Miracle-dz/UniFAR-FTUs huggingface dataset:
Editorial: Population genomic architecture: Conserved polymorphic sequences (CPSs), not linkage disequilibrium

The human extended major histocompatibility complex (MHC) region, ~7.7 megabases (Mb) in the middle of the short arm of chromosome 6, is one of the most gene-dense and polymorphic regions of the human genome (Horton et al., 2004; Shiina et al., 2009; Kulski et al., 2022). MHC haplotype characterization originated largely from genetic studies in the 1960s–1990s by Ceppellini et al. (1967) and the research groups of Chester Alper (Alper et al., 1983; Awdeh et al., 1983; Yunis et al., 2003) and Roger Dawkins (Degli-Esposti et al., 1992; Degli-Esposti et al., 1995; Dawkins et al., 1999). In this Research Topic, we introduced the term “conserved polymorphic sequences” (CPSs) to encompass both Mb-length haplotypes, labeled currently either as conserved extended haplotypes or ancestral haplotypes, and their haplotypic fragments (“fixed” or “frozen” blocks). The relevance of CPSs includes: 1) an improved understanding of MHC genomic architecture-laying the foundation for other regions; 2) their use in testing genetic models for both meiotic recombination and trait association; and 3) providing insight into population genetics and evolution. Linkage disequilibrium (LD) and other expectation-maximization (EM) analyses of unrelated genotypes fail to detect most of the larger CPS variants but often detect their small (5–200 kb) blocks (Walsh et al., 2003; Alper et al., 2006). The technical explanation(s) for these differences remain unresolved. The Research Topic includes original work, a minireview, a commentary, and a mechanistic model for CPSs at high population frequency. The CPS mechanistic model may apply to any genomic region or vertebrate species (Dawkins and Lloyd). Alper reviewed CPS conceptual development. The identification of high population frequency Mb-length MHC haplotypes resulted from observed shorter (140 kb) MHC-encoded complement gene haplotypes (“complotypes”; Alper et al., 1983) in strong LD with HLA class I and class II haplotypic variants. Later publications demonstrated both the intervening genetic “fixity” (essentially fixed DNA sequence) among each of those long-range population haplotypes and their extension from the telomeric end of the HLA class I region to the centromeric end of HLA class II (e.g., OPEN ACCESS
Assessing MR-compatibility of somatosensory stimulation devices: A systematic review on testing methodologies

Functional magnetic resonance imaging (fMRI) has been extensively used as a tool to map the brain processes related to somatosensory stimulation. This mapping includes the localization of task-related brain activation and the characterization of brain activity dynamics and neural circuitries related to the processing of somatosensory information. However, the magnetic resonance (MR) environment presents unique challenges regarding participant and equipment safety and compatibility. This study aims to systematically review and analyze the state-of-the-art methodologies to assess the safety and compatibility of somatosensory stimulation devices in the MR environment. A literature search, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines, was performed in PubMed, Scopus, and Web of Science to find original research on the development and testing of devices for somatosensory stimulation in the MR environment. Nineteen records that complied with the inclusion and eligibility criteria were considered. The findings are discussed in the context of the existing international standards available for the safety and compatibility assessment of devices intended to be used in the MR environment. In sum, the results provided evidence for a lack of uniformity in the applied testing methodologies, as well as an in-depth presentation of the testing methodologies and results. Lastly, we suggest an assessment methodology (safety, compatibility, performance, and user acceptability) that can be applied to devices intended to be used in the MR environment. Systematic review registration https://www.crd. york.ac. uk/prospero/, identifier CRD42021257838.
Genome-wide analysis of Hsp40 and Hsp70 gene family in four cotton species provides insights into their involvement in response to Verticillium dahliae and abiotic stress

