A Framework to Identify Antigen-Expanded T Cell Receptor Clusters Within Complex Repertoires

Common approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire provides a global view that is limited only in terms of theoretical sensitivity due to the depth of available sampling; however, the assignment of antigen specificities within TCR repertoires has become a bottleneck. This study combines antigen-driven expansion, deep TCR sequencing, and a novel analysis framework to show that homologous ‘Clusters of Expanded TCRs (CETs)’ can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse uncultured repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity.

Sensitivity study of ring-shaped electrostatic sensor based on nonparametric estimation

In this paper, aiming at the problem of the electrostatic sensor signal satisfying the gaussian distribution, the non-parametric kernel estimation method is introduced, and the electrode induction model of the electrostatic sensor is finally fitted by combining the goodness of fit and the simulation data samples. This model satisfies the gaussian distribution and the electrostatic signal satisfying the gaussian distribution is given in the theory. Maxwell simulation software was used to simulate the theoretical sensitivity of the electrostatic sensor and the axial and radial spatial sensitivity characteristics of different sensor parameters were obtained. Within a certain range, the relative permittivity of the insulating tube is also discussed. Finally, an insulating tube with a relative permittivity of 3 is selected as the material of the insulating tube. Finally, the experiment is carried out on the experimental equipment and the conclusions obtained in the article are confirmed.

A framework to identify antigen-expanded T Cell Receptor (TCR) clusters within complex repertoires

Common approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire offers a global view whose theoretical sensitivity is limited only by the depth of available sampling. However, assignment of antigen specificities within TCR repertoires has become a bottleneck. Here, we combine antigen-driven expansion, deep TCR sequencing and a novel analysis framework to show that homologous "Clusters of Expanded TCRs (CETs)" can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse unexpanded repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity.

Diferencias en el análisis de datos desde distintas versiones de la Teoría Fundamentada

La teoría fundamentada (TF) es una metodología de investigación ampliamente conocida y utilizada en las ciencias sociales. Tiene varias versiones (Teoría Fundamentada Glaseriana, Straussiana, Dimensional, Constructivista y Análisis Situacional) que muestran diferencias que tienden a generar cierta confusión en su estudio y uso. Es el caso del proceso de análisis de datos. Para identificar estas diferencias, se realizó una revisión intencionada de la literatura publicada en los últimos 20 años en español, portugués e inglés. Hicimos una búsqueda sistemática en cinco bases de datos científicas y Google Scholar Beta. Fueron seleccionados 72 textos, incluidos libros y artículos de los cuales 31 están escritos por los principales referentes de cada versión y 41 escritos por otros autores y autoras que contribuyen a la comprensión del método. El análisis de estos textos permitió identificar elementos comunes y diferencias significativas. Los resultados encontrados revelan cinco aspectos comunes entre las versiones: comparación constante, muestreo teórico, elaboración de memorandos, sensibilidad teórica y saturación teórica. Asimismo, se encontró diferencias significativas en el proceso de análisis de datos, las corrientes filosóficas de cada versión, la teoría generada, los datos recolectados como entrevistas, entre otros. En particular, el proceso de análisis en las cinco versiones tiene aspectos comunes, pero los procedimientos utilizados son diferentes. Finalmente, se elaboraron representaciones gráficas para facilitar la comprensión del análisis de datos. El artículo facilita a los investigadores, especialmente a los nuevos, reconocer cómo y cuándo encajar en los diversos aspectos utilizados para el análisis de datos, especialmente si los requisitos de la investigación obligan a mezclar o fusionar algunas perspectivas durante el proceso de análisis.Grounded Theory (TF) is a widely known and widely used research methodology in the social sciences. It has various versions (Glaserian Grounded Theory, Straussian, Dimensional, Constructivist and Situational Analysis) show differences that tend to generate some confusion in their study and use. It is the case with the data analysis process. To identify these differences, we carried out an intentional review of the literature published in the last 20 years in Spanish, Portuguese, and English. We did a systematic search in five scientific databases and Google Scholar Beta. We selected 72 texts, included books and articles. They were 31 of them written by the main referents of each version and, 41 were written by other authors who contribute to the understanding of the method. The analysis of these texts allowed us to identify common elements and significant differences. The results that we found reveal five common aspects between the versions: constant comparison, theoretical sampling, elaboration of memoranda, theoretical sensitivity, and theoretical saturation. Also, we found we find significant differences in the data analysis process, the philosophical currents of each version, the theory generated, the data collected as interviews, among others. In particular, the analysis process in the five versions has common aspects, but the procedures used are different. Finally, we elaborate graphical representations to facilitate understanding of data analysis. The article makes it easier for investigators, especially new ones, to recognize how and when to fit in the various aspects used for data analysis, especially if the research requirements force you to mix or merge some perspectives during the analysis process.

Anxieties and Coping among Filipino New Fathers with Postnatal Depression

Existing evidence suggests that postnatal depression is common in fathers of newborns among low- and middle-income countries because parents from this region experience socioeconomic difficulties. Common socioeconomic difficulties include educational attainment, employment status, and monthly income. Through the number of available participants, this study screened 50 new fathers coming from barangays of Cabanatuan City, Province of Nueva Ecija, Philippines. This study made use of the Becks Depression Inventory to carefully select new fathers without depression before childbirth. Remaining participants were administered Edinburgh Postnatal Depression Scale (EPDS) and Gotland Male Depression Scale (GMDS) 24–72 hours after the childbirth. From this, the researcher was left with seven new fathers who were invited for an in-depth interview. Using the role strain theory and depressive symptoms from the EPDS and GMDS, the researcher drafted a general idea of where to begin the interview. Structured questions were followed to meet the theoretical sensitivity and domains of the tools used (EPDS and GMDS). Qualitative analysis revealed FEAR among new fathers with Postnatal Depression coming from difficulties in financial responsibility, emotional responses, adaptability and role transition.

Numerical analysis of effective refractive index ultrasonic sensor based on Cantilever arm structure slot-based dual-micro-ring resonator

We propose a novel ultrasonic sensor structure composed of Cantilever arm structure slot dual-micro-ring resonators (DMRR). We present a theoretical analysis of transmission by using the coupled mode theory. The mode field distributions and sound pressure distributions of transmission spectrum are obtained from 3D simulations based on Comsol Multi-physics (COMSOL) method. Our ultrasonic sensor exhibits theoretical sensitivity as high as [Formula: see text], which is 22 times higher than that of the single slot-based micro-ring ultrasonic sensor. Our ultrasonic sensor offers higher sensitivity and a larger detection frequency range than conventional piezoelectric-based ultrasound transducer. The results show that the sensing characteristics of our system can be optimized through changing the position and the angle of sound field. Our ultrasonic sensor is with an area of [Formula: see text], the [Formula: see text]-factor can be approximately [Formula: see text] with radius of [Formula: see text]. We detect an angular range of [Formula: see text] to [Formula: see text] and a minimum distance of [Formula: see text]. Finally, we calculate the Cantilever arm structure slot DMRR array ultrasonic sensor’s optical performance. Our proposed design provides a promising candidate for a hydrophone.

Theoritical Sensitivity: Mengungkap Konsep dalam Penelitian Ilmiah Kajian Sastra

Penelitian ini membuktikan bahwa dalam sebuah penelitian ilmiah dibutuhkan sensitivitas teoritis (theoretical sensitivity). Dengan menggunakan argumentasi akademik yang telah dikemukakan oleh komunitas akademik lainnya, melalui grounded theory penelitian ini mengungkapkan bahwa teoritisasi data dilakukan secara induktif yaitu didasarkan pada temuan dan analisis pelbagai data observasi empirik di lapangan (grounded in data). Penelitian ini tidak sependapat dengan komunitas akademik Chicago School of Sociology yang menggunakan deductive qualitative analysis dalam proses theory-building. Penelitian ini mendukung perspektif theoretical sensitivity Barney G. Glaser (Theoretical Sensitivity: Advances in the Methodology of Grounded Theory: 1978) dan Barney G. Glaser & Anselm L. Strauss (The Discovery of Grounded Theory: 1967 & Awareness of Dying: 1965) yang menyatakan bahwa dalam sebuah penelitian, theoretical sensitivity memegang peranan kunci tehadap pelbagai data di lapangan/fenomena masalah yang diteliti dalam kerangka teoritis untuk dilakukan build theory. Berdasarkan asumsi teoritik Glaser dan Strauss tersebut, theoretical sensitivity sangat mungkin untuk digunakan dalam penelitian ilmiah seperti kajian sastra. Penelitian ini mengeksplorasi implementasi theoritical sensitivity dalam kajian novel Saman karya Ayu Utami dan Perempuan Berkalung Sorban karya Abidah el Khaliqy dengan hasil penelitian berupa lahirnya konsep genre sastra wangi dan sastra feminis Islam.[The paper talks a scientific study that requires theoretical sensitivity. With academic arguments that puts forward by the academic community, grounded theory in the research reveals inductive data theoritization based on findings and analysis of various empirical observational data in the field research. The article does not agree with the Chicago School of Sociology Scholar, which uses deductive qualitative analysis in the theory-building process. The study supports the theoretical sensitivity perspective of Barney G. Glaser and Anselm L. Strauss. Both of these scholar stated that a study on theoretical sensitivity has a key role in various data in the field or problem phenomena being studied in the theoretical framework for a build theory. Based on the theoretical assumptions of Barney G. Glaser and Anselm L. Strauss, theoretical sensitivity is very likely to be used in scientific research such as literature studies. This paper explores the implementation of theoretical sensitivity in the study of the novel “Saman” by Ayu Utami and “Perempuan Berkalung Sorban” by Abidah el Khaliqy. This study gives the new Persepective of fragrant literary genres and Islamic feminist literature.]

Magnetoencephalography Using Optically Pumped Magnetometers

This chapter explores one of the most promising alternatives to superconducting quantum-interference devices (SQUIDs) as the fundamental building block of magnetoencephalography (MEG) systems: optically pumped magnetometers (OPMs). OPMs exploit the spin properties of alkali atoms, using a technique known as optical pumping to prepare a gas of atoms such that its opacity to laser light becomes a sensitive marker of a local magnetic field. The theoretical sensitivity of the OPM surpasses even that of the SQUID, and OPMs operate without cryogenic cooling. Moreover, they are small and lightweight, offering the potential for development of a flexible MEG system, which could be adapted to any head shape and in principle could become wearable such that subjects could move freely during data acquisition. Because the external surface of an OPM is at approximately body temperature, the sensing volume can be placed close to the head, increasing the signal strength. When operated in the spin exchange relaxation-free (SERF) regime, their bandwidth is suited to MEG acquisition, and their dynamic range, although limited, is acceptable.

Cirrus Cloud Identification from Airborne Far-Infrared and Mid-Infrared Spectra

Airborne interferometric data, obtained from the Cirrus Coupled Cloud-Radiation Experiment (CIRCCREX) and from the PiknMix-F field campaign, are used to test the ability of a machine learning cloud identification and classification algorithm (CIC). Data comprise a set of spectral radiances measured by the Tropospheric Airborne Fourier Transform Spectrometer (TAFTS) and the Airborne Research Interferometer Evaluation System (ARIES). Co-located measurements of the two sensors allow observations of the upwelling radiance for clear and cloudy conditions across the far- and mid-infrared part of the spectrum. Theoretical sensitivity studies show that the performance of the CIC algorithm improves with cloud altitude. These tests also suggest that, for conditions encompassing those sampled by the flight campaigns, the additional information contained within the far-infrared improves the algorithm’s performance compared to using mid-infrared data only. When the CIC is applied to the airborne radiance measurements, the classification performance of the algorithm is very high. However, in this case, the limited temporal and spatial variability in the measured spectra results in a less obvious advantage being apparent when using both mid- and far-infrared radiances compared to using mid-infrared information only. These results suggest that the CIC algorithm will be a useful addition to existing cloud classification tools but that further analyses of nadir radiance observations spanning the infrared and sampling a wider range of atmospheric and cloud conditions are required to fully probe its capabilities. This will be realised with the launch of the Far-infrared Outgoing Radiation Understanding and Monitoring (FORUM) mission, ESA’s 9th Earth Explorer.

Traumatic pneumothorax mapping using computed tomography to assess optimal area to scan with POCUS

ABSTRACTIntroductionIt is traditionally taught that the location to place an ultrasound probe to detect a pneumothorax with point-of-care ultrasound (POCUS) is the anterior chest, given the theory that air will collect at the least dependent area in the supine patient. There is a wide variety of scanning protocols with varying accuracy and completeness. We sought to assess the optimal area to scan for diagnosing pneumothorax by mapping the location of traumatic pneumothorax on computed tomography (CT).MethodsPatients were selected after a retrospective cohort of adult patients who presented to a regional trauma center with a pneumothorax diagnosed on CT. Data were extracted using a standardized data collection tool, and 20% of charts were reviewed by two reviewers. Predefined zones were used to map the areas of pneumothoraces. Theoretical sensitivity and 95% confidence intervals (CIs) are reported.ResultsA total of 203 traumatic pneumothoraces were reviewed from 2006 to 2016. The majority of the pneumothoraces were found in an area defined by the para-sternal border and the mid-clavicular line from the inferior aspect of the clavicle to the physiologic lung point (liver on the right, heart on the left). The theoretical sensitivity for pneumothorax of scanning this area was 91.6% (95% CI, 86.9–95%).ConclusionThis study suggests any POCUS scanning protocol for traumatic pneumothorax should include an area from the inferior border of the clavicle at the parasternal border down to the liver or cardiac lung points and then the mid clavicular line down to the liver or cardiac lung points.