Miracle-dz/UniFAR-FTUs huggingface dataset:
Glaucoma Diagnostic Capability of Global and Regional Measurements of Isolated Ganglion Cell Layer and Inner Plexiform Layer

Purpose: To compare glaucoma diagnostic capability of global/regional macular layer parameters in different-sized grids. Materials and Methods: Serial horizontal spectral-domain optical coherence tomography scans of macula were obtained. Automated macular grids with diameters of 3, 3.45, and 6 mm were used. For each grid, 10 parameters (total volume; average thicknesses in 9 regions) were obtained for 5 layers: macular retinal nerve fiber layer (mRNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), ganglion cell-inner plexiform layer (GCIPL; GCL+IPL), and ganglion cell complex (GCC; mRNFL+GCL+IPL). Results: Sixty-nine normal eyes (69 subjects) and 87 glaucomatous eyes (87 patients) were included. For the total volume parameter, the area under the receiver operating characteristic curves (AUCs) in 6-mm grid were larger than the AUCs in 3- and 3.45-mm grids for GCL, GCC, GCIPL, and mRNFL (all P<0.020). For the average thickness parameters, the best AUC in 6-mm grid (T2 region for GCL, IPL, and GCIPL; I2 region for mRNFL and GCC) was greater than the best AUC in 3-mm grid for GCL, GCC, and mRNFL (P<0.045). The AUC of GCL volume (0.920) was similar to those of GCC (0.920) and GCIPL (0.909) volume. The AUC of GCL T2 region thickness (0.942) was similar to those of GCC I2 region (0.942) and GCIPL T2 region (0.934) thickness. Conclusions: Isolated macular GCL appears to be as good as GCC and GCIPL in glaucoma diagnosis, while IPL does not. Larger macular grids may be better at detecting glaucoma. Each layer has a characteristic region with the best glaucoma diagnostic capability.
The Role of Carbon Dioxide in Host-Finding by Mosquitoes (Diptera: Culicidae): A Review

From a critical review of the literature, it is concluded that the role of carbon dioxide in host-seeking by mosquitoes comprises two distinct actions. Firstly, it acts as an attractant’, orientation towards the host being mediated by kinesis and optomotor anemotaxis. When tested in the absence of moving air currents, orientation to the source is not possible and only the kinetic or activating effect is manifested. Moreover, in the absence of other host factors, sustained flight takes place only in response to intermittent pulses of carbon dioxide; this response is not elicited in uniformly permeated airstreams. Secondly, carbon dioxide has a combined action with warm moist convection currents
Large Vessel Cerebral Atherosclerosis Is Not in Direct Association with Neuropathological Lesions of Alzheimer’s Disease

Introduction: Cerebral hypoperfusion caused by large vessel atherosclerosis has been suggested to be associated with the pathogenesis of sporadic Alzheimer’s disease (AD). Atherosclerosis and AD share risk factors such as age, diabetes, hypercholesterolemia, hypertension and apolipoprotein E ε4 (APOE ε4) allele. We studied the association between atherosclerosis of the circle of Willis (CW) and AD neuropathology in a large autopsy sample. Methods: The present study comprised a consecutive autopsy series (n = 466) representing noninstitutionalized general population aged 50 years and over (mean 70.8, SD 11.5 years). The atherosclerosis of CW was scored semiquantitatively and the amyloid plaque (AP) load in the frontal cortex and the number of neurofibrillary tangles (NFT) in the hippocampus were measured. Results: In a linear regression model, AP percentage area was associated with age (p < 0.0001) and APOE ε4 allele (p < 0.0001), but not with CW score (p = 0.70) or gender (p = 0.11). Similarly, the NFT count was predicted only by age (p > 0.0001), and not by CW score (p = 0.36), gender (p = 0.41) or APOE ε4 allele (p = 0.072). Conclusion: Our results suggest that cerebral large vessel atherosclerosis is not in direct association with APs or NFTs – hallmarks of AD neuropathology.
Stability of flat spacetime in quantum gravity.