Introduction: Cotton is an important economic crop to provide natural fibers as raw materials to textile industry, and is significantly affected by biotic and abiotic stress during the whole growth stage, in which Verticillium wilt (VW) caused by Verticillium dahliae is one of the most destructive disease to lead to a significant yield reduction. Heat shock proteins (Hsps) are important molecular chaperones, and play crucial roles in plant growth, development, resistance to biotic and abiotic stress. Hsp40 and Hsp70 are two key Hsps in cell chaperone network, however, the function and regulatory mechanism of Hsp40 and Hsp70 members in VW resistance and abiotic stress in cotton are largely unknown. Methods and Results: Herein, a systematic and comprehensive analysis of Hsp40s and Hsp70s in four cotton species of Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense were performed. A total of 291 Hsp40s and 171 Hsp70s identified in four Gossypium species. Sequence analysis revealed that all Hsp40 proteins contained J domain that provides the binding sites to Hsp70. Protein-protein interaction prediction analysis displayed that GhHsp40-55 might interact with GhHsp70-2 and GhHsp70-13, suggesting their potential function as protein complex. Promoter cis-acting element analysis demonstrated that multiple cis-elements related to disease and stress response consists in GhHsp40 and GhHsp70 promoters. Further expression analysis showed that eight GhHsp40s (Hsp40-2,4,8,11,20,23,53,55) and seven GhHsp70s (Hsp70-2,3,6,8,13,19,22) were up-regulated after V. dahliae infection. In addition, five GhHsp40s (Hsp40-2,8,11,53,55) and four GhHsp70s (Hsp70-3,6,8,13) were up-regulated after salt treatment, six GhHsp40s (Hsp40-4,11,20,23) and three GhHsp70s (Hsp70-2,8,19) were up-regulated after drought treatment, four GhHsp40s (Hsp40-2,11,20,23) and four GhHsp70s (Hsp70-3,6,19,22) were up-regulated after temperature treatment, suggesting these Hsps have possible important function in the process of abiotic stress response. Discussion: Our results lay a foundation for understanding the function of Hsp40 and Hsp70 in the resistance against V. dahliae and abiotic stress, and elucidating the regulatory mechanism of the protein complex, evolution and molecular mechanism under stress.
Addressing blood-brain-tumor-barrier heterogeneity in pediatric brain tumors with innovative preclinical models

Brain tumors represent the leading cause of disease-related mortality and morbidity in children, with effective treatments urgently required. One factor limiting the effectiveness of systemic therapy is the blood-brain-barrier (BBB), which limits the brain penetration of many anticancer drugs. BBB integrity is often compromised in tumors, referred to as the blood-brain-tumor-barrier (BBTB), and the impact of a compromised BBTB on the therapeutic sensitivity of brain tumors has been clearly shown for a few selected agents. However, the heterogeneity of barrier alteration observed within a single tumor and across distinct pediatric tumor types represents an additional challenge. Herein, we discuss what is known regarding the heterogeneity of tumor-associated vasculature in pediatric brain tumors. We discuss innovative and complementary preclinical model systems that will facilitate real-time functional analyses of BBTB for all pediatric brain tumor types. We believe a broader use of these preclinical models will enable us to develop a greater understanding of the processes underlying tumor-associated vasculature formation and ultimately more efficacious treatment options.
Using a deep-learning approach to infer and forecast the Indonesian Throughflow transport from sea surface height

The Indonesian Throughflow (ITF) connects the tropical Pacific and Indian Oceans and is critical to the regional and global climate systems. Previous research indicates that the Indo-Pacific pressure gradient is a major driver of the ITF, implying the possibility of forecasting ITF transport by the sea surface height (SSH) of the Indo-Pacific Ocean. Here we used a deep-learning approach with the convolutional neural network (CNN) model to reproduce ITF transport. The CNN model was trained with a random selection of the Coupled Model Intercomparison Project Phase 6 (CMIP6) simulations and verified with residual components of the CMIP6 simulations. A test of the training results showed that the CNN model with SSH is able to reproduce approximately 90% of the total variance of ITF transport. The CNN model with CMIP6 was then transformed to the Simple Ocean Data Assimilation (SODA) dataset and this transformed model reproduced approximately 80% of the total variance of ITF transport in the SODA. A time series of ITF transport, verified by Monitoring the ITF (MITF) and International Nusantara Stratification and Transport (INSTANT) measurements of ITF, was then produced by the model using satellite observations from 1993 to 2021. We discovered that the CNN model can make a valid prediction with a lead time of 7 months, implying that the ITF transport can be predicted using the deep-learning approach with SSH data.
Smoothing with Mixed Model Software

