Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing for Weak Instruments in Two Sample Summary Data Multivariable Mendelian Randomisation

Here we show that under the assumption that the instruments are uncorrelated the two sample conditional F-statistic FTS in equation (7) in the main text is equivalent to the one sample conditional F-statistic FSW . The individual level conditional F-statistic derived by Sanderson and Windmeijer (2016), FSW , has been shown elsewhere to be an F-test version of the Basmann statistic for overidentification1,2,3,4. Here we show that FTS is the two-sample equivalent of the same Basmann statistic and therefore it follows that FTS is equivalent to FSW , the equivalent test for individual level data. This equivalence implies that the Stock-Yogo critical values for weak instruments used to test for weak instruments in individual level data are also the appropriate values to compare FTS to to identify weak instruments in two sample Mendelian randomisation. 5,6,1 Although the effect of any particular SNP on different exposures in the model may be correlated we assume throughout that the SNPs themselves are independent of each other. This is not an unreasonable assumption in the context of two-sample MVMR where results from Genome-wide Association Studies are used for each sample. In this context the SNPs used for the analysis are pruned to remove correlated SNPs as standard procedure ensuring that the instruments used in the analysis are independent. The estimation considered, in the one sample setting, is;
Distributed thermal tasks on many-body systems through a single quantum machine

We propose a configuration of a single three-level quantum emitter embedded in a non-equilibrium steady electromagnetic environment, able to stabilize and control the local temperatures of a target system it interacts with, consisting of a collection of coupled two-level systems. The temperatures are induced by dissipative processes only, without the need of further external couplings for each qubit. Moreover, by acting on a set of easily tunable geometric parameters, we demonstrate the possibility to manipulate and tune each qubit temperature independently over a remarkably broad range of values. These findings address one standard problem in quantum-scale thermodynamics, providing a way to induce a desired distribution of temperature among interacting qubits and to protect it from external noise sources.
Tackling the Saturation of Oxygen: The Use of Phosphorus and Sulfur as Proxies within the Neutral Interstellar Medium of Star-forming Galaxies

The abundance of oxygen in galaxies is widely used in furthering our understanding of galaxy formation and evolution. Unfortunately, direct measurements of O/H in the neutral gas are extremely difficult to obtain, as the only O i line available within the Hubble Space Telescope (HST) UV wavelength range (1150–3200 Å) is often saturated. As such, proxies for oxygen are needed to indirectly derive O/H via the assumption that solar ratios based on local Milky Way sight lines hold in different environments. In this paper we assess the validity of using two such proxies, P ii and S ii, within more typical star-forming environments. Using HST-Cosmic Origins Spectrograph (COS) far-UV (FUV) spectra of a sample of nearby star-forming galaxies (SFGs) and the oxygen abundances in their ionized gas, we demonstrate that both P and S are mildly depleted with respect to O and follow a trend, log(P ii/S ii) , in excellent agreement with the solar ratio of over the large range of metallicities (0.03–3.2 Z⊙) and H i column densities ( (H i)/cm−2] =18.44–21.28) spanned by the sample. From literature data we show evidence that both elements individually trace oxygen according to their respective solar ratios across a wide range of environments. Our findings demonst-rate that the solar ratios of and can both be used to derive reliable O/H abundances in the neutral gas of local and high-redshift SFGs. The difference between O/H in the ionized- and neutral gas phases is studied with respect to metallicity and H i content. The observed trends are consistent with galactic outflows and/or star formation inefficiency affecting the most metal-poor galaxies, with the possibility of primordial gas accretion at all metallicities.
Application of afxy-code for parameterization of ionization yield function Y in the atmosphere for primary cosmic ray protons

In this work is obtained new approximation for the yield function Y for cosmic ray induced ionization in the Earth atmosphere on the basis of simulated data. The parameterization is obtained using inverse nonlinear problem solution with afxy(analyze fx=y)-code. Short description of the methods is given. The found approximation is for primary proton nuclei, inclined up to 70 degrees zenith angle. This permits to estimate the direct ionization by primary cosmic rays explicitly. The parameterization is applicable to the entire atmosphere, from ground level to upper atmosphere. Several implications of the found parameterization are discussed.
Surface plasmon–polariton wave propagation guided by a metal slab in a sculptured nematic thin film

Surface plasmon–polariton (SPP) wave propagation guided by a metal slab in a periodically nonhomogeneous sculptured nematic thin film (SNTF) was studied theoretically. The morphologically significant planes of the SNTF on both sides of the metal slab could either be aligned or twisted with respect to each other. The canonical boundary-value problem was formulated, solved for SPP wave propagation, and examined to determine the effect of slab thickness on the multiplicity and the spatial profiles of SPP waves. Decrease in slab thickness was found to result in more intense coupling of two metal/SNTF interfaces. But when the metal slab becomes thicker, the coupling between the two interfaces reduces and eventually SPP waves localize to one of the two metal/SNTF interfaces. The greater the coupling between the two metal/SNTF interfaces, the smaller is the phase speed. Both the phase speed and the attenuation of an SPP wave also depend on the twist between the morphologically significant planes of the SNTF on the two sides of the metal slab.
The Synoptic All-Sky Infrared (SASIR) Survey

We are proposing to conduct a multicolor, synoptic infrared (IR) imaging survey of the Northern sky with a new, dedicated 6.5-meter telescope at San Pedro M\'artir (SPM) Observatory. This initiative is being developed in partnership with astronomy institutions in Mexico and the University of California. The 4-year, dedicated survey, planned to begin in 2017, will reach more than 100 times deeper than 2MASS. The Synoptic All-Sky Infrared (SASIR) Survey will reveal the missing sample of faint red dwarf stars in the local solar neighborhood, and the unprecedented sensitivity over such a wide field will result in the discovery of thousands of z ~ 7 quasars (and reaching to z > 10), allowing detailed study (in concert with JWST and Giant Segmented Mirror Telescopes) of the timing and the origin(s) of reionization. As a time-domain survey, SASIR will reveal the dynamic infrared universe, opening new phase space for discovery. Synoptic observations of over 10^6 supernovae and variable stars will provide better distance measures than optical studies alone. SASIR also provides significant synergy with other major Astro2010 facilities, improving the overall scientific return of community investments. Compared to optical-only measurements, IR colors vastly improve photometric redshifts to z ~ 4, enhancing dark energy and dark matter surveys based on weak lensing and baryon oscillations. The wide field and ToO capabilities will enable a connection of the gravitational wave and neutrino universe - with events otherwise poorly localized on the sky - to transient electromagnetic phenomena.
Modelling the cost-effectiveness of hepatitis A vaccination in South Africa

The World Health Organization (WHO) recommends the consideration of introducing routine hepatitis A vaccination into national immunization schedules for children younger than 1 year old in countries with intermediate HAV endemicity. Recent data suggest that South Africa is transitioning from high to intermediate HAV endemicity, thus it is important to consider the impact and cost of potential routine hepatitis A vaccination strategies in the country. An age-structured compartmental model of hepatitis A transmission was calibrated with available data from South Africa, incorporating direct costs of hepatitis A treatment and vaccination. We used the calibrated model to evaluate the impact and costs of several childhood hepatitis A vaccination scenarios from 2023 to 2030. We assessed how each scenario impacted the burden of hepatitis A (symptomatic hepatitis A cases and mortality) as well as calculated the incremental cost per DALY averted as compared to the South African cost-effectiveness threshold. All costs and outcomes were discounted at 5%. For the modelled scenarios, the median estimated cost of the different vaccination strategies ranged from $1.71 billion to $2.85 billion over the period of 2023 to 2030, with the cost increasing for each successive scenario and approximately 39-52% of costs being due to vaccination. Scenario 1, which represented the administration of one dose of the hepatitis A vaccine in children < 2 years old, requires approximately 5.3 million vaccine doses over 2023-2030 and is projected to avert a total of 136,042 symptomatic cases [IQR: 88,842-221,483] and 31,106 [IQR: 22,975- 36,742] deaths due to hepatitis A over the period of 2023 to 2030. The model projects that Scenario 1 would avert 8,741 DALYs over the period of 2023 to 2030, however is not cost-effective against the South African cost-effectiveness threshold with an ICER per DALY averted of $21,006. While Scenario 3 and 4 included the administration of more vaccine doses and averted more symptomatic cases of hepatitis A, these scenarios were absolutely dominated owing to the population being infected before vaccination through the mass campaigns at older ages. The model was highly sensitivity to varying access to liver transplant in South Africa. When increasing the access to liver transplant to 100% for baseline and Scenario 1, the ICER for Scenario 1 becomes cost-effective against the CET (ICER = $2,425). Given these findings, we recommend further research is conducted to understand the access to liver transplants in South Africa to better estimate the cost of liver transplant care for hepatitis A patients. The modelling presented in this paper has been used to develop a user-friendly application for vaccine policy makers to further interrogate the model outcomes and consider the costs and benefits of introducing routine hepatitis A vaccination in South Africa.
Automatic Image-To-Map-Registration of Remote Sensing Data

With this paper, a fully automatic system for the registration of satellite image data with vector GIS data is presented. The implemented approach is based on polygonal objects which are extracted from the image (region growing segmentation) and from the GIS data set (merging of polygons with the same object class). Based on absolute affine invariant features, corresponding pairs of objects are determined by a backtracking depth-first tree search algorithm. Investigations concerning the robustness and discrimination power of the used absolute affine invariants are presented. Within the tree search algorithm, unary and binary constraints are applied in order to find a consistent subset of polygon pairs from all matching hypothesis. Furthermore, a coarse global affine transformation is determined in this step. Based on this transformation, all hypothesis being consistent with the global transformation are determined in a verification step. An individual affine transformation for each object pair is computed by using the formalism of standard positions. , The individual transformations are refined for each verified sensor-model polygon pair in a refinement step. Finally, homologuous points (GCPs) with prefixed standard deviation of the residuals are extracted from the polygon boundaries. The whole process is exemplarily applied to a 25km x 20km section of the German ATKIS Vector data base and corresponding original SPOT PAN data. In this work, only forest polygons were used.
Association of cardiorespiratory fitness with the risk factors of cardiovascular disease: Evaluation using the Japan step test from the National Institute of Occupational Safety and Health

Cardiorespiratory fitness (CRF) is an important factor for evaluating cardiovascular disease (CVD) risk. We recently developed a novel method (National Institute of Occupational Safety and Health, Japan step test [JST]) for evaluating CRF in workers; its criterion validity has been investigated. However, its association with health risk must be confirmed before its application in the workplace. Therefore, we aimed to determine the association of JST‐evaluated CRF with the prevalence of CVD risk among Japanese workers.
Draft Genome Sequences of Dickeya Species Associated with Soft Rot Diseases in Pineapple (Ananas comosus) and Banana (Musa spp.)

Dickeya species cause soft rots on many commercial crops. Here, we present the draft genomes of Dickeya oryzae (BRIP 64262) and Dickeya zeae (BRIP 64263) isolates causing soft rot on banana (Musa spp.) and pineapple (Ananas comosus) plants, respectively. This expands the range of available genomes from plant-pathogenic Dickeya species. ABSTRACT Dickeya species cause soft rots on many commercial crops. Here, we present the draft genomes of Dickeya oryzae (BRIP 64262) and Dickeya zeae (BRIP 64263) isolates causing soft rot on banana (Musa spp.) and pineapple (Ananas comosus) plants, respectively. This expands the range of available genomes from plant-pathogenic Dickeya species.
COMMUNICATION IN XYZ ALL-TO-ALL QUANTUM NETWORKS WITH A MISSING LINK

We explicitate the relation between Hamiltonians for networks of interacting qubits in the XYZ model and graph Laplacians. We then study evolution in networks in which all sites can communicate with each other. These are modeled by the complete graphKn and called all-to-all networks. It turns out that Kn does not exhibit perfect state transfer (PST). However, we prove that deleting an edge in Kn allows PST between the two non-adjacent sites, when n is a multiple of four. An application is routing a qubit over n different sites, by switching off the link between the sites that we wish to put in communication. Additionally, we observe that, in certain cases, the unitary inducing evolution in Kn is equivalent to the Grover operator.
Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila

Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.
Commonality and Individuality-Based Subspace Learning

Subspace learning (SL) plays a key role in various learning tasks, especially those with a huge feature space. When processing multiple high-dimensional learning tasks simultaneously, it is of great importance to make use of the subspace extracted from some tasks to help learn others, so that the learning performance of all tasks can be enhanced together. To achieve this goal, it is crucial to answer the following question: How can the commonality among different learning tasks and, of equal importance, the individuality of each single learning task, be characterized and extracted from the given datasets, so as to benefit the subsequent learning, for example, classification? Existing multitask SL methods usually focused on the commonality among the given tasks, while neglecting the individuality of the learning tasks. In order to offer a more general and comprehensive framework for multitask SL, in this article, we propose a novel method dubbed commonality and individuality-based SL (CISL). First, we formally define the notions and objective functions of both commonality and individuality with respect to multiple SL tasks. Then, we design an iterative algorithm to solve the formulated objective functions, with the convergence of the algorithm being guaranteed. To show the generality of the proposed method, we theoretically analyze its connections to existing single-task and multitask SL methods. Finally, we demonstrate the necessity and effectiveness of incorporating both commonality and individuality by interpreting the learned subspaces and comparing the performance of CISL (in terms of the subsequent classification accuracy) with that of classical and state-of-the-art SL approaches on both synthetic and real-world multitask datasets. The empirical evaluation validates the effectiveness of the proposed method in characterizing the commonality and individuality for multitask SL.
QQVALUE: Stata module to generate quasi-q-values by inverting multiple-test procedures

