jimnoneill/paper-to-field-training huggingface dataset:
Ectopic gene conversion in prokaryotic and yeast genomes

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The repair of double strand DNA breaks is important to genomic stability. Gene conversions are non-reciprocal exchanges of DNA created through the repair of double strand DNA breaks. Relatively few studies have looked at examining the similarities and differences of the physical characteristics of ectopic gene conversions (conversions between non-allelic genes) within and between diverse lineages of prokaryotes and yeast. I found that several factors affect the frequency of ectopic gene conversions in prokaryotes and yeast. The size and organization of multigene families affects how often genes are converted. In E. coli a positive correlation was found between gene family size and conversion frequency. In yeast, I found that intra-chromosomal gene conversions are more frequent than inter-chromosomal conversions. The amount of sequence similarity between the converted genes affects their conversion frequency. I found that long conversions tend to occur between highly similar homologs. In addition, the sequence similarity requirements are not uniform for every organism. For example, I found indications that the life-style of the organism affects the stringency of sequence similarity requirements for ectopic gene conversion. I determined that ectopic gene conversions occur more frequently and require significantly less flanking similarity in the pathogenic bacteria strains than in the non-pathogenic. The functional importance of the converted genes affects how frequently they are converted. Genes that have been functionally maintained throughout evolution are ectopically converted less frequently than genome specific paralogs. Nucleotide distance between homologous genes affects their ectopic conversion frequency. In paralogous multigene families of yeast, gene conversions occur more frequently between genes which are close together on the same chromosome than between dispersed homologs. Converted regions are not uniformly distributed along the length of genes. Converted regions tend to be clustered near the 3' end of genes in yeast but not in prokaryotes. I also looked at the effects of gene conversions on nucleotide composition of yeast genes and found that repeated ectopic gene conversions between dispersed homologs tend to increase the converted genes GC-content.
Time Horizon: Intersections of Deep Time and Biographical Time on the West Shore, Stromness, Orkney

Field: Social Sciences (Social Sciences)

What is the significance of a human life in relation to the timespan of the geological processes that shape and reshape the terrain under our feet? Here, we ask how we might think on a planetary scale while being grounded in the everyday, tracing the relationship between biographical time and geological formation. Examining social relationships through the materiality of sandstone, uranium, and concrete, this paper presents a collaborative deep time practice, realised through the iterative process of walking, reading and inscribing a specific site, the West Shore of Stromness, Orkney.
Serum analytes as predictors of disease recurrence and the duration of invasive disease-free survival in patients with triple negative breast cancer enrolled in the OXEL trial treated with immunotherapy, chemotherapy, or chemoimmunotherapy

Field: Medicine (Health Sciences)

Background The OXEL study ( NCT03487666 ) was a phase II trial of patients with triple negative breast cancer (TNBC) with residual disease following neoadjuvant chemotherapy, randomized to receive immunotherapy (anti-programmed cell death protein 1, nivolumab), chemotherapy (capecitabine), or chemoimmunotherapy. We previously reported on the primary endpoint of the OXEL trial, demonstrating that a peripheral immunoscore based on circulating immune cells reflecting immune activation was increased in patients treated with immunotherapy. However, compared with cell-based immune assays, sera assays are more cost-effective, less labor-intensive, and samples easier to obtain. Here, we report on differences in serum analytes between treatment arms and associations with clinical response. Methods Patients (n=38) were assayed for 97 serum analytes before and after 6 and 12 weeks of therapy. Serum analytes were assessed for changes with therapy, and as predictors of disease recurrence and the duration of invasive disease-free survival (iDFS) in both single analyte analyses and machine learning models. Results Levels of specific analytes at baseline and changes in levels at early time points on treatment preceding recurrence were associated with eventual development of disease recurrence and/or the duration of iDFS. These associations varied based on the therapy patients received. Immunotherapy led to enrichment in pro-inflammatory analytes following treatment, whereas chemotherapy resulted in overall decreases. Changes seen in patients receiving chemoimmunotherapy more closely resembled those observed in patients receiving immunotherapy alone as opposed to chemotherapy alone. Furthermore, logistic regression and Cox proportional hazard models, developed using machine learning methods, demonstrated that combinations of serum analytes were more predictive of disease recurrence and iDFS duration than analyses of single serum analytes. Notably, the multivariable models that predicted patient outcomes were highly specific to the class of treatment patients received. Conclusions In patients with TNBC with residual disease after neoadjuvant chemotherapy, treatment with immunotherapy alone or chemoimmunotherapy resulted in enhanced immune activation compared with chemotherapy alone as measured by changes in serum analyte levels. Distinct serum analytes, both at baseline and as changes after therapy, predicted clinical outcomes for patients receiving immunotherapy alone, chemotherapy alone, or chemoimmunotherapy. Trial registration number NCT03487666 .
Measuring the effectiveness of quality assurance systems in the construction industry

