Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunization with gingipain A hemagglutinin domain of Porphyromonas gingivalis induces IgM antibodies binding to malondialdehyde-acetaldehyde modified low-density lipoprotein

Treatment of periodontitis has beneficial effects on systemic inflammation markers that relate to progression of atherosclerosis. We aimed to investigate whether immunization with A hemagglutinin domain (Rgp44) of Porphyromonas gingivalis (Pg), a major etiologic agent of periodontitis, would lead to an antibody response cross-reacting with oxidized low-density lipoprotein (OxLDL) and how it would affect the progression of atherosclerosis in low-density lipoprotein receptor-deficient (LDLR-/-) mice. The data revealed a prominent IgM but not IgG response to malondialdehyde-acetaldehyde modified LDL (MAA-LDL) after Rgp44 and Pg immunizations, implying that Rgp44/Pg and MAA adducts may share cross-reactive epitopes that prompt IgM antibody production and consequently confer atheroprotection. A significant negative association was observed between atherosclerotic lesion and plasma IgA to Rgp44 in Rgp44 immunized mice, supporting further the anti-atherogenic effect of Rgp44 immunization. Plasma IgA levels to Rgp44 and to Pg in both Rgp44- and Pg-immunized mice were significantly higher than those in saline control, suggesting that IgA to Rgp44 could be a surrogate marker of immunization in Pg-immunized mice. Distinct antibody responses in plasma IgA levels to MAA-LDL, to Pg lipopolysaccharides (Pg-LPS), and to phosphocholine (PCho) were observed after Rgp44 and Pg immunizations, indicating that different immunogenic components between Rpg44 and Pg may behave differently in regard of their roles in the development of atherosclerosis. Immunization with Rgp44 also displayed atheroprotective features in modulation of plaque size through association with plasma levels of IL-1α whereas whole Pg bacteria achieved through regulation of anti-inflammatory cytokine levels of IL-5 and IL-10. The present study may contribute to refining therapeutic approaches aiming to modulate immune responses and inflammatory/anti-inflammatory processes in atherosclerosis.
The self-referenced DLR 3D-modeler

In the context of 3-D scene modeling, this work aims at the accurate estimation of the pose of a close-range 3-D modeling device, in real-time and passively from its own images. This novel development makes it possible to abandon using inconvenient, expensive external positioning systems. The approach comprises an ego-motion algorithm tracking natural, distinctive features, concurrently with customary 3-D modeling of the scene. The use of stereo vision, an inertial measurement unit, and robust cost functions for pose estimation further increases performance. Demonstrations and abundant video material validate the approach.
Patterning, specification, and differentiation in the developing hypothalamus

Owing to its complex structure and highly diverse cell populations, the study of hypothalamic development has historically lagged behind that of other brain regions. However, in recent years, a greatly expanded understanding of hypothalamic gene expression during development has opened up new avenues of investigation. In this review, we synthesize existing work to present a holistic picture of hypothalamic development from early induction and patterning through nuclear specification and differentiation, with a particular emphasis on determination of cell fate. We will also touch on special topics in the field including the prosomere model, adult neurogenesis, and integration of migratory cells originating outside the hypothalamic neuroepithelium, and how these topics relate to our broader theme. WIREs Dev Biol 2015, 4:445–468. doi: 10.1002/wdev.187
Phosphodiesterase (PDE5) inhibition assay for rapid detection of erectile dysfunction drugs and analogs in sexual enhancement products.

Products marketed as dietary supplements for sexual enhancement are frequently adulterated with phosphodiesterase-5 (PDE5) inhibitors, which are erectile dysfunction drugs or their analogs that can cause adverse health effects. Due to widespread adulteration, a rapid screening assay was developed to detect PDE5 inhibitors in adulterated products. The assay employs fluorescence detection and is based on measuring inhibition of PDE5 activity, the pharmacological mechanism shared among the adulterants. Initially, the assay reaction scheme was established and characterized, followed by analysis of 9 representative PDE5 inhibitors (IC50 , 0.4-4.0 ng mL-1 ), demonstrating sensitive detection in matrix-free solutions. Next, dietary supplements serving as matrix blanks (n = 25) were analyzed to determine matrix interference and establish a threshold value; there were no false positives. Finally, matrix blanks were spiked with 9 individual PDE5 inhibitors, along with several mixtures. All 9 adulterants were successfully detected (≤ 5 % false negative rate; n = 20) at a concentration of 1.00 mg g-1 , which is over 5 times lower than concentrations commonly encountered in adulterated products. A major distinction of the PDE5 inhibition assay is the ability to detect adulterants without prior knowledge of their chemical structures, demonstrating a broad-based detection capability that can address a continuously evolving threat of new adulterants. The PDE5 inhibition assay can analyze over 40 samples simultaneously within 15 minutes and involves a single incubation step and simple data analysis, all of which are advantageous for combating the widespread adulteration of sex-enhancement products.
Nutrition Status of Young Elite Female German Football Players.

PURPOSE To investigate energy intake, energy expenditure, and the nutritional status of young female elite football players using 7-day food and activity records and blood parameters. METHODS A total of 56 female elite football players [14.8 (0.7) y] completed the requested food and activity protocols. Misreporting was assessed by the ratio of energy intake to energy expenditure. The food records were analyzed concerning energy and macronutrient and micronutrient intakes, and energy expenditure was calculated using predictive equations. Hematological data and 25-hydroxyvitamin D serum concentrations were determined. RESULTS Mean energy intake was 2262 (368) kcal/d [40.5 (7.0) kcal/kg/d] and estimated EE averaged 2403 (195) kcal/d. Fifty-three percent of the players exhibited an energy availability <30 kcal/kg lean body mass; 31% of the athletes consumed <5 g/kg carbohydrates and 34% consumed <1.2 g/kg proteins. A large proportion of players (%) had intakes below the recommended daily allowance of folate (75%), vitamin D (100%), iron (69%), and calcium (59%). Ferritin and 25-hydroxyvitamin D serum levels were below the recommendations of 59% and 38%, respectively. CONCLUSIONS A remarkable number of players failed to meet the energy balance and the recommended carbohydrate and protein intakes. Low iron and 25-hydroxyvitamin D serum levels were observed showing a suboptimal nutrition status of some young female football players. As a consequence, strategies have to be developed for a better information and application of sport nutrition practice among young female football players.
Alternative measures of between‐study heterogeneity in meta‐analysis: Reducing the impact of outlying studies

Meta‐analysis has become a widely used tool to combine results from independent studies. The collected studies are homogeneous if they share a common underlying true effect size; otherwise, they are heterogeneous. A fixed‐effect model is customarily used when the studies are deemed homogeneous, while a random‐effects model is used for heterogeneous studies. Assessing heterogeneity in meta‐analysis is critical for model selection and decision making. Ideally, if heterogeneity is present, it should permeate the entire collection of studies, instead of being limited to a small number of outlying studies. Outliers can have great impact on conventional measures of heterogeneity and the conclusions of a meta‐analysis. However, no widely accepted guidelines exist for handling outliers. This article proposes several new heterogeneity measures. In the presence of outliers, the proposed measures are less affected than the conventional ones. The performance of the proposed and conventional heterogeneity measures are compared theoretically, by studying their asymptotic properties, and empirically, using simulations and case studies.
Complex pattern detection and specification from multiscale environmental variables for biodiversity applications

Biodiversity scientists often need to define and detect scenarios of interest from data streams concern meteorological sensors. Such streams are characterized by their heterogeneity across spatial and temporal scales, which hampers construction of scenarios. To help them in this task, this paper proposes the use of the theory of Complex Event Processing (CEP) to detect complex event patterns in this context.
Consecutive epigenetically-active agent combinations act in ID1-RUNX3-TET2 and HOXA pathways for Flt3ITD+ve AML

Co-occurrence of Flt3ITD and TET2 mutations provoke an animal model of AML by epigenetic repression of Wnt pathway antagonists, including RUNX3, and by hyperexpression of ID1, encoding Wnt agonist. These affect HOXA over-expression and treatment resistance. A comparable epigenetic phenotype was identified among adult AML patients needing novel intervention. We chose combinations of targeted agents acting on distinct effectors, at the levels of both signal transduction and chromatin remodeling, in relapsed/refractory AML’s, including Flt3ITD+ve, described with a signature of repressed tumor suppressor genes, involving Wnt antagonist RUNX3, occurring along with ID1 and HOXA over-expressions. We tracked patient response to combination of Flt3/Raf inhibitor, Sorafenib, and Vorinostat, pan-histone deacetylase inhibitor, without or with added Bortezomib, in consecutive phase I trials. A striking association of rapid objective remissions (near-complete, complete responses) was noted to accompany induced early pharmacodynamic changes within patient blasts in situ, involving these effectors, significantly linking RUNX3/Wnt antagonist de-repression (80%) and ID1 downregulation (85%), to a response, also preceded by profound HOXA9 repression. Response occurred in context of concurrent TET2 mutation/hypomorphy and Flt3ITD+ve mutation (83% of complete responses). Addition of Bortezomib to the combination was vital to attainment of complete response in Flt3ITD+ve cases exhibiting such Wnt pathway dysregulation.
Coordinate interferometric system for measuring the position of a sample with infrared telecom laser diode

We report on a design of an interferometric position measuring system for control of a sample stage in an e-beam writer with reproducibility of the position on nanometer level and resolution below nanometer. We introduced differential configuration of the interferometer where the position is measured with respect to a central reference point to eliminate deformations caused by thermal and pressure effects on the vacuum chamber. The reference is here the electron gun of the writer. The interferometer is designed to operate at infrared, telecommunication wavelength due to the risk of interference of stray light with sensitive photodetectors in the chamber. The laser source is here a narrow-linewidth DFB laser diode with electronics of our own design offering precision and stability of temperature and current, low-noise, protection from rf interference, and high-frequency modulation. Detection of the interferometric signal relies on a novel derivative technique utilizing hf frequency modulation and phase-sensitive detection.
The E3 Ubiquitin Ligase Siah-1 Suppresses Avian Reovirus Infection by Targeting p10 for Degradation

ABSTRACT Avian reovirus (ARV) causes viral arthritis, chronic respiratory diseases, retarded growth, and malabsorption syndrome. The ARV p10 protein, a viroporin responsible for the induction of cell syncytium formation and apoptosis, is rapidly degraded in host cells. Our previous report demonstrated that cellular lysosome-associated membrane protein 1 (LAMP-1) interacted with p10 and was involved in its degradation. However, the molecular mechanism underlying LAMP-1-mediated p10 degradation remains elusive. We report here that the E3 ubiquitin ligase seven in absentia homolog 1 (Siah-1) is critical for p10 ubiquitylation. Our data show that Siah-1 ubiquitylated p10 and targeted it for proteasome degradation. Furthermore, the ubiquitylation of p10 by Siah-1 required the participation of LAMP-1 by forming a multicomponent complex. Thus, LAMP-1 promotes the proteasomal degradation of p10 via interacting with both p10 and the E3 ligase Siah-1. These data establish a novel host defense mechanism where LAMP-1 serves as a scaffold for both Siah-1 and p10 that allows the E3 ligase targeting p10 for ubiquitylation and degradation to suppress ARV infection. IMPORTANCE Avian reovirus (ARV) is an important poultry pathogen causing viral arthritis, chronic respiratory diseases, retarded growth, and malabsorption syndrome, leading to considerable economic losses to the poultry industry across the globe. The ARV p10 protein is a virulence factor responsible for the induction of cell syncytium formation and apoptosis and is rapidly degraded in host cells. We previously found that cellular lysosome-associated membrane protein 1 (LAMP-1) interacts with p10 and is involved in its degradation. Here we report that the E3 ubiquitin ligase seven in absentia homolog 1 (Siah-1) ubiquitylated p10 and targeted it for proteasomal degradation. Furthermore, the ubiquitylation of p10 by Siah-1 required the participation of LAMP-1 by forming a multicomponent complex. Thus, LAMP-1 serves as an adaptor to allow Siah-1 to target p10 for degradation, thereby suppressing ARV growth in host cells.
Genotyping Oral Commensal Bacteria to Predict Social Contact and Structure

