Miracle-dz/UniFAR-FTUs huggingface dataset:
CVD-associated SNPs with regulatory potential drive pathologic non-coding RNA expression

Background Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) appearing in non-coding genomic regions in CVDs. The SNPs may alter gene expression by modifying transcription factor (TF) binding sites and lead to functional consequences in cardiovascular traits or diseases. To understand the underlying molecular mechanisms, it is crucial to identify which variations are involved and how they affect TF binding. Methods The SNEEP (SNP exploration and analysis using epigenomics data) pipeline was used to identify regulatory SNPs, which alter the binding behavior of TFs and link GWAS SNPs to their potential target genes for six CVDs. The human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs), monoculture cardiac organoids (MCOs) and self-organized cardiac organoids (SCOs) were used in the study. Gene expression, cardiomyocyte size and cardiac contractility were assessed. Results By using our integrative computational pipeline, we identified 1905 regulatory SNPs in CVD GWAS data. These were associated with hundreds of genes, half of them non-coding RNAs (ncRNAs), suggesting novel CVD genes. We experimentally tested 40 CVD-associated non-coding RNAs, among them RP11-98F14.11, RPL23AP92, IGBP1P1, and CTD-2383I20.1, which were upregulated in hiPSC-CMs, MCOs and SCOs under hypoxic conditions. Further experiments showed that IGBP1P1 depletion rescued expression of hypertrophic marker genes, reduced hypoxia-induced cardiomyocyte size and improved hypoxia-reduced cardiac contractility in hiPSC-CMs and MCOs. Conclusions IGBP1P1 is a novel ncRNA with key regulatory functions in modulating cardiomyocyte size and cardiac function in our disease models. Our data suggest ncRNA IGBP1P1 as a potential therapeutic target to improve cardiac function in CVDs.
Computational modelling of 1D blood flow with variable mechanical properties and its application to the simulation of wave propagation in the human arterial system

In this paper we numerically investigate a one‐dimensional model of blood flow in human arteries using both a discontinuous Galerkin and a Taylor–Galerkin formulation. The derivation of the model and the numerical schemes are detailed and applied to two model numerical experiments. We first study the effect of an intervention, such the implantation of a vascular prosthesis (e.g. a stent), which leads to an abrupt variation of the mechanical characteristics of an artery. We then discuss the simulation of the propagation of pressure and velocity waveforms in the human arterial tree using a simplified model consisting of the 55 main arteries. Copyright © 2003 John Wiley & Sons, Ltd.
Alpaca single B cell interrogation and heavy-chain-only antibody discovery on an optofluidic platform

In vivo discovery approaches for single domain antibodies such as VHH have been limited by the lack of methodologies available for camelid B cell interrogation. Here, we report a novel application of the Berkeley Lights Beacon® optofluidic platform to the discovery of heavy-chain-only antibodies by screening single B cells from alpacas immunized with two different targets. Custom methods for alpaca B cell enrichment, culture, on-Beacon IgG2/3 detection, and sequencing were developed and used to discover target-specific VHH candidates from an alpaca immunized with either human prostate specific membrane antigen (PSMA) or a second blinded target, in a proof-of-concept study. PSMA-specific VHH hits discovered on the Beacon were recombinantly expressed as VHH-Fc, purified, and characterized using label-free techniques. All but one VHH-Fc bound PSMA with a single-digit nanomolar affinity, and four candidates were successfully humanized in silico using a rapid bulk humanization approach. In addition, next-generation repertoire sequencing was performed at longitudinal timepoints after immunization, uncovering additional variants within the clonal lineages of the validated hits discovered on the Beacon platform. The establishment of this single B cell VHH discovery workflow extends the powerful Beacon technology to enable rapid discovery of VHH directly from natural camelid immune repertoires.
Continuous Quantum Measurement of Cold Alkali-Atom Spins

The field of quantum metrology concerns the physical measurement of sensors with a precision comparable to fundamental limits set by quantum mechanics. It is possible to outperform naive interpretations of these limits by using entangled states of the sensor system. One example is that of a spin-squeezed state, in which the uncertainty of one variable is decreased at the expense of another while still obeying Heisenberg's uncertainty principle, improving rotation sensitivity along a chosen axis. These states are potentially useful in devices including atomic clocks, inertial sensors, and magnetometers. Any model of a quantum metrology device must respect the fact that physical measurements are not passive, as imagined classically, but necessarily invasive. Far from being a negative feature, well-understood quantum measurement can conditionally drive a system into desirable entangled states, including spin-squeezed states. Furthermore, the fundamental randomness of this process can, in principle, be removed with real-time feedback control, motivating an adaptation of classical feedback concepts to the quantum realm. In this thesis, I describe these ideas in the context of one experimental example. A laser-cooled cloud of cesium spins is polarized along one axis via optical pumping and, subsequently, a linearly polarized far-off resonant probe beam traverses the sample. Due to the interaction Hamiltonian, the optical polarization rotates by an amount nominally proportional to one spin component of the collective spin state, enacting a weak, continuous, nondemolition measurement of that collective variable. This optical Faraday rotation is then measured with a polarimeter and the inherently noisy result used to condition the collective atomic state via a quantum filter, or stochastic master equation. Ideally, this process is capable of producing spin-squeezed states via the measurement itself. The details of this measurement are investigated in depth, including a derivation of the nonideal polarizability Hamiltonian, an analysis of the projection process with control, and a derivation of the magnetometry sensitivity. Experimentally, we demonstrate continuous measurement of the collective spin state with a large single-shot signal-to-noise ratio and verify many predictions of the model. Finally, we describe attempts to observe the atomic projection noise, which would infer the preparation of spin-squeezed states.
Modeling and imaging of attenuation in biological media

La these est consacree a l'etude des problemes inverses lies a la localisation des sources acoustiques et elastiques dans des milieux attenues a partir de mesures a la frontiere, et de leurs applications a l'imagerie medicale. Nous presentons des algorithmes efficaces et stables pour compenser les effets d'attenuation sur la resolution d'image. Nous developpons des algorithmes bases sur la transformee de Radon pour recuperer la distribution de pression initiale dans les milieux attenues, avec et sans conditions aux limites imposees. Nous appliquons le theoreme de phase stationnaire a un operateur d'attenuation mal conditionne pour corriger l'effet d'attenuation et nous utilisons des methodes de regularisation TV-Tikhonov pour traiter les problemes de mesure partielle. Nous revisitons les methodes de retournement temporel pour les milieux ideaux (sans perte d'energie) et nous les etendons aux milieux attenuees. Comme des ondes attenuees ne sont pas reversibles en temps, nous utilisons la strategie de back-propagation des approximations regulieres des ondes adjointes attenuees pour reconstituer les sources de facon stable avec une correction d'attenuation d'ordre 1. Pour les milieux acoustiques, nous presentons une strategie alternative basee sur un pre-traitement des donnees pour les corrections d'ordre superieur. Aux milieux elastiques, les donnees consistent en des ondes de cisaillement et des pressions couplees. Nous proposons une approche originale basee sur la decomposition de Helmholtz avec des poids. En outre, nous introduisons des algorithmes efficaces d'imagerie avec des poids pour localiser les sources de bruit acoustique par des techniques de cross-correlation et en utilisant une version regularisee de back-propagateurs pour corriger l'attenuation. Nous avons egalement localise les sources de bruit spatialement correlees, et nous estimons la matrice de correlation entre eux. Afin d'etendre les algorithmes de detection d'anomalies elastiques aux milieux visco-elastiques, nous derivons une expression de la fonction de Green visco-elastique isotrope. Ensuite, nous proposons une technique de correction d'attenuation pour un milieu quasi-incompressible et prouver que l'on peut acceder a la fonction de Green ideale (non visqueux) a partir de la fonction de Green visco-elastique en inversant un operateur differentiel ordinaire. Enfin, nous fournissons quelques fonctions de Green visco-elastiques anisotropes, dans le but d'etendre nos resultats aux milieux anisotropes
The diffuse clouds towards Cyg OB2 No. 5 and No. 12

We have investigated, in the 13CO(1-0) line, the region between the stars Cyg OB2 No. 5 and No, 12. The integrated intensity contour map reveals the existence of a condensation at 12 km s-1 (core C), north-west of Cyg OB2 No. 5, with a core-halo structure. The morphology and the derived physical parameters make it quite similar to core A, previously discovered towards Cyg OB2 No. 12. A second condensation at 7 km s -1, near Cyg OB2 No. 12, has been mapped in the same line (1-0) of 13CO. A summary of different observations, in all spectral regions, towards Cyg OB2 No. 5 and No. 12 is presented to provide the material for a further comprehensive discussion of this intricate and still intriguing region.
Iterative learning control with forgetting factor for linear distributed parameter systems with uncertainty

Iterative learning control is an intelligent control algorithm which imitates human learning process. Based on this concept, this paper discussed iterative learning control problem for a class parabolic linear distributed parameter systems with uncertainty coefficients. Iterative learning control algorithm with forgetting factor is proposed and the conditions for convergence of algorithm are established. Combining the matrix theory with the basic theory of distributed parameter systems gives rigorous convergence proof of the algorithm. Finally, by using the forward difference scheme of partial differential equation to solve the problems, the simulation results are presented to illustrate the feasibility of the algorithm.
Becoming Sustainable Together: ESG Data Commons for Fintech Startups

Environmental, social, and corporate governance (ESG) reporting has become an important instrument for the sustainable transition of the next generation of business-startup. Nonetheless, poor ESG data quality impedes effective reporting, especially in domains such as Fintech where top-down ESG metrics may overlook pertinent material issues. This action research study applies a design probe in the form of the notion of an ESG data commons to explore possible strategies to improve ESG data quality in Fintech startup. By reporting on the initial results of an ongoing study of a Danish Fintech startup cluster, we develop a practice-based approach that highlights the changing processes, teleoaffective structures, and sociomaterial dynamics of ESG data commons. We contribute to information systems (IS) research in two areas. First, we contribute to the call for a data-driven approach to ESG reporting. Second, the study extends the IS design literature by applying data commons as a design probe.
Optical sorting and manipulation of microscopic particles

Over the last few decades, the use of light to control and manipulate microscopic particles has become widespread. These methods are enabling new areas of research to flourish across the physical and biological sciences. This thesis describes investigations into both optical trapping and the closely related field of optical sorting. It documents the development of a variety of new techniques. The thesis begins with a short review of optical trapping and existing methods for sorting mixtures of microscopic particles. The first half of this chapter highlights some of the reasons behind optical trapping’s rapid growth in popularity. By reviewing an array of methods for sorting particles and discussing the relative merits of each, the case for optical sorting is established. The second chapter describes research into using a spatial light modulator to create three-dimensional optically trapped colloidal structures using the time-sharing technique. Limiting factors inherent in the technology are discussed in detail. The third chapter reviews a sophisticated particle-tracking software package that has proved to be a considerable success. It was developed explicitly with colloidal microscopy in mind and experimental plots produced by the software are used throughout the thesis. Experimental studies have been performed into the behaviour of microscopic particles moving under the influence of two classes of propagation-invariant beams: Mathieu beams and Bessel beams. The Bessel beam studies have been complimented by a theoretical model and have led ultimately to a new method for the static optical sorting of both solid particles and biological cells, with particular emphasis on human blood. The fifth and final chapter describes how re-configurable optical devices can be implemented to spatially separate different colloidal species. A new method for creating arbitrary
Forming short-period earth-like planets via a collision-merger scenario

Abstract We present a new formation mechanism to produce short-period Earth-like planets in the late stage of planet formation, through a collision-merger scenario. In this scenario, a planetary embryo is directly thrown into a close-in orbit after a collision with another embryo, and then the larger merged body is seized by the central star as a hot Earth-like planet.
Low‐temperature photoluminescence studies of chemical‐vapor‐deposition‐grown 3C‐SiC on Si

26 cubic SiC (3C‐Sic) films grown on (100) Si by way of chemical vapor deposition (CVD) with SiC film thicknesses ranging from 600 A to 25 μm have been studied by photoluminescence at 2 K. The ‘‘defect‐related’’ W band near 2.15 eV appears in very thin‐film samples. The G band near 1.90–1.92 eV and its phonon side bands G 1 and G 2 are believed to be related to dislocations and extended defects. The ratio ρ of the intensities of the G band and the strongest nitrogen‐bound exciton (N‐BE) TO(X) line may be used as a figure of merit for crystalline perfection in CVD 3C‐SiC films. General formulas for the band‐gap shift due to an axial stress, including three special cases—hydrostatic pressure and uniaxial and biaxial stress—are derived and applied to the CVD 3C‐SiC/Si system. An experimental relationship of stress in these epitaxial films of 3C‐SiC as a function of depth is obtained. It is shown that a 1–3 μm transition layer greatly reduces the interface misfit strain. For films thicker than 3 μm the film stress decreases slightly with increase of film thickness. The effects of biaxial stress on the relative intensities of N‐BE lines are experimentally studied. It is reported that biaxial stress in the SiC/Si system depresses the intensity of the no‐phonon line as well as the TA, LA, and LO phonon transitions of the N‐BE spectrum.
Team decision theory and information structures in optimal control problems--Part II

General dynamic team decision problems with linear information structures and quadratic payoff functions are studied. The primitive random variables are jointly Gaussian. No constraints on the information structures are imposed except causality. Equivalence relations in information and in control functions among different systems are developed. These equivalence relations aid in the solving of many general problems by relating their solutions to those of the systems with "perfect memory. " The latter can be obtained by the method derived in Part I. A condition is found which enables each decision maker to infer the information available to his precedents, while at the same time the controls which will affect the information assessed can be proven optimal. When this condition fails, upper and lower bounds of the payoff function can still be obtained systematically, and suboptimal controls can be obtained.
NUMERICAL SIMULATION OF PARTICLE BREAKUP/COALESCENCE PROCESSES IN SHOCK WAVES

The numerical simulations to assess particle breakup/coalescence processes while passing through oblique shocks are performed. Gas-particle two phase flow are addressed by one-way coupled population balance equation (PBE) using the direct quadrature method of moments (DQMOM) for heterogeneous particles. Air-water droplet system is solved within the flow field over the 2-d wedge-shaped bodies (10 and 15 deg). The current study focuses on quantifying the effect of particle phase characteristics (0.05 µm < D43 < 0.45 µm, 0.05 < mf < 0.45) before the oblique shock on the particle size after the shock. The effect of shock strength by changing inflow Mach number (1.5 < M1 < 2.5) is assessed too. It is observed that the collision processes occurs when inflow particle D43 is 0.05 µm in all currently considered shock waves. Collision-breakup interface within the flow field behind the shock wave is identified too.
CYCLOTRON-RESONANCE MASS OF TWO-DIMENSIONAL ELECTRONS IN GAN/ALXGA1-XN HETEROSTRUCTURES

The electron cyclotron-resonance (CR) mass of quasi-two-dimensional electrons in GaN/AlxGa1-xN heterostructures is studied theoretically. The correction to the CR mass due to electron-phonon interaction is investigated, taking into account band nonparabolicity, the occupation effect, and the screening of the electron-phonon coupling. The dependence of the CR mass on the electron density and on the magnetic field strength is displayed in detail, and the calculated CR mass agrees well with a recent experiment. We found that the effective electron-phonon coupling strength in GaN heterostructures is reduced below the bulk value.
The EPED pedestal model and edge localized mode-suppressed regimes: Studies of quiescent H-mode and development of a model for edge localized mode suppression via resonant magnetic perturbations