Field: Decision Sciences (Social Sciences)

Many large construction companies in the UK are now operating a quality assurance (QA) system to ISO 9000, yet there seems to be no available evidence that they have developed any way of measuring the “effectiveness” of their systems in meeting prescribed quality objectives. This paper discusses the difficulties faced in attempting to develop a model in the form of a matrix to measure the effectiveness of QA systems.
Urine and Serum Sex Steroid Profile in Testosterone-Treated Transgender and Hypogonadal and Healthy Control Men

Field: Medicine (Health Sciences)

Urine antidoping detection tests in T-treated transgender men can be interpreted like those of T-treated hypogonadal men and are unaffected by time since last T dose. Serum steroids are more sensitive to detect exogenous T administration early but not later after the last T dose.
Abstract 3249: a-TIGIT mediates antitumor activity through multiple mechanisms of action involving activation of intratumor effector T cells and depletion of regulatory T cells

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Abstract T cell Immunoreceptor with Ig and ITIM domains (TIGIT) is a co-inhibitory receptor expressed by lymphocytes, preferentially CD8+ T cells, NK, as well as regulatory T cells (Treg). TIGIT can be bound by several ligands including CD155 and CD112 that are frequently expressed by tumor cells. In cancer, TIGIT expression is upregulated on conventional T cells and even more on regulatory T cells. Co-expression with exhaustion markers such as PD-1 is common, giving a strong rationale for blocking TIGIT as a therapeutic approach for reversing T or NK cell dysfunction linked with cancer progression. The mechanism of action of novel a-TIGIT monoclonal antibody (mAb) was characterized in vivo in the murine CT26 tumor model. This model mimics the human situation based on expression of TIGIT ligands on tumor cells and infiltration by effector and regulatory T cells that express higher levels of TIGIT compared to splenocytes. Two different isotypes (mIgG2a and mIgG1) of a-TIGIT mAb were used to evaluate anti-tumor efficacy, with only the mIgG2a, deleting isotype able to induce strong antitumor efficacy. The importance of Fc gamma receptors (FcγR) for the antitumor efficacy of a-TIGIT activity was further demonstrated by the use of mice KO for activatory FcγR or by depletion of NK cells which also resulted in the loss of a-TIGIT activity. The anti-tumor efficacy of a-TIGIT mAb was associated with an increased activity of conventional CD8+ and CD4+ T cells but also with a preferential depletion of Treg within the tumor microenvironment. This activity also correlated with full occupancy of TIGIT receptor in mice. As it has been shown that TIGIT is expressed on tumor cells in certain hematological cancers, we also established a model of EL4 tumor with engineered TIGIT expression. In this model, a-TIGIT demonstrates a strong antitumor effect that strictly depends on the isotype of the mAb. Finally, the activity of a-TIGIT was tested in less immunogenic models including of pancreatic PancO2 cancer where it demonstrated some tumor growth delay as a single agent and very strong combination potential with other immune checkpoints. In summary, these results show that antitumor mediated efficacy of a-TIGIT mAb depends upon target binding and also on interaction with FcγR. These findings support the clinical evaluation of a-TIGIT mAb able to engage those receptors. Citation Format: Julie Preillon, Sofie Denies, Diane Jamart, Matthew J. Carter, Mark S. Cragg, Gregory Driessens. a-TIGIT mediates antitumor activity through multiple mechanisms of action involving activation of intratumor effector T cells and depletion of regulatory T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3249.
Supplemental Material: Contemporaneous crust-derived I- and S-type granite magmatism and normal faulting on Tinos, Delos, and Naxos, Greece: Constraints on Aegean orogenic collapse

Field: Earth and Planetary Sciences (Physical Sciences)

<p>Further method details and complete results for granite geochemistry, Sr-Nd isotope analysis, and U-Pb geochronology.</p>
Men Like These

Field: Arts and Humanities (Social Sciences)