Social network structure is a fundamental determinant of human health, from infectious to chronic diseases. However, quantitative and unbiased approaches to measuring social network structure are lacking. We hypothesized that genetic relatedness of oral commensal bacteria could be used to infer social contact between humans, just as genetic relatedness of pathogens can be used to determine transmission chains of pathogens. We used a traditional, questionnaire survey-based method to characterize the contact network of the School of Public Health at a large research university. We then collected saliva from a subset of individuals to analyze their oral microflora using a modified deep sequencing multilocus sequence typing (MLST) procedure. We examined micro-evolutionary changes in the S. viridans group to uncover transmission patterns reflecting social network structure. We amplified seven housekeeping gene loci from the Streptococcus viridans group, a group of ubiquitous commensal bacteria, and sequenced the PCR products using next-generation sequencing. By comparing the generated S. viridans reads between pairs of individuals, we reconstructed the social network of the sampled individuals and compared it to the network derived from the questionnaire survey-based method. The genetic relatedness significantly (p-value < 0.001) correlated with social distance in the questionnaire-based network, and the reconstructed network closely matched the network derived from the questionnaire survey-based method. Oral commensal bacterial are thus likely transmitted through routine physical contact or shared environment. Their genetic relatedness can be used to represent a combination of social contact and shared physical space, therefore reconstructing networks of contact. This study provides the first step in developing a method to measure direct social contact based on commensal organism genotyping, potentially capable of unmasking hidden social networks that contribute to pathogen transmission.
Improved Iteratively Reweighted Least Squares for Unconstrained Smoothed 퓁q Minimization

In this paper, we first study $\ell_q$ minimization and its associated iterative reweighted algorithm for recovering sparse vectors. Unlike most existing work, we focus on unconstrained $\ell_q$ minimization, for which we show a few advantages on noisy measurements and/or approximately sparse vectors. Inspired by the results in [Daubechies et al., Comm. Pure Appl. Math., 63 (2010), pp. 1--38] for constrained $\ell_q$ minimization, we start with a preliminary yet novel analysis for unconstrained $\ell_q$ minimization, which includes convergence, error bound, and local convergence behavior. Then, the algorithm and analysis are extended to the recovery of low-rank matrices. The algorithms for both vector and matrix recovery have been compared to some state-of-the-art algorithms and show superior performance on recovering sparse vectors and low-rank matrices.
Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics

Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through biomimetic NPCs consisting of Nsp1 domains attached to the inner surface of solid-state nanopores. We examine both wildtype FG-domains and hydrophilic SG-mutants. FG-nanopores showed a clear selectivity as transport receptors can translocate across the pore whereas other proteins cannot. SG mutant pores lack such selectivity. To unravel this striking difference, we present coarse-grained molecular dynamics simulations that reveal that FG-pores exhibit a high-density, nonuniform protein distribution, in contrast to a uniform and significantly less-dense protein distribution in the SG-mutant. We conclude that the sequence-dependent density distribution of disordered proteins inside the NPC plays a key role for its conductivity and selective permeability.
The inner‐rod component of Shigella flexneri type 3 secretion system, MxiI, is involved in the transmission of the secretion activation signal by its interaction with MxiC

The virulence of Shigella mainly resides in the use of a Type 3 Secretion System (T3SS) to inject several proteins inside the host cell. Three categories of proteins are hierarchically secreted: (1) the needle components (MxiH and MxiI), (2) the translocator proteins which form a pore (translocon) inside the host cell membrane, and (3) the effectors interfering with the host cell signaling pathways. In the absence of host cell contact, the T3SS is maintained in an “off” state by the presence of a tip complex. We have previously identified a gatekeeper protein, MxiC, which sequesters effectors inside the bacteria probably by interacting with MxiI, the inner‐rod component. Upon cell contact and translocon insertion, a signal is most likely transmitted from the top of the needle to the base, passing through the needle and allowing effectors release. However, the molecular mechanism underlying the transmission of the activation signal through the needle is still poorly understood. In this work, we investigate the role of MxiI in the activation of the T3SS by performing a mutational study. Interestingly we have shown that mutations of a single residue in MxiI (T82) induce an mxiC‐like phenotype and prevent the interaction with MxiC. Moreover, we have shown that the L26A mutation significantly reduces T3 secretion. The L26A mutation impairs the interaction between MxiI and Spa40, a keystone component of the switch between needle assembly and translocators secretion. The L26A mutation also sequesters MxiC. All these results highlight the crucial role of MxiI in regulating the secretion and transmitting the activation signal of the T3SS.
Progressive Resistance Training in Elderly HIV-Positive Patients: Does it Work?

BACKGROUND Elderly people present alterations in body composition and physical fitness, compromising their quality of life. Chronic diseases, including HIV/AIDS, worsen this situation. Resistance exercises are prescribed to improve fitness and promote healthier and independent aging. Recovery of strength and physical fitness is the goal of exercise in AIDS wasting syndrome. OBJECTIVE This study describes a case series of HIV-positive elderly patients who participated in a progressive resistance training program and evaluates their body composition, muscular strength, physical fitness and the evolution of CD4+ and CD8+ cell counts. METHODS Subjects were prospectively recruited for nine months. The training program consisted of three sets of 8–12 repetitions of leg press, seated row, lumbar extension and chest press, performed with free weight machines hts, twice/week for one year. Infectious disease physicians followed patients and reported all relevant clinical data. Body composition was assessed by anthropometric measures and dual-energy x-ray absorptiometry before and after the training program. RESULTS Fourteen patients, aged 62–71 years old, of both genders, without regular physical activity who had an average of nine years of HIV/AIDS history were enrolled. The strengths of major muscle groups increased (74%–122%, p=0.003–0.021) with a corresponding improvement in sit-standing and walking 2.4 m tests (p=0.003). There were no changes in clinical conditions and body composition measures, but triceps and thigh skinfolds were significantly reduced (p=0.037). In addition, there were significant increases in the CD4+ counts (N=151 cells; p=0.008) and the CD4+/CD8+ ratio (0.63 to 0.81, p=0.009). CONCLUSION Resistance training increased strength, improved physical fitness, reduced upper and lower limb skinfolds, and were associated with an improvement in the CD4+ and CD4+/CD8+ counts in HIV positive elderly patients without significant side effects.
Web-based Supplementary Materials for Selection of Effects in Cox Frailty Models by Regularization Methods

Note here that the linear predictors ηij(t) depend on the parameter vector δ, compare equation (1). This is suppressed here for notational convenience. The vectors s β and s α have dimension p and (r + 1)M , respectively, while the vectors s pen i are of dimension q. The penalty matrix Aξ0,ξ,ζ is a block-diagonal matrix of the form Aξ0,ξ,ζ = diag(Aξ0 ,Aξ,ζ). The first matrix Aξ0 = ξ0∆ T M∆M corresponds to the penalization of the squared differences between adjacent spline coefficients α0 of the baseline hazard from equation (6), with ∆M denoting the ((M − 1) ×M)-dimensional difference operator matrix of degree one from equation (5). The second matrix Aξ,ζ results from a local quadratical approximation of the penalty in equation (4), following Oelker