the patterns were varied systematically. There were three levels of N (6, 12 or 24 elements) and three levels of V (circles, squares or hexagons occupying all, one half or one third of the element locations for all levels of N ). Subjects were instructed that they would be required in a post‐test to recognize the patterns, among patterns which had not appeared; they were also informed that the patterns had been constructed according to a set of simple rules, but the nature of these rules was not made fully explicit. The EEG was quantified by means of low‐frequency analysis, yielding measures of abundance (theta, alpha and beta) and mean dominant frequency. For the recognition task, nine stimulus items were embedded among 45 items. Recognition efficiency was measured by means of the signal detection theory discrimination index ( d' ). The results were as follows: (i) Both N and V were inversely related to alpha abundance ( P &lt; 0.01); (ii) the strongest relationship between stimulus parameters and the EEG held for N and EEG beta activity (13.5–19.5 Hz; P &lt; 0.001), where again the EEG and N were inversely related; (iii) there was a significant ( P &lt; 0.05) direct relationship between N and theta activity; (iv) contrary to prediction, mean dominant alpha frequency decreased as 'N increased; (v) d' correlated significantly with a number of effects for N , i.e. subjects who exhibited greatest EEG discriminability of items during exposure of the patterns, subsequently obtained the higher detection scores in the recognition task. The work described therefore demonstrates that not only do stimulus parameters have systematic effects upon brain activity as measured by the EEG, but that such effects have functional value and reflect aspects of efficiency. The results are fully compatible with arousal theory constructs relating physiological reactivity and performance.

Topic: EEG and Brain-Computer Interfaces
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
The Maha-prajapati Bhiksuni Sutra

Rightly named for Maha-prajapati, the first bhiksuni (Buddhist nun), this sutra depicts the story of how the Buddha’s foster-mother, in her sixties at Kapilavatthu (the Buddha’s birthplace), begged the Buddha earnestly and continually to admit her and five hundred other lay women of the Sakya tribe into the monastic order. Viewed from the “Buddha-Only Vehicle” perspective of The Lotus Sutra, The Maha-prajapati Bhiksuni Sutra reveals the Buddha’s compassionate will and vow to help the female practitioners consummate their quest for the ultimate nirvana—becoming a Buddha. In addition, He thus fulfilled His filial piety for His foster-mother. Though founded on The Eight Commands That Demand Respect for the Bhiksus (the eight rules prescribed by the Buddha as the precondition for admitting women into the monastic order), this sutra is not based on a secular patriarchic/male-chauvinist discriminatory view of the Sangha regarding women. What distinguishes this sutra from other sutras is that in it the Buddha explicated in great detail the women’s delusive 84 sentiments and postures and explained the reasons to reach Arhaship by getting rid of the 84 feminine sentiments and postures.

Topic: Indian and Buddhist Studies
Subfield: Religious studies
Field: Arts and Humanities
Domain: Social Sciences
Non-Convulsive Status Epilepticus following Liver Transplantation

Neurological complications following liver transplantation are more common than after other organ transplants. These complications include seizure in about 8% of cases, which is associated with morbidity and mortality. Seizure should be treated immediately, and the process of differential diagnosis has to be performed appropriately in order to avoid permanent neurologic deficit. We herein report a case of status epilepticus after liver transplantation. The status epilepticus was treated promptly and the cause of seizure was assessed. The patient was discharged without any complication.

Topic: Neurological Complications and Syndromes
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Craniofacial Dysostosis With Syringomyelia and Associated Anomalies

A 16-year old boy had craniofacial dysostosis, hydrocephalus, and syringomyelia. Other anomalies included platybasia, a Klippel-Feil anomaly, webbed toes, and a cutaneous hemangioma. Evaluation included cerebral angiography, ventriculography, and myelography.