In a previous paper, a modified effective-action formalism was developed which produces equations satisfied by the expectation value of the field, rather than the usual in-out average. Here this formalism is applied to a quantized scalar field in a background which is a small perturbation from Minkowski spacetime. The one-loop effective field equation describes the back reaction of created particles on the gravitational field, and is calculated in this paper to linear order in the perturbation. In this way we rederive an equation first found by Horowitz using completely different methods. This equation possesses exponentially growing solutions, so we confirm Horowitz's conclusion that flat spacetime is unstable in this approximation to the theory. The new derivation shows that the field equation is just as useful as the one-loop approximation to the in-out equation, contrary to earlier arguments. However, the instability suggests that the one-loop approximation cannot be trusted for gravity. These results are compared with the corresponding situation in QED and QCD.
Automated torso organ segmentation from 3D CT images using conditional random field

This paper presents a segmentation method for torso organs using conditional random field (CRF) from medical images. A lot of methods have been proposed to enable automated extraction of organ regions from volumetric medical images. However, it is necessary to adjust empirical parameters of them to obtain precise organ regions. In this paper, we propose an organ segmentation method using structured output learning which is based on probabilistic graphical model. The proposed method utilizes CRF on three-dimensional grids as probabilistic graphical model and binary features which represent the relationship between voxel intensities and organ labels. Also we optimize the weight parameters of the CRF using stochastic gradient descent algorithm and estimate organ labels for a given image by maximum a posteriori (MAP) estimation. The experimental result revealed that the proposed method can extract organ regions automatically using structured output learning. The error of organ label estimation was 6.6%. The DICE coefficients of right lung, left lung, heart, liver, spleen, right kidney, and left kidney are 0.94, 0.92, 0.65, 0.67, 0.36, 0.38, and 0.37, respectively.
Speed-up of Neuromorphic Adiabatic Quantum Computation by Local Adiabatic Evolution

Farhi et al. have proposed an adiabatic quantum computation (AQC), which can be applied to NP-problems if one can know an appropriate Hamiltonian for a target problem. We have proposed a neuromorphic adiabatic quantum computation (NAQC) as the AQC with energy dissipation and an efficient method for designing a final Hamiltonian in consideration of the analogy with a neural network. The NAQC can be applied to optimization problems if its cost function can be expressed in a quadratic form. And successful operations have been confirmed by numerical simulations. In addition, local adiabatic evolution for quantum search have proposed by Roland et al. in order to speed-up the calculation time. In this paper, we show preliminary results for NAQC with local adiabatic evolution by numerical simulations.
OFF‐alpha and OFF‐beta ganglion cells in cat retina. I: Intracellular electrophysiology and HRP stains

Six OFF‐alpha ganglion cells and a single OFF‐beta ganglion cell were penetrated with intracellular microelectodes and marked with horseradish peroxidase (HRP) in a perfused cat eyecup. Gaussian center radii (Rc) ranging from 40 to 217 μm were measured for receptive fields mapped with slits, values in agreement with previous extracellular reports. ON and OFF response components revealed nearly identical Rc's and center locations. Although Gaussian diameters (2Rc) were about 80% of dendritic field diameters overall, in this sample dendritic and receptive fields were not well correlated. Spatial tuning of ganglion cells was evidenced in peaked amplitude‐vs.‐width functions, fit by difference‐of‐Guassians models. Such plots yielded Rc values about 40% less than position‐vs amplitude plots. Rs values for surrounds ranged from 200 to 1,700 μm.
Salmonella enterica serovar Typhimurium effectors SopB, SopE, SopE2 and SipA disrupt tight junction structure and function

Salmonella enterica serovar Typhimurium is a major cause of human gastroenteritis. Infection of epithelial monolayers by S. Typhimurium disrupts tight junctions that normally maintain the intestinal barrier and regulate cell polarity. Tight junction disruption is dependent upon the Salmonella pathogenicity island‐1 (SPI‐1) type 3 secretion system but the specific effectors involved have not been identified. In this study we demonstrate that SopB, SopE, SopE2 and SipA are the SPI‐1‐secreted effectors responsible for disruption of tight junction structure and function. Tight junction disruption by S. Typhimurium was prevented by inhibiting host protein geranylgeranylation but was not dependent on host protein synthesis or secretion of host‐derived products. Unlike wild‐type S. Typhimurium, ΔsopB, ΔsopE/E2, ΔsipA, or ΔsipA/sopB mutants, ΔsopB/E/E2 and ΔsipA/sopE/E2 mutants were unable to increase the permeability of polarized epithelial monolayers, did not disrupt the distribution or levels of ZO‐1 and occludin, and did not alter cell polarity. These data suggest that SPI‐1‐secreted effectors utilize their ability to stimulate Rho family GTPases to disrupt tight junction structure and function.
Optimal impedance matching design for broadband Archimedean spiral antennas

This paper presents an optimization problem formulation to design broadband antennas with optimal impedance matching considering that the source impