Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear Perturbation Theory for Structural Dynamic Systems

A novel nonlinear perturbation theory for structural dynamic systems is developed that can provide an exact relationship between the perturbation of structural parameters and the perturbation of modal parameters. A system of governing equations based on the developed theory is further derived, which can be utilized for general applications, such as structural reanalyses, eigendata modification, model updating, and damage identification, suitable for all types of structures including mechanical systems, framed structures, and continua. Neither model reduction nor mode shape expansion is required for modal updating and damage identification because information about incomplete measured modal data can be directly employed. The developed theory successfully avoids adopting a Taylor series expansion procedure and then the derivatives of modal parameters are not required. Computational procedures based on the derived nonlinear governing equations are presented for eigendata modification, model updating, and damage identification. The Jacobi transformation method and the accelerated modal method are introduced to make the proposed techniques particularly suitable for cases with a very large perturbation of structural parameters. Finally, two numerical examples are given to demonstrate the effectiveness of the proposed techniques. The results show that the modified modal parameters can be predicted exactly even for cases with a large modification of structural parameters, and the analytical model can be adjusted correctly using the information about limited modal data available.
Transcription factors IRF8 and PU.1 are required for follicular B cell development and BCL6-driven germinal center responses

Significance The functions of transcription factors IRF8 and PU.1 in B cell activation and differentiation have been poorly understood due to redundancy between the family members. By using Mb1-Cre–mediated B cell-specific deletion of Irf8 and Spi1 (encoding PU.1), we provide evidence here that (i) double deletion of IRF8 and PU.1 resulted in severe deficiency in follicular and germinal center B cells; (ii) antibody affinity maturation was compromised in double-mutant mice; and (iii) the expression of BCL6 was dependent on IRF8 and PU.1, indicating the existence of an IRF8/PU.1–BCL6 axis in the initiation phase of the germinal center response. Our data thus reveal that IRF8 and PU.1 are indispensable for the development of late-stage B cells. The IRF and Ets families of transcription factors regulate the expression of a range of genes involved in immune cell development and function. However, the understanding of the molecular mechanisms of each family member has been limited due to their redundancy and broad effects on multiple lineages of cells. Here, we report that double deletion of floxed Irf8 and Spi1 (encoding PU.1) by Mb1-Cre (designated DKO mice) in the B cell lineage resulted in severe defects in the development of follicular and germinal center (GC) B cells. Class-switch recombination and antibody affinity maturation were also compromised in DKO mice. RNA-seq (sequencing) and ChIP-seq analyses revealed distinct IRF8 and PU.1 target genes in follicular and activated B cells. DKO B cells had diminished expression of target genes vital for maintaining follicular B cell identity and GC development. Moreover, our findings reveal that expression of B-cell lymphoma protein 6 (BCL6), which is critical for development of germinal center B cells, is dependent on IRF8 and PU.1 in vivo, providing a mechanism for the critical role for IRF8 and PU.1 in the development of GC B cells.
Modelling iceberg motion: A multiple‐time‐series approach

From the report of Ball, Gaskill, and Lopez (1981), it appears that the main determinants of the motion of icebergs are oceanic and atmospheric conditions (or their interaction) rather than the characteristics of the iceberg itself. The data from file 3 thus seem to be of less importance in explaining iceberg motion. In addition, many data are missing from that file. The data on the rate and direction of the ocean current (files 1 and 2) and on the atmospheric and oceanic conditions (file 5) were taken at the platform or in its vicinity. It is not clear if these data are pertinent in studying the motion of an iceberg which is far from the platform. Because of the abovementioned facts and the complicated way some factors seem to influence the iceberg motion (Ball, Gaskill, and Lopez, 1981; Smith and Banke, 1983; Hsiung and Aboul-Azm, 1982; Mountain, 1980), only the tracking data (file 4) were considered in the analysis. For many of the 114 icebergs listed, either there are only a few readings or there are long periods with no readings. Seven icebergs were selected for study, each having a relatively large number of readings at regular intervals. The icebergs considered and their characteristics are presented in Table 1 below. Iceberg no. 91001 was observed during a period of 313 hours, but clearly it grounded at some point. Only the 91 observations made while it was in motion were considered.
Computational Identification of RNA-Seq Based miRNA-Mediated Prognostic Modules in Cancer

Systematic identification of miRNA prognostic signature can help decipher the effects of biomarkers in cancer treatment. A number of previous studies have only characterized a single miRNA as a promising prognostic biomarker. There is currently a trend toward combining several miRNAs as a panel of prognostic signatures, but few attempts to explain the mechanism of miRNA combination. Throughout this paper, we refer to “miRNA-mediated prognostic modules” and propose a novel computational approach called ProModule to analyze prognostic biomarkers from the module perspective. ProModule works in two main stages: it first uses univariate and multivariable Cox proportional hazard regressions to find individual miRNA biomarkers and then employs a clustering method to systematically detect miRNA-mediated modules with statistical prognostic significance. We applied ProModule to three data sets in bladder cancer, breast cancer, and liver cancer, and identified several miRNA prognostic modules for each data set. We found that miRNA prognostic modules have more powerful prognostic value than individuals while presenting coherent miRNA–miRNA expression as well as significant functional enrichment, and thus are likely to be biologically meaningful. Availability: ProModule is implemented in R and available at https://github.com/chupan1218/ProModule.
LuAG:Ce fibers for high energy calorimetry

The main objective of this contribution is to point out the potentialities of cerium doped LuAG single crystal as pixels and fibers. We first show that after optimization of growth conditions using Bridgman technology, this composition exhibits very good performances for scintillating applications (up to 26 000 photons/MeV). When grown with the micropulling down technology, fiber shapes can be obtained while the intrinsic performances are preserved. For the future high energy experiments requiring new detector concepts capable of delivering much richer informations about x- or gamma-ray energy deposition, unusual fiber shaped dense materials need to be developed. We demonstrate in this frame that cerium doped LuAG is a serious candidate for the next generation of ionizing radiation calorimeters.
The Life Cycle of the Madden–Julian Oscillation

Abstract A composite life cycle of the Madden–Julian oscillation (MJO) is constructed from the cross covariance between outgoing longwave radiation (OLR), wind, and temperature. To focus on the role of convection, the composite is based on episodes when a discrete signal in OLR is present. The composite convective anomaly possesses a predominantly zonal wavenumber 2 structure that is confined to the eastern hemisphere. There, it propagates eastward at about 5 m s−1 and evolves through a systematic cycle of amplification and decay. Unlike the convective anomaly, the circulation anomaly is not confined to the eastern hemisphere. The circulation anomaly displays characteristics of both a forced response, coupled to the convective anomaly as it propagates across the eastern hemisphere, and a radiating response, which propagates away from the convective anomaly into the western hemisphere at about 10 m s−1. The forced response appears as a coupled Rossby–Kelvin wave while the radiating response displays predom.
A similarity analysis of curves

The authors propose a method for comparing two samples of curves. The notion of similarity between two curves is the basis of three statistics they suggest for testing the null hypothesis of no difference between the two groups. They exploit standard tools from functional data analysis to preprocess the observed curves and use the permutation distribution under the null hypothesis to obtain p‐values for their tests. They explore the operating characteristics of these tests through simulations and as an application, compare the ganglioside distribution in brain tissue between old and young rats.
Electrical‐transport measurements on fragile single crystals to 7.5 GPa in the diamond anvil cell

A four‐probe method is presented for the study of electrical‐transport properties of materials ranging from insulators to metals. Development of several experimental procedures and apparatuses and the fabrication of a composite gasket has permitted quasihydrostatic electrical resistivity measurements of fragile single crystals. Using a fluid to transmit pressure to the sample, the integrity of the crystal is assured. Pressures to 7.5 GPa have been obtained using the diamond anvil cell.
Graphical exploration in comparing covariance matrices

A graphical technique for comparing variance-covariance matrices of several populations is proposed. These "h-plots" display each population's variance-covariance configuration by projecting it onto the plane of closest fit, i.e., along the first two principal axes. It is shown how to construct these h-plots and inspect them for linear combinations of variables on which the populations differ. It is further shown how, under normality assumptions, one may use the h-plots to approximate simultaneous tests of significance on the variance comparisons. An illustration is examined in detail to show the practical usefulness of the proposed technique for data analysis and testing.
JAFROC analysis revisited: figure-of-merit considerations for human observer studies

Jackknife alternative free-response receiver operating characteristic (JAFROC) is a method for measuring human observer performance in localization tasks. JAFROC is being increasingly used to evaluate imaging modalities because it has been shown to have greater statistical power than conventional receiver operating characteristic (ROC) analysis, which neglects location information. JAFROC neglects the non-lesion localization marks ("false positives") on abnormal images. JAFROC1 is an alternative method that includes these marks. Both methods are lesion-centric in the sense that they assign equal importance to all lesions; an image with many lesions would tend to dominate the performance metric, and clinically less significant lesions are treated identically as more significant ones. In this paper weighted JAFROC and JAFROC1 analyses are described that treat each abnormal image (not each lesion) as a unit of measurement and account for different lesion clinical significances (weights). Lesion-centric and weighted methods were tested using a simulator that includes multiple-reader multiple-case multiple-modality location level correlations. For comparison, ROC analysis was also tested where the rating of the highest rated mark on an image was assumed to be its "ROC" rating. The testing involved random numbers of lesions per image, random weights, case-mixes (ratio of normal to abnormal images) and different correlation structures. We found that for either JAFROC or JAFROC1, both lesion-centric and weighted analyses had correct NH behavior and comparable statistical powers. For either lesion-centric or weighted analyses JAFROC1 yielded the highest power, followed by JAFROC and ROC yielded the least power, confirming a recent study using a less flexible single-reader dual-modality simulator. Provided the number of normal cases is not too small, JAFROC1 is the preferred method for analyzing human observer free-response data. For either JAFROC or JAFROC1 weighted analysis is preferable.
Identification of bacterial communities related to handling in commercial white-leg shrimp (Litopenaeus vannamei) using metagenomic analysis

Post-harvest handling, which includes the use of cold chains and proper hygiene, plays a critical role in maintaining fish quality and food safety. The bacterial community in white-leg shrimp will be affected by differences in the level of hygiene used in traditional and modern markets. This study was aimed to isolate bacterial DNA and identify bacterial communities on the surface of shrimps sold in the commercial market using metagenomic analysis. The research methods covered the isolation of bacterial DNA followed by the metabarcoding analysis of 16S rRNA and bioinformatics analysis. The sequence abundance of bacteria in White-leg shrimp samples were dominated by the genus Myroides, with a relative abundance of 49.18% in traditional markets and 84.89% in modern markets. Bacterial DNA from the skin surface of shrimp from traditional and modern markets has been isolated. The samples of shrimp from traditional markets had a higher relative abundance and diversity of bacteria than samples from modern markets.
The Restricted Boltzmann Machine Ansatz through Adiabiatic Routes

We discuss the expressive power of the quantum restricted Boltzmann machine Ansatz in order to represent faithfully the operation process of a quantum spin-glass system undergoing an adiabatic quantum computation process. We address both the representability and the trainability problems associated to the restricted Boltzmann machine Ansatz when we try to describe the ground state of a quantum Ising spin-glass in a transverse field. In our approach, we obtain the ground state of the system using exact diagonalization and find the optimal restricted Boltzman machine. Our preliminary results show that due to the complex spin-glass landscape, for some topologies of the restricted Bolztmann machine, the parameters of the representation are hard to be found.
The ocean response to El Nino Southern Oscillation (ENSO) in the Bali Sea: a model study

The Bali Sea (BS) is connected to the Java Sea and Makassar Strait in the north and is one of the main outflow straits of the Indonesian Throughflow (ITF) in Lombok Strait (LS). Local ocean dynamics and their variability may be controlled significantly by the ITF. This study aims to investigate the interannual variation of circulation, mixed layer depth, and isotherm of 20°C, by performing a simulation of fine- a resolution 1/84° ocean circulation model of CROCO between 2010-2020 with a focus on El Nino 2015 (EN2015) and La Nina 2020 (LN2020) events. The model validation reproduces well the satellite-derived SST and SSH dataset with a correlation coefficient of >0.9. The model demonstrated an anti-clockwise circulation of the ITF in the BS, entering via the northern and exiting into the LS via the southern area. This circulation changes drastically during the ENSO event, where the ITF transport inflow is weaker and shallower during EN2015, compared to a much stronger and deeper ITF inflow during LN2020. Accordingly, shallower mixed layer depth and depth of isotherm of 20°C are found during EN2015, and vice versa. Coherence of these parameters with NINO3.4 is very significant (>-0.89) with a phase lag of 1.7 months.
Barium sulfate and pigment admixture for photoacoustic and x-ray contrast imaging of the gut

Abstract. Significance X-ray imaging is frequently used for gastrointestinal imaging. Photoacoustic imaging (PAI) of the gastrointestinal tract is an emerging approach that has been demonstrated for preclinical imaging of small animals. A contrast agent active in both modalities could be useful for imaging applications. Aim We aimed to develop a dual-modality contrast agent comprising an admixture of barium sulfate with pigments that absorb light in the second near-infrared region (NIR-II), for preclinical imaging with both x-ray and PAI modalities. Approach Eleven different NIR-II dyes were evaluated after admixture with a 40% w/v barium sulfate mixture. The resulting NIR-II absorption in the soluble fraction and in the total mixture was characterized. Proof-of-principle imaging studies in mice were carried out. Results Pigments that produced more uniform suspensions were assessed further for photoacoustic contrast signal at a wavelength of 1064 nm that corresponds to the output of the Nd:YAG laser used. Phantom imaging studies demonstrated that the pigment-barium sulfate mixture generated imaging contrast in both x-ray and PAI modalities. The optimal pigment selected for further study was a cyanine tetrafluoroborate salt. Ex-vivo and whole-body mouse imaging demonstrated that photoacoustic and x-ray contrast signals co-localized in the intestines for both imaging modalities. Conclusion These data demonstrate that commercially-available NIR-II pigments can simply be admixed with barium sulfate to generate a dual-modality contrast agent appropriate for small animal gastrointestinal imaging.
Updated contour plots for the design of p/sup +/ emitters of silicon solar cells

The contours of constant dark saturation current density, J/sub 0e/, photogenerated current density lost by recombination, J/sub lost/ and sheet resistance, /spl rhosub se/, as a function of the surface dopant density and the thickness of the emitter are given for boron-doped regions, with application to silicon solar cells. Although similar calculations and graphs have already been published, the present ones have been generated using an updated value for the intrinsic carrier density, n/sub i/. Contour plots of the emitter-limited ideal solar cell efficiency are also included for the common case of a combined passivated/metal contacted surface. The latter plots show the main features of the optimum emitters. <<ETX>>
The transfer lemma for Graff tori and Arnold diffusion time

Let $H_\mu, 0 < \mu < < 1$ be a small perturbation of size $\mu$ of an initially hyperbolic Hamiltonian system. We prove that Graff tori satisfy the transitivity property : if $T_1, T_2$ and $T_3$ are three Graff tori such that $W^+(T_1)$ (resp. $W^+(T_2))$ and $W^-$ $(T_2)$ (resp. $W^-$ $(T_3))$ intersect transversally in a given energy level $H$ with an angle of order $\mu$, then $W^+(T_1)$ and $W^-$ $(T_3)$ intersect transversally in $H$ with an angle of order $\mu- c(\mu)$, with $c(\mu)$ exponentially small in $\mu$. The proof is based on a quantitative version of the $\lambda$-lemma for Graff tori called the transfer lemma. This result allows us to compute the Arnold diffusion time along transition chains for initially hyperbolic Hamiltonian systems. We prove that this time is polynomial in the inverse of the perturbing parameter.
Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-Analysis

The omicron variant is thought to cause less olfactory dysfunction than previous variants of SARS-CoV-2, but the reported prevalence differs greatly between populations and studies. Our systematic review and meta-analysis provide information regarding regional differences in prevalence as well as an estimate of the global prevalence of olfactory dysfunction based on 62 studies reporting information on 626,035 patients infected with the omicron variant. Our estimate of the omicron-induced prevalence of olfactory dysfunction in populations of European ancestry is 11.7%, while it is significantly lower in all other populations, ranging between 1.9% and 4.9%. When ethnic differences and population sizes are considered, the global prevalence of omicron-induced olfactory dysfunction in adults is estimated to be 3.7%. Omicron’s effect on olfaction is twofold to tenfold lower than that of the alpha or delta variants according to previous meta-analyses and our analysis of studies that directly compared the prevalence of olfactory dysfunction between omicron and previous variants. The profile of the prevalence differences between ethnicities mirrors the results of a recent genome-wide association study that connected a gene locus encoding an odorant-metabolizing enzyme, UDP glycosyltransferase, to the extent of COVID-19-related loss of smell. Our analysis is consistent with the hypothesis that this enzyme contributes to the observed population differences.
Exploring Reproductive Health Decision Experiences and Preferences of Women With Pediatric-Onset Inflammatory Bowel Diseases

Abstract Background Women with inflammatory bowel diseases (IBDs), such as Crohn’s disease or ulcerative colitis, face several disease-specific concerns related to their reproductive health decisions. This study explored the reproductive health decision-making experiences and preferences of women with IBD to discover ways to improve this aspect of comprehensive care. Methods We recruited women ages 18–44 years with IBD to participate in individual, semistructured interviews exploring their experiences and attitudes toward parenthood, pregnancy, contraception, and family planning care. Two independent coders performed analysis using an inductive and deductive coding approach and identified key themes. Results Twenty-one women with IBD participated in interviews (average age 24.7 ± 5.9 years, range 18–43 years; average age of diagnosis 14.1 ± 2.0 years). We identified 4 key themes: (1) Nulliparous women who do not currently desire pregnancy appear to lack reproductive health knowledge; (2) Women with IBD lack clarity regarding the role IBD plays in contraceptive choice; (3) Related to pregnancy, women are concerned about the heredity of IBD, antepartum disease activity, and the safety of their current medications; (4) Women with IBD typically default to their reproductive health provider for reproductive health care and counseling, but they expect their gastroenterologist to initiate relevant reproductive health discussions with them and to provide information in the context of their disease. Conclusions Women have concerns about the effects of IBD on pregnancy, parenthood, and contraceptive choice; however, many have had limited or no discussion with their gastroenterologist about the topic.
Effect of the surface charge on ion transport through nanoslits

A description of ion transport through geometrically defined nanoslits is presented. It is characterized by the effective surface charge density and was obtained by impedance spectroscopy measurements of electrolytes with different physico-chemical properties. The fluid channels were fabricated in a Pyrex-Pyrex field assisted bonding process with an intermediate layer of amorphous silicon. The height of the nanoslits was defined by the 50 nm thickness of the amorphous silicon layer. Two microfluidic channels, containing electrodes for the characterization of the nanoslits, maintained fresh liquid on both sides of the nanoapertures. By changing the KCl concentration of the electrolyte, a conductance plateau (in log-log scale) was observed due to the dominance of the effective surface charge density, resulting in an excess of mobile counterions in the nanoslits at low salt concentrations. The effective surface charge density of the Pyrex nanoslits could be modified by changing the pH of the solution. It was verified that at higher pH values the nanoslit conductance increased. Field-effect experiments allowed changing the effective surface charge density as well. The polarity of the external voltage could be chosen such that the effective surface charge density was increased or decreased, resulting in a higher or lower nanoslit conductance. This regulation of ionic flow can be exploited for the fabrication of nanofluidic devices