qqvalue is similar to the R package p.adjust. It inputs a single variable, assumed to contain P-values calculated for multiple comparisons, in a dataset with 1 observation per comparison. It outputs a new variable, containing the quasi-q-values corresponding to these P-values, calculated by inverting a multiple-test procedure specified by the user. These quasi-q-values represent, for each corresponding P-value, the minimum uncorrected P-value threshold for which that P-value would be in the discovery set, assuming that the specified multiple-test procedure was used on the same set of input P-values to generate a corrected P-value threshold. These minimum uncorrected P-value thresholds may represent familywise error rates or false discovery rates, depending on the procedure used. Optionally, qqvalue may output other variables, containing the various intermediate results used in calculating the quasi-q-values. The multiple-test procedures available for qqvalue are a subset of those available using the multproc module of the smileplot package, which can be downloaded from SSC.
Causal, Bayesian, & non-parametric modeling of the SARS-CoV-2 viral load distribution vs. patient’s age

The viral load of patients infected with SARS-CoV-2 varies on logarithmic scales and possibly with age. Controversial claims have been made in the literature regarding whether the viral load distribution actually depends on the age of the patients. Such a dependence would have implications for the COVID-19 spreading mechanism, the age-dependent immune system reaction, and thus for policymaking. We hereby develop a method to analyze viral-load distribution data as a function of the patients’ age within a flexible, non-parametric, hierarchical, Bayesian, and causal model. The causal nature of the developed reconstruction additionally allows to test for bias in the data. This could be due to, e.g., bias in patient-testing and data collection or systematic errors in the measurement of the viral load. We perform these tests by calculating the Bayesian evidence for each implied possible causal direction. The possibility of testing for bias in data collection and identifying causal directions can be very useful in other contexts as well. For this reason we make our model freely available. When applied to publicly available age and SARS-CoV-2 viral load data, we find a statistically significant increase in the viral load with age, but only for one of the two analyzed datasets. If we consider this dataset, and based on the current understanding of viral load’s impact on patients’ infectivity, we expect a non-negligible difference in the infectivity of different age groups. This difference is nonetheless too small to justify considering any age group as noninfectious.
Is the CMB cold spot a gate to extra dimensions?

One of the most striking features found in the cosmic microwave background data is the presence of an anomalous cold spot (CS) in the temperature maps made by the Wilkinson Microwave Anisotropy Probe (WMAP). This CS has been interpreted as the result of the presence of a collapsing texture, perhaps coming from some early universe grand unified theory (GUT) phase transition. In this work we propose an alternative explanation based on a completely different kind of texture which appears in a natural way in a broad class of brane-world models. This type of texture, known as a brane-skyrmion, can be understood as a hole in the brane which makes it possible to pass through them along the extra-dimensional space. The typical scales needed for the proposed brane-skyrmions to correctly describe the observed CS can be as low as the electroweak scale.
Determinants of mammography screening participation–a cross-sectional analysis of the German population-based Gutenberg Health Study (GHS)

Purpose We investigated the association between social inequality and participation in a mammography screening program (MSP). Since the German government offers mammography screening free of charge, any effect of social inequality on participation should be due to educational status and not due to the financial burden. Methods The ‘Gutenberg Health Study’ is a cohort study in the Rhine-Main-region, Germany. A health check-up was performed, and questions about medical history, health behavior, including secondary prevention such as use of mammography, and social status are included. Two indicators of social inequality (equivalence income and educational status), an interaction term of these two, and different covariables were used to explore an association in different logistic regression models. Results A total of 4,681 women meeting the inclusion criteria were included. Only 6.2% never participated in the MSP. A higher income was associated with higher chances of ever participating in a mammography screening (odds ratios (OR): 1.67 per €1000; 95%CI:1.26–2.25, model 3, adjusted for age, education and an interaction term of income and education). Compared to women with a low educational status, the odds ratios for ever participating in the MSP was lower for the intermediate educational status group (OR = 0.64, 95%CI:0.45–0.91) and for the high educational status group (0.53, 95%CI:0.37–0.76). Results persisted also after controlling for relevant confounders. Conclusions Despite the absence of financial barriers for participation in the MSP, socioeconomic inequalities still influence participation. It would be interesting to examine whether the educational effect is due to an informed decision.
Octonionic geometry and conformal transformations

We describe space-time using split octonions over the reals and use their group of automorphisms, the non-compact form of Cartan's exceptional Lie group G2, as the main geometrical group of the model. Connections of the G2-rotations of octonionic 8D space with the conformal transformations in 4D Minkowski space-time are studied. It is shown that the dimensional constant needed in these analysis naturally gives the observed value of the cosmological constant.