Topic: Congenital limb and hand anomalies
Subfield: Developmental Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Reliability Analysis of a Steel Frame

A steel frame with haunches is designed according to Eurocodes. The frame is exposed to self-weight, snow, and wind actions. Lateral-torsional buckling appears to represent the most critical criterion, which is considered as a basis for the limit state function. In the reliability analysis, the probabilistic models proposed by the Joint Committee for Structural Safety (JCSS) are used for basic variables. The uncertainty model coefficients take into account the inaccuracy of the resistance model for the haunched girder and the inaccuracy of the action effect model. The time invariant reliability analysis is based on Turkstra's rule for combinations of snow and wind actions. The time variant analysis describes snow and wind actions by jump processes with intermittencies. Assuming a 50-year lifetime, the obtained values of the reliability index b vary within the range from 3.95 up to 5.56. The cross-profile IPE 330 designed according to Eurocodes seems to be adequate. It appears that the time invariant reliability analysis based on Turkstra's rule provides considerably lower values of b than those obtained by the time variant analysis.

Topic: Structural Load-Bearing Analysis
Subfield: Civil and Structural Engineering
Field: Engineering
Domain: Physical Sciences
Effect of temperature on incorporation of <scp>l</scp>-lysine-U-C<sup>14</sup> into testicular proteins

The incorporation of l-lysine-U-C 14 into proteins of slices of rat testis, liver, kidney, and spleen has been investigated following a 1-hr incubation period at temperatures of 20, 26, 32, 37.5, and 44 C. In the testis, maximal incorporation of labeled lysine into protein occurred at 32 C, whereas in the liver, kidney, and spleen the maximal incorporation of isotope into protein occurred at 37.5 C. The data obtained indicate that the enzymatic systems involved in the incorporation of labeled lysine into proteins of the rat testis are more heat labile than those of rat liver, kidney, and spleen. It is suggested that the increased heat lability of the protein-synthesizing systems of the testis may offer a partial explanation for the deleterious effects of temperature on spermatogenesis occurring in cases of cryptorchism.

Topic: Metabolism and Genetic Disorders
Subfield: Clinical Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Ocean Mesoscale Eddy Diffusivity (Abernathey and Marshall, 2013)

Surface mesoscale diffusivities as defined in the paper:<br>Abernathey, R. P., and J. Marshall (2013), Global surface eddy diffusivities derived from satellite altimetry, J. Geophys. Res. Oceans, 118, 901–916, doi:10.1002/jgrc.20066.

Topic: Oceanographic and Atmospheric Processes
Subfield: Oceanography
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Holes in Architecture: A Queer Eye on a Design Method

This article analyzes the formation of a conceptual persona in a narrative which some architects use in the design process. It focuses on a description of such a persona borrowed from Gilles Deleuze and Félix Guattari’s What is Philosophy? It presents the work of three architects who explore how this persona can express a corporeal, public and emotional presence; elaborating on relations which extend beyond the design task and engage with their cultural context. The task all three were given is to design a glory hole that links divided lovers. The actuality of this configuration asks the inhabitants to imagine the presence of the other much like the architects would in the design process. The research is novel allowing architects to truly indulge in exploring the presence of sexual desire and longing in public space.

Topic: Art, Politics, and Modernism
Subfield: Visual Arts and Performing Arts
Field: Arts and Humanities
Domain: Social Sciences
Crisis management as practice in small‐ and medium‐sized enterprises during the first period of COVID‐19

Abstract This article draws attention to the social context and working methods in crisis management. Based on 1000 interviews with business leaders in Swedish small‐ and medium‐sized enterprises (SMEs), we analyze crisis management in practice and ask: What social contexts do business leaders use in crisis management, and what working methods do they rely on? Most companies in this study do not have any form of crisis group; rather, they deal with issues reactively as they occur. Few of the companies work continuously with a crisis plan and only slightly more than half of those that have crisis plans report that it has been helpful in dealing with the COVID‐19 situation. The study concludes that Swedish SMEs seem reliant upon a process that has an emerging nature whereby decisions are largely based on gut feeling. However, the companies in our sample that experienced a significant revenue decline due to the COVID‐19 situation report that they employ a more centralized and deductive approach with reports and documents as a basis for their work. The study contributes to a developed understanding of how crisis management works in practice.

Topic: Public Relations and Crisis Communication
Subfield: Communication
Field: Social Sciences
Domain: Social Sciences