jimnoneill/paper-to-field-training huggingface dataset:
Risk Factors for Emergency Room and Hospital Care Among Patients With Solid Tumors on Immune Checkpoint Inhibitor Therapy

Field: Medicine (Health Sciences)

Objectives: Immune checkpoint inhibitors (ICIs) are being increasingly used across cancer types. Emergency room (ER) and inpatient (IP) care, common in patients with cancer, remain poorly defined in this specific population, and risk factors for such care are unknown. Methods: We retrospectively reviewed charts for patients with solid tumors who received >1 ICI dose at 1 of 2 sites from January 1, 2011 to April 28, 2017. Demographics, medical history, cancer diagnosis/therapy/toxicity details, and outcomes were recorded. Descriptive data detailing ER/IP care at the 2 associated hospitals during ICI therapy (from first dose to 3 mo after last dose) were collected. The Fisher exact test and multivariate regression analysis was used to study differences between patients with versus without ER/IP care during ICI treatment. Results: Among 345 patients studied, 50% had at least 1 ER visit during ICI treatment and 43% had at least 1 IP admission. Six percent of ER/IP visits eventually required intensive care. A total of 12% of ER/IP visits were associated with suspected or confirmed immune-related adverse events. Predictors of ER care were African-American race (odds ratio [OR]: 3.83, P =0.001), Hispanic ethnicity (OR: 3.12, P =0.007), and coronary artery disease (OR: 2.43, P =0.006). Predictors of IP care were African-American race (OR: 2.38, P =0.024), Hispanic ethnicity (OR: 2.29, P =0.045), chronic kidney disease (OR: 3.89, P =0.006), angiotensin converting enzyme inhibitor/angiotensin receptor blocker medication use (OR: 0.44, P =0.009), and liver metastasis (OR: 2.32, P =0.003). Conclusions: Understanding demographic and clinical risk factors for ER/IP care among patients on ICIs can help highlight disparities, prospectively identify high-risk patients, and inform preventive programs aimed at reducing such care.
Religious pluralism in theological education

Field: Arts and Humanities (Social Sciences)

In this essay, I will try to explain and ground a conviction that I share with many colleagues in the Christian theological community: that one of the reasons why Christian theological education is not adequately doing its job of mediating between culture and religion has to do with the mono-religions character of most Christian theology today. Theological educators are going about their job on the basis of an exclusive, or too restrictive, use of Christian tradition and experience. They have closed themselves to, or are not sufficiently open to, other religious traditions and identities.
Natural Antibody in Mammary Tumor Virus-Infected Mice That Reacts With Intracytoplasmic A Particles of Mouse Mammary Tumors

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

By an indirect immunofluorescence technique with prolonged serum incubation on murine mammary tumor (MT) slices, 179 of 424 mice examined were found to possess natural serum antibody (antibodies) that reacted with intracytoplasmic A particles (iAp) of MT cells. The immunologic specificity of this antibody was supported by absorption and blocking experiments. Furthermore, a strong similarity was seen between the mouse antibody reaction on various MT and the fluorescence pattern of rabbit anti-iAp antiserum on these tumors. In female mice, incidence and geometric mean titers of the antibody in part were correlated to the spontaneous MT frequency of the mouse strains examined. Some mice of the strains XVII/Bin and CBA/BinfXVII/Bin, hitherto regarded as "free" of the mouse mammary tumor virus (MuMTV), also contained anti-iAp antibody in their sera. In contrast to MuMTV)-producing CBA/Bin micethese animals did not possess detectable spontaneous antibody reacting with MuMTV-B particles. Therefore, hypothetically, the antibody response in these mice might be induced by incomplete MuMTV expression. In the strain CBA/Bin, females 4 months old and older possessed the antibody in significantly higher geometric mean titers when compared to 4-week-old female mice. The history of lactation seemed to have no influence on the titer of antibody. In the comparatively high MT strains CBA/Bin and C3H/Bin, adult (4-month-old) females had the antibody in significantly higher levels when compared to age-matched males.
Analogue of a Laplace-Runge-Lenz vector for particle orbits (timelike geodesics) in Schwarzschild spacetime

Field: Physics and Astronomy (Physical Sciences)

In Schwarzschild spacetime, the timelike geodesic equations, which define particle orbits, have a well-known formulation as a dynamical system in coordinates adapted to the timelike hypersurface containing the geodesic. For equatorial geodesics, the resulting dynamical system is shown to possess a conserved angular quantity and two conserved temporal quantities, whose properties and physical meaning are analogues of the conserved Laplace-Runge-Lenz vector, and its variant known as Hamilton's vector, in Newtonian gravity. When a particle orbit is projected into the spatial equatorial plane, the angular quantity yields the coordinate angle at which the orbit has either a turning point (where the radial velocity is zero) or a centripetal point (where the radial acceleration is zero). This is the same property as the angle of the respective Laplace-Runge-Lenz and Hamilton vectors in the plane of motion in Newtonian gravity. The temporal quantities yield the coordinate time and the proper time at which those points are reached on the orbit. In general, for orbits that have a single turning point, the three quantities are globally constant; for orbits that possess more than one turning point, the temporal quantities are just locally constant as they jump at every successive turning point, while the angular quantity similarly jumps only if an orbit is precessing. This is analogous to the properties of a generalized Laplace-Runge-Lenz vector and generalized Hamilton's vector which are known to exist for precessing orbits in post-Newtonian gravity. The angular conserved quantity can be used to define a direct analogue of these vectors at spatial infinity.
Improving Control of Torsional Vibrations of Motor-Driven Reciprocating Compressors

Field: Engineering (Physical Sciences)

Abstract Torsional vibrations establish a remarkable risk for decreased reliability and availability of motor-driven reciprocating compressors in oil and gas industry. This risk can be significantly reduced by careful analysis and design of torsional drive trains. A drive train is composed of separate parts, as motor, coupling, flywheel and compressor. These components are usually produced by separate manufacturers. Thus, the control of torsional vibrations requires seamless cooperation between the system integrator and component suppliers. Torsional analysis is based on the inertia, stiffness and damping properties of the train components. Usually, the chosen motor manufacturer provides this data to the system integrator. In addition to the mechanical properties, electric motors are characterized by the magnetic stiffness and damping induced by the magnetic fields in the air-gap between the rotor and stator. The main aim of this paper is to describe the modelling of magnetic effects in general terms as part of the drive train torsional analysis. The second aim is to show the significance of the magnetic stiffness and damping particularly in motor-driven reciprocating compressors with a soft coupling. This paper describes a recently introduced approach for the modelling of magnetic effects. This approach combines the accuracy of Finite Element Method (FEM) with the portability of parametric space-vector models. This is enabled by the linearization of the electromagnetic behavior in the operation point of the motor. The significance of portability follows from the typical procedure of torsional analysis and design carried out usually by the system integrator. The calculation example is a motor-driven reciprocating compressor with a soft coupling. It is well-known that in these motor-compressors the effect of magnetic stiffness is significant due to several natural frequencies and excitation orders below the motor supply frequency. In general, the magnetic stiffness increases the natural frequencies, and the magnetic damping decreases the oscillation amplitudes of the lowest torsional modes. The calculation example shows that the accuracy of the analytic formulae can be clearly increased by the presented new method. In addition, the calculation results demonstrate the significance of magnetic stiffness and damping in motor-driven compressors with a soft coupling. Thus, the reliability and availability of these compressor trains can be improved by including the magnetic effects into the analysis.
The Development of Ataxia Telangiectasia Mutated Kinase Inhibitors

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Radiation and genotoxic drugs are two of the cornerstones of current cancer treatment strategy. However, this type of therapy often suffers from radio- or chemo-resistance caused by DNA repair mechanisms. With the aim of increasing the efficacy of these treatments, there has been great interest in studying DNA damage responses (DDR). Among the plethora of signal and effector proteins involved in DDR, three related kinases ATM (ataxia telangiectasia mutated), ATR (ATM and Rad3-related) and DNA-PK (DNA-dependent protein kinase) play the main roles in initiation and regulation of signaling pathways in response to DNA double and single strand breaks (DSB and SSB). ATM inhibitors, as well as those of ATR and DNA-PK, provide an opportunity to sensitize cancer cells to therapy. Moreover, they can lead to selective killing of cancer cells, exploiting a concept known as synthetic lethality. However, only a very few selective inhibitors have been identified to this date. This mini-review is focused both on the development of selective inhibitors of ATM and other inhibitors which have ATM as one of their targets.
The Channels of Song in Calpurnius Siculus and in Virgil's Georgics

Field: Arts and Humanities (Social Sciences)

In a song exchange in his second Eclogue, Calpurnius presents the canales through which water is piped to a garden as equivalent to a pastoral singer's pipe, anticipating his innovative use of canales to denote musical pipes at Ecl. 4.76. Calpurnius's choice of the term suggests a metaphorical reading of Virgil's two references to canales in the Georgics as conduits for water and honey. Calpurnius makes explicit Virgil's implicit association of irrigation through canales with the nourishing value of song. This double sense of canales dramatizes a productive relationship between human song and the natural landscape in Calp. Ecl. 2.
A New Dataset, Notation Software, and Representation for Computational Schenkerian Analysis

Field: Arts and Humanities (Social Sciences)

Schenkerian Analysis (SchA) is a uniquely expressive method of music analysis, combining elements of melody, harmony, counterpoint, and form to describe the hierarchical structure supporting a work of music. However, despite its powerful analytical utility and potential to improve music understanding and generation, SchA has rarely been utilized by the computer music community. This is in large part due to the paucity of available high-quality data in a computer-readable format. With a larger corpus of Schenkerian data, it may be possible to infuse machine learning models with a deeper understanding of musical structure, thus leading to more "human" results. To encourage further research in Schenkerian analysis and its potential benefits for music informatics and generation, this paper presents three main contributions: 1) a new and growing dataset of SchAs, the largest in human- and computer-readable formats to date (>140 excerpts), 2) a novel software for visualization and collection of SchA data, and 3) a novel, flexible representation of SchA as a heterogeneous-edge graph data structure.
Intertumor and intratumor heterogeneity of PIK3CA mutations in extramammary Paget’s disease

Field: Medicine (Health Sciences)

Abstract Although the prognosis of patients with extramammary Paget’s disease (EMPD) treated with radical resection is good, the prognosis of EMPD with distant metastasis is very poor. PIK3CA mutations predict a good response to PIK3CA inhibitors. The aim of this study was to investigate the occurrence rate of PIK3CA mutations (including multiple mutations [MM]) related to the intertumor and intratumor heterogeneity in EMPD and to evaluate the correlation between these mutations and clinical parameters of EMPD. We performed droplet digital polymerase chain reaction to detect PIK3CA mutations (E542K, E545K, H1047R, and MM) in 68 patients with EMPD. In addition, we investigated the presence of PIK3CA mutations at multiple sites in 16 patients with PIK3CA mutations to assess the intratumor heterogeneity of PIK3CA mutations in EMPD. The frequency of one or more PIK3CA mutations in patients with EMPD was 30.8% (21/68). The frequency of E542K, E545K, H1047R, and MM were 10.2% (7/68), 13.2% (9/68), 11.7% (8/68), and 4.4% (3/68), respectively. No significant correlation was found between PIK3CA mutation patterns and clinical parameters. Of the 21 patients with PIK3CA mutations, 16 with tissue samples that could be analyzed at multiple sites were examined. The proportion of patients with the same PIK3CA mutations at all sites was 12.5% (2/16). The proportion of patients with the same PIK3CA mutations at least two or more sites, but not at all sites, was 31.2% (5/16). The proportion of patients with no PIK3CA mutations at other sites was 37.5% (6/16). The proportion of patients with other PIK3CA mutations at other sites was 18.7% (3/16). There is intertumor and intratumor heterogeneity of PIK3CA mutations. PIK3CA mutations in EMPD may be progressor mutations in EMPD.
Effect of traffic routes on the trace element concentration in plants in the Warsaw agglomeration

Field: Environmental Science (Physical Sciences)

Abstract This work presents the results of an analysis of concentration levels of selected trace metals (Pb, Zn, Cu, Cd) in plants and soil near the main roads of the Warsaw agglomeration. The aim of the study was to assess the degree of contamination by selected trace elements of plants growing at different distances from the road (directly at the roadside and 50 meters away from the road) and to examine the relationship between the concentration of the tested parameters in the soil and their content in the plant. It was found that the lack of clear differentiation in the levels of all heavy metals in plants depending on the distance from the road was associated with the possibility of considerable pollutant migration. In addition, it was found that dandelion usually reveals higher concentrations of heavy metals than meadow-grass.
Sensing Dying Cells in Health and Disease

Field: Medicine (Health Sciences)

Kidney injury molecule-1 (KIM-1), also known as T-cell Ig and mucin domain-1 (TIM-1), is a widely recognized biomarker for AKI, but its biological function is less appreciated. KIM-1/TIM-1 belongs to the T-cell Ig and mucin domain family of conserved transmembrane proteins, which bear the characteristic six-cysteine Ig-like variable domain. The latter enables binding of KIM-1/TIM-1 to its natural ligand, phosphatidylserine, expressed on the surface of apoptotic cells and necrotic cells. KIM-1/TIM-1 is expressed in a variety of tissues and plays fundamental roles in regulating sterile inflammation and adaptive immune responses. In the kidney, KIM-1 is upregulated on injured renal proximal tubule cells, which transforms them into phagocytes for clearance of dying cells and helps to dampen sterile inflammation. TIM-1, expressed in T cells, B cells, and natural killer T cells, is essential for cell activation and immune regulatory functions in the host. Functional polymorphisms in the gene for KIM-1/TIM-1, HAVCR1 , have been associated with susceptibility to immunoinflammatory conditions and hepatitis A virus–induced liver failure, which is thought to be due to a differential ability of KIM-1/TIM-1 variants to bind phosphatidylserine. This review will summarize the role of KIM-1/TIM-1 in health and disease and its potential clinical applications as a biomarker and therapeutic target in humans.
Processing the spectroscopic data

Field: Physics and Astronomy (Physical Sciences)

Context: The Gaia Data Release 2 (DR2) contains the first release of radial velocities complementing the kinematic data of a sample of about 7 million relatively bright, late-type stars. // \n \nAims: This paper provides a detailed description of the Gaia spectroscopic data processing pipeline, and of the approach adopted to derive the radial velocities presented in DR2. // \n \nMethods: The pipeline must perform four main tasks: (i) clean and reduce the spectra observed with the Radial Velocity Spectrometer (RVS); (ii) calibrate the RVS instrument, including wavelength, straylight, line-spread function, bias non-uniformity, and photometric zeropoint; (iii) extract the radial velocities; and (iv) verify the accuracy and precision of the results. The radial velocity of a star is obtained through a fit of the RVS spectrum relative to an appropriate synthetic template spectrum. An additional task of the spectroscopic pipeline was to provide first-order estimates of the stellar atmospheric parameters required to select such template spectra. We describe the pipeline features and present the detailed calibration algorithms and software solutions we used to produce the radial velocities published in DR2. // \n \nResults: The spectroscopic processing pipeline produced median radial velocities for Gaia stars with narrow-band near-IR magnitude GRVS ≤ 12 (i.e. brighter than V ~ 13). Stars identified as double-lined spectroscopic binaries were removed from the pipeline, while variable stars, single-lined, and non-detected double-lined spectroscopic binaries were treated as single stars. The scatter in radial velocity among different observations of a same star, also published in Gaia DR2, provides information about radial velocity variability. For the hottest (Teff ≥ 7000 K) and coolest (Teff ≤ 3500 K) stars, the accuracy and precision of the stellar parameter estimates are not sufficient to allow selection of appropriate templates. The radial velocities obtained for these stars were removed from DR2. The pipeline also provides a first-order estimate of the performance obtained. The overall accuracy of radial velocity measurements is around ~200–300 m s−1, and the overall precision is ~1 km s−1; it reaches ~200 m s−1 for the brightest stars.
Organisational development, appreciative inquiry and the development of Psychologically Informed Environments (PIEs): part two: the pilot study and evaluation

Field: Social Sciences (Social Sciences)

Purpose – Part One of this duo of papers outlined the appreciative inquiry (AI) philosophy, a strengths-based “positive psychology” and organisational development (OD) approach which is intrinsically creative and generative, and has been found to work well in many fields. The purpose of this paper is to describe its application in homeless hostels and demonstrates the benefits of using AI with the staff and residents, as both a personal development and an OD tool for hostels who want to become a psychologically informed environment (PIE). Design/methodology/approach – This is a case study exploring a new approach to the development of a PIE. The background of the approach and the way it contributes to a PIE as described in Part One is briefly summarised, and the implementation pilot project is discussed; the appreciative conversation and the 5 D cycle are key AI “tools” which were used. The inclusion of positive psychology approaches is referenced. In addition, in the spirit of evidence-generating practice in PIEs, preliminary quantitative and qualitative findings are reported to identify the outcomes of the approach – including client motivation, desire to build positive relationships, and increased emotional awareness. Findings – Residents responded very well to the approach, and a high proportion continued to apply their learning, making major steps towards independent living. This was backed up by quantitative data demonstrating effective outcomes for the supported housing sector, and qualitative themes start to illuminate the psychological processes behind the outcomes. The openness of PIEs to alternative psychologies is further demonstrated. The model was rolled out to other Westminster hostels. Originality/value – AI is well-established as an OD process and less well known as a personal development approach; but has not previously been articulated as a tool for working with hostel residents or for developing PIEs. This strength-based approach is an alternative to some of the problem-based psychological approaches that have been used. In addition, the AI intervention illustrated defining features of a PIE such as reflective awareness.
Parvo virus infection − an unusual cause of pleural efusion in an immunocompetent patient

Field: Medicine (Health Sciences)

Pleural and pulmonary manifestations of Parvo virus infection are exceedingly rare. Here, we describe an immunocompetent patient with Parvo virus infection who presented with lymphocytic, exudative effusion. Though, this presentation is rare, it may be looked for, if a patient presents with rash and pleural effusion.