Smoothing methods that use basis functions with penalization can be formulated as fits in a mixed model framework. One of the major benefits is that software for mixed model analysis can be used for smoothing. We illustrate this for several smoothing models such as additive and varying coefficient models for both S-PLUS and SAS software. Code for each of the illustrations is available on the Internet.
Magnetoelastic coupling in DyMn2O5 via infrared spectroscopy

as a function of temperature and magnetic ﬁeld inorder to elucidate the magnetic ordering-induced lattice distortions. Spin-lattice coupling in this geometricallyfrustrated multiferroic is evidenced by small frequency shifts of several phonon modes at various magneticordering temperatures, vibrational frequency shifts between 60 and 65 K from which we extract large couplingconstants, and magnetic-ﬁeld dependence of numerous phonons. We analyze these results in terms of locallattice distortions and discuss the consequences for the ferroelectric polarization and magnetodielectric effect.DOI: 10.1103/PhysRevB.78. 064307 PACS number s : 75.47. Lx, 75.80. q, 78.20. Ls, 78.30. j
Sampling Errors of Variance Components in Small Sample Multifacet Generalizability Studies

The paper describes the small sample stability of least square estimates of variance components within the context of generalizability theory. Monte Carlo methods are used to generate data conforming to some selected multifacet generalizability designs to illustrate the sampling behavior of variance component estimates. Based on the findings, recommendations are made concerning the design of efficient small sample generalizability studies.
Correction for Nonindependence of Sample Observations in ANOVA "F" Tests

Abstract This article derived a modified F test that includes a correction for nonindependence of between-groups and within-groups sample values in ANOVA designs. A computer-simulation study induced correlations between and within treatment groups and examined their influence on the probability of Type I and Type II errors for normal and non-normal distributions. Nonindependence severely altered the usual F tests in one-way ANOVA for all distributions. Between-groups correlations, which can result from violations of random assignment, depressed the probability of Type I errors far below the nominal significance level and markedly increased the probability of Type II errors. Within-groups correlations, which can result from violations of random sampling, had the reverse effect. The modified F test restored these probabilities to their previous values and was more powerful than conventional within-subjects ANOVA. Non-normality and nonindependence were additive. An ordinary F test performed on the ranks of s.
Nonparametric Two-Sample Tests of Longitudinal Data with Termination Events

In longitudinal data, observations of response variables occur at fixed or random time points, and can be stopped by a termination event. When comparing longitudinal data for two groups, such irregular observation behavior must be considered to yield suitable results. In this article, we propose the use of nonparametric tests based on the difference between weighted cumulative mean functions for comparing two mean functions with an adjustment for difference in the timing of termination events. We also derive the asymptotic null distributions of the test statistics and examine their small sample properties through simulations. We apply our method to data from a study of liver cirrhosis.
Optical Characterization in Microelectronics Manufacturing