The EPED model predicts the H-mode pedestal height and width based upon two fundamental and calculable constraints: (1) onset of non-local peeling-ballooning modes at low to intermediate mode number, (2) onset of nearly local kinetic ballooning modes at high mode number. We present detailed tests of the EPED model in discharges with edge localized modes (ELMs), employing new high resolution measurements, and finding good quantitative agreement across a range of parameters. The EPED model is then applied for the first time to quiescent H-mode (QH), finding a similar level of agreement between predicted and observed pedestal height and width, and suggesting that the model can be used to predict the critical density for QH-mode operation. Finally, the model is applied toward understanding the suppression of ELMs with 3D resonant magnetic perturbations (RMP). Combining EPED with plasma response physics, a new working model for RMP ELM suppression is developed. We propose that ELMs are suppressed when a “wall”.
Modeling Symmetry, Asymmetry, and Change in Ordered Scales with Midpoints Using Adjacent Category Logit Models for Discrete Data

Likert scales and bipolar adjective scales are often used to measure attitudes and opinions. To model the dependence of the scale on covariates, investigators typically (1) assign interval scores to scale categories, using these in regression analyses; (2) collapse categories to compare responses above and below a middle category; or (3) estimate a model for the cumulative distribution, for example, a proportional odds model. Problems with Approaches 1 and 2 are obvious. However, Approach 3 is not easily used to address the concerns of researchers who work with these scales because cumulative probabilities are employed. Thus, this article constructs adjacent category logit models for analyzing such scales. The models, which incorporate discrete covariates, are linear in the logits, hence equivalent to log-linear models. The Appendix shows how to fit the models using standard software for estimating log-linear models. To illustrate, the author models the distribution of political views in the 1977 General Social Survey, by sex and education, as well as a 20-year series on sex role attitudes, using new models for trends.
Finite-difference methods for the solution of special eighth-order boundary-value problems

A family of finite-difference methods is developed for the solution of special nonlinear eighth-order boundary-value problems. Methods with second-, fourth-, sixth- and eighth-order covergence are contained in the family. The problem is also solved by writing the eighth-order differential equation as a system of four second-order differential equations. A second-order method is then used to obtain the solution.
THE MOON AS PHOTOGRAPHED BY LIGHT OF DIFFERENT COLORS

The photographs of the Moon, shown in Plate II, are illustrative of a number taken in light of different colors during the month of September, 1926, by Miss Dorothy Applegate and myself. The observations were begun on September 14, when the age of the Moon was seven days, and were continued at intervals of a day or two until the 29th, when the lunar age was 22 days. They therefore cover the middle period of the lunation, between waxing and waning crescents. The photographs were made as part of a general color survey of the brighter planets and the Moon, which has been in progress at the Lick Observatory for a number of years. The colors used were ultra-violet, violet, green, orange, red, and extreme red light. The colors were isolated by the familiar methods of filter photography, the application of which to the work in progress here is described in an earlier pàper. It will perhaps meet the requirements of this note to give the wave-lengths for the colors used in taking the pictures shown in the plate ; these are, approximately, 3600 A for ultra-violet, and 7600 A for extreme red. Photographs of the Moon by light of distinct spectral regions have been taken by a number of previous observers and some of the more obvious alterations with color have already been described. R. W. Wood seems to have been the first to undertake observations of this kind. He remarked especially a dark region near Aristarchus on photographs taken by ultra-violet light, that appeared only in greatly reduced intensity on those taken by light of longer wave-lengths. Wood was followed within a short time by Miethe and Seegert who, while they worked within a 1 These Publications, 36, 239, 1924. * M.N. , 70, 226, 1910; Pop. Astron. 18, 67, 1910. *A.N. , 188, 10, 239, 371, 1911.