As a forerunner to television, the cinema was the only medium for visual projections of the air war, and the sole opportunity mass audiences had to see actual combat footage, or the men and aircraft involved. Newsreels and MOI short films were the two means of presenting such information, the former 'hot' propaganda, and the latter 'warm', because of the time differences involved and the relative immediacy of their contents. Newsreels could not compete with the BBC and press for the speed of response in breaking the news, but they could cover topical themes from a slightly broader perspective with reference to specific events such as very high RAF claims for aircraft shot down on a particular day, or the award of medals to pilots. The MOI's short films did not attempt to address 'hot' news events but instead covered broader, 'public information' themes that chimed with newsreel coverage such as a justification for the RAF's cumulative enemy aircraft totals, or a day in the life of a fighter pilot. In some respects newsreel and MOI film content was similar when it came to the RAF's pilots, some film clips used in both, or access to the 'fighter boys' resulting in unavoidably similar footage. Newsreel companies invariably used a light and frequently humorous narrative style; the MOI's 'shorts' tended to be more sober and — although they tried to avoid it — were more officious in tone. However, for cinemagoers the key difference between the two probably did not lay so much in what was said, but who was saying it.KeywordsShort FilmGood FightFighter PilotFighter StationGround CrewThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
The Impact of Modern Industrialized Dietary Sodium Intake on the Plasma Proteome

Field: Medicine (Health Sciences)

Abstract BACKGROUND High dietary sodium intake is associated with cardiovascular disease. We investigated the influence of sodium intake on the plasma proteome. METHODS Prospectively recruited normotensive participants underwent 2 controlled dietary sodium interventions to evaluate hormonal and proteomic (1,512 proteins) changes: sodium-restriction resembling ancestral hunter-gatherer intake (~10 mEq/day, ~230 mg/day) and sodium-loading resembling modern industrialized intake (~200 mEq/day, ~4,600 mg/day). Twenty-four hour urine collections were obtained after each diet. Plasma proteomic changes were assessed with correction for false discovery. RESULTS Participants achieved a 24-h urinary sodium excretion of 16 mEq/L when sodium-restricted and 249 mEq/L when sodium-loaded. Thirty-eight proteins displayed statistically significant changes with 15 additional proteins exhibiting notable trends that did not reach statistical significance. The most apparent changes were increases in proteins related to fibrosis and the extracellular matrix (ECM) when sodium-loaded, whereas sodium-restriction increased proteins related to immune/inflammatory pathways and the renin-angiotensin system (RAS)-kallikrein-kinin system (KKS)-complement pathway. NT-proBNP, FUMH (fumarate hydratase), LKHA4 (leukotriene A(4) hydrolase), COFA1 (collagen alpha-1(V) chain), COF2 (cofilin-2), BMP-4, and TGF-β RIII had the greatest increases when sodium-loaded, whereas renin, thrombin, apo A-1 (apolipoprotein A-1), FABPA (fatty acid binding protein), and LEAP-1 (hepcidin) had the greatest increases when sodium-restricted. CONCLUSIONS When compared to a sodium-restricted diet resembling ancestral intake, the modern industrialized dietary sodium intake increased proteins related to fibrosis and the ECM, and decreased proteins related to the RAS, KKS, immunity, and inflammation. These findings in normotensive people provide an atlas of proteomic changes, and biological pathways, that may contribute to hypertension and other sodium-related disorders.
The fluoride concentration in the drinking water of towns in the Transvaal, Orange Free State and Natal.

Field: Environmental Science (Physical Sciences)

In previous studies the water fluoride content of the larger cities in South Africa, and smaller towns in the Cape Province were recorded. This project was extended to include smaller towns (500 or more inhabitants) in the Transvaal, Orange Free State and Natal. Drinking water was collected in polypropylene containers and the fluoride content determined potentiometrically. The information obtained made it possible to compile a table setting out the fluoride content of the drinking water in these smaller towns. The study confirms a previous observation that water from boreholes has the highest (p < 0.05), and fountains the lowest fluoride content.
Slave Narratives and the Rhetoric of Author Portraiture

Field: Arts and Humanities (Social Sciences)

âSlave Narratives and the Rhetoric of Author Portraitureâ places the author portraits of slave narratives within the historical contexts of illustrated texts generally, and the genre of slave narratives specifically. The essay begins with an examination of author portraiture from its earliest use in print publication, where the author portrait was an often ironic "zone of transaction" between the reader and the text's narrator. With the emergence of slave narratives, however, the essay argues that slave narrativesâ author portraits were serious evidence to prove the authenticity of slave narratives as autobiographies. Further, slave narratives' author portraits sought to evidence the irrational relationship of apparent skin color to race categories during the era of American slavery. The essay finds that the frontispiece author portraits were both proof of authorship/authenticity, and critical evidence of miscegenation's dire consequences. Yet the current editions of slave narratives often manipulate and, in many cases omit these portraits and thereby create a subtle but important crisis of authority in the slave narrative genre.
SH1149466.09FU

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
A Torsional Contact Problem for an Indented Half-Space

Field: Engineering (Physical Sciences)

This paper is concerned with the torsion of a rigid disk bonded to the bottom of a cylindrical indentation on an elastic half-space. By virtue of Fourier sine and cosine transforms, the mixed boundary value problem in classical elastostatics is shown to be reducible to a pair of integral equations, of which one possesses a generalized Cauchy singular kernel. With the aid of the theory of analytic functions, the inherent fractional-order singularity in the contact problem is rendered explicit. Illustrative results on the torsional stiffness of the base of the indentation and the corresponding contact stress distribution are presented for engineering applications.
Active portfolio management: The power of the Treynor-Black model

Field: Economics, Econometrics and Finance (Social Sciences)

Abstract: The performance of active portfolio methods critically depends on the forecasting ability of the security analyst. The Treynor-Black model provides an efficient way of implementing active investment strategy. Despite its potential benefits, the Treynor-Black model appears to have had little impact on the financial community, mainly because it has been believed that the precision threshold of alpha forecasts used as inputs to the model is too high. We seek to lower the threshold of forecast precision needed to beat a passive-portfolio strategy by improving the econometric methods used in constructing portfolios from security analyst forecasts. We apply shrinkage estimation to beta coefficients and to discount functions for forecasts of stock abnormal returns. OLS estimates, Least Absolute Deviations (LAD) estimates and shrinkage LAD estimates are compared by contribution to portfolio performance. Despite correlations between forecasts and realizations of abnormal returns as low as 0.04, the shrinkage LAD methodology yields superior performance in outof-sample experiments.
An Analysis of the Liberal Arts in Introductory Meteorology Courses

Field: Social Sciences (Social Sciences)

A questionnaire was designed to probe the degree to which specific pedagogical tasks or techniques are incorporated into introductory meteorology courses. Responses from higher education institutions showed that there is a large deviation among colleges with regard to the inclusion of liberal arts within the course structure. Though the results are generally positive, there are three specific areas that warrant attention. 1) Students need to be integrated into the learning process. 2) Students' writing skills need to be improved. 3) Instructors need to illustrate the advancements in the science of meteorology in their courses.
Modélisation de la dynamique couplée des plasmas magnétosphérique et ionosphérique.

Field: Physics and Astronomy (Physical Sciences)

The interaction of the solar wind with the terrestrial magnetic field induces in the magnetosphere an electric field responsible of the motion (or convection) of the plasma from the tail to the Earth. The magnetospheric particles interact with the ionosphere, the ionized part of the Earth's atmosphere. They modify the electrical properties of the ionospheric conductor, particularly the electric field distribution which moves the magnetospheric plasma. The Centre d'Etude Spatiale des Rayonnements built a numerical model describing self-consistently the magnetospheric convection coupled with the ionosphere. We modified this code in order :
1) to include the effects of the asymmetry between the two north and south hemispheres due to the solar illumination
2) to replace the used dipolar magnetic field model by a more realistic model The first numerical results show the large effect of the inter-hemispheric asymmetry on the ionospheric plasma dynamics but that the magnetosphere is relatively insensitive to these effects. They also show that the use of a magnetic field topology more realistic than the one of a dipole is necessary to reproduce the observations
An energy and environmental assessment of road transport fuels

Field: Energy (Physical Sciences)

This paper assesses the conventional and alternative fuels for road transport from the energy and environmental viewpoints. Energy security, the potential supplies of petroleum and feedstocks for alternative fuels, and existing alternative fuel programmes are discussed. A review of the formation of the main vehicular pollutants is given and comparisons of the emissions from road vehicles using conventional and alternative fuels are made. Comparisons are also made among six transport fuel options by considering several factors that influence choice, and a possible long–term development in road transport energy consumption by fuel type is presented.