To successfully construct semiconductor devices, the semiconductor industry must measure fundamental material parameters, especially when developing new materials; measure the quality of the material as it is grown; accurately determine the details of thin films, quantum wells, and other microstructures that control or affect device performance; and measure properties of the devices themselves. Properties that need to be determined, therefore, include basic band structure and transport parameters, such as energy gap values and carrier scattering times; the presence and concentration of impurities and defects; alloy parameters; layer thicknesses; the distribution of materials in complex structures; and many others. This process of determining a wide range of material, structural, and device parameters is called characterization. The semiconductor industry uses many characterization methods which draw on electrical, chemical, and other approaches. Among these, optical characterization techniques, defined as those using electromagnetic radiation from the ultraviolet to the far infrared, stand out because they arc nondestructive and require minimal sample preparation since no contacts arc needed. These features arc of great importance for production use or to examine finished devices. Another benefit is that, unlike electrical methods which require fixed contacts, optical techniques can give two- or three-dimensional maps of properties over the extent of a semiconductor wafer. The six techniques described in this paper (cllipsometry, infrared spectroscopy, microscopy, modulation spectroscopy, photolumincscence, and Raman scattering) were chosen because they are currently or potentially widely used in the industry; they measure a broad array of semiconductor parameters; and they operate in different regions of the electromagnetic spectrum. The discussion of each technique indicates the basic semiconductor quantities measured, gives the scientific basis of the technique, and indicates how the measurement is made. Illustrative examples from the literature are discussed in detail, showing applications to important semiconductor materials. More information can be obtained from the detailed list of references included.
Statistical structure of speech sound classes is congruent with cochlear nucleus response properties

Natural sounds possess considerable statistical structure. Lewicki (2002, Nature Neuroscience, 5(4):356-363) used independent components analysis (ICA) to reveal the statistical structure of environmental sounds, animal vocalizations, and human speech. Each sound class exhibited distinct statistical properties, but filters that optimally encoded speech closely resembled response properties in the mammalian auditory nerve. This and other analyses of statistical properties of speech examine only global structure without considering systematic variability in different speech sound classes, while acoustic/phonetic analyses of these classes are agnostic to their statistical structure. Here, statistical structure was investigated in principled subdivisions of speech: consonants organized by manner of articulation, and vowels organized by vocal tract configuration. Analyses reveal systematic differences for local statistical structure in speech: statistically optimal filters in ICA were highly diverse for differ.
Spin-wave lineshape in two-dimensional K2CuF4: neutron experiments and theory

The authors interpret the spin-wave lineshape in the two-dimensional ferromagnet K2CuF4 by a theory developed for small wavelengths, as is relevant for inelastic neutron scattering, applicable for temperatures both above and below the Curie temperature. The agreement between theory and experimental results is rather good. However, at high temperatures, when the spin-wave lineshape is very broad, the present theory, which is available for energies near the spin-wave energy omega q, gives only qualitative results.
The X-ray surface brightness distribution and spectral properties of six early-type galaxies

Detailed analysis is presented of the Einstein X-ray observations of six early-type galaxies. The results show that effective cooling is probably present in these systems, at least in the innermost regions. Interaction with the surrounding medium has a major effect on the X-ray surface brightness distribution at large radii, at least for galaxies in clusters. The data do not warrant the general assumptions of isothermality and gravitational hydrostatic equilibrium at large radii. Comparison of the X-ray surface brightness profiles with model predictions indicate that 1/r-squared halos with masses of the order of 10 times the stellar masses are required to match the data. The physical model of White and Chevalier (1984) for steady cooling flows in a King law potential with no heavy halo gives a surface brightness distribution that resembles the data if supernovae heating is present. 57 references.
Reflecting Brownian motion in a cusp

Let C be the cusp {(x, y): x ≥ 0, −x β ≤ y ≤ x β } where β > 1. Set ∂C 1 = {(x, y): x ≥ 0, y = −x β } and ∂C 2 = {(x, y): x ≥ 0, y = x β }. We study the existence and uniqueness in law of reflecting Brownian motion in C. The angle of reflection at ∂C j \{0} (relative to the inward unit normal) is a constant θ j ∈ (−π/2, π/2), and is positive iff the direction of reflection has a negative first component in all sufficiently small neighborhoods of 0. When θ 1 + θ 2 ≤ 0, existence and uniqueness in law hold. When θ 1 + θ 2 > 0, existence fails. We also obtain results for a large class of asymmetric cusps. We make essential use of results of Warschawski on the differentiability at the boundary of conformal maps
Optimal wavelength selection for noncontact reflection photoplethysmography

In this work, we obtain backscattered signals from human forehead for wavelengths from 380 to 980 nm. The results reveal bands with strong pulsatile signals that carry useful information. We describe those bands as the most suitable wavelengths in the visible and NIR regions from which heart and respiratory rate parameters can be derived using long distance non-contact reflection photoplethysmography analysis. The latter results show the feasibility of a novel technique for remotely detection of vital signs in humans. This technique, which may include morphological analysis or maps of tissue oxygenation, is a further step to real non-invasive remote monitoring of patients.
Effects of displacement and rate saturation on the control of statically unstable aircraft

Methodologies are presented for the analysis and design of stability augmentation control laws for aircraft in which "hard" displacement and rate limiting are significant. Candidate control laws are derived using the linearquadratic (LQ) regulator. Analytical and computational estimates of the stability limits imposed by control saturation are presented using state trajectories, as well as describing functions and eigenvalue computation. Analysis also includes an investigation of the interaction of the state-space saturation and stability boundaries for various choices of LQ weighting matrices. For minimum energy control, the saturation and stability boundaries are shown to be parallel. In this case, there is a direct relation between the solution to the matrix Riccati equation and the aircraft's open-loop dynamics. V IRTUALLY all aircraft control system actuation mechanisms possess "hard" limits on deflection and rate of deflection, and accounting for these limits is particularly important for aircraft designed with relaxed or negative static stability. Relaxed static stability generally leads to reduced weight and trim drag, both of which enhance the aircraft's performance.1 Relaxed static stability also may lead to increased control activity.2 For such aircraft, consideration must be given to the effects of control saturation on the initiation and, more importantly, the arrestment of dynamic motions, if departure from controlled flight is to be prevented. It may be possible to provide hardware actuation limits large enough so that normal disturbances and command inputs do not force the controls and to their mechanical, hydraulic, or electrical "stops"; however, there is no guarantee that commanded control deflections or rates will not exceed any established limit. Therefore, it is important to define the region within which stability and satisfactory response can be assured. This paper explores the effects of deflection and rate saturation on the stability of a statically unstable aircraft. This paper also reports on the development of methodologies for the analysis and design of stability augmentation control laws, with emphasis on response to initial conditions. (Command response is presented in Ref. 3 is the subject of a separate paper.11) Candidate stability augmentation system (SAS) control laws are derived using optimal control theory, with the linear-quadratic (LQ) regulator taken as the fundamental solution. Analytical and computational estimates of the stability limits imposed by control saturation are presented.
An efficient unified systolic architecture for the computation of discrete trigonometric transforms

In this paper, a novel unified systolic architecture which can efficiently implement various discrete trigonometric transforms (DXT) including the discrete Fourier transform (DFT), the discrete Hartley transform (DHT), the discrete cosine transform (DCT), and the discrete sine transform (DST) is described. Based on Clenshaw's recurrence formula, a set of efficient recurrences for computing the DXT is developed first. Then, the inherent symmetry of the trigonometric functions is further exploited to render a hardware-efficient, systolic structure. For the computation of any N-point DXT of interest, the proposed structure requires only about N/2 multipliers and N adders, thus providing substantial hardware savings compared with previous works. Furthermore, the new scheme can be easily adapted to compute any type of DXT with only minor modification. The complete I/O buffers have been addressed as well which allows for a continuous flow of successive blocks of input data and transformed results in natural order.
IRAS observations of dust heating and energy balance in the Rho Ophiuchi dark cloud

The equilibrium process dust emission in the Rho Ophiuchi dark cloud is studied. The luminosity of the cloud is found to closely match the luminosity of the clouds's known embedded and external radiation sources. There is no evidence for a large population of undetected low-luminosity sources within the cloud and unknown external heating is also only a minor source of energy. Most of the cloud's luminosity is emitted in the mid-to-far-IR. Dust temperature maps indicate that the dust is not hot enough to heat the gas to observed temperatures. A simple cloud model with a radiation field composed of flux HD 147889, S1, and Sco OB2 associations predicts the observed IRAS 60 to 100 micron in-band flux ratios for a mean cloud density n(H2) = 1400. Flattened 12 and 25 micron observations show much extended emission in these bands, suggesting stochastic heating of very small grains or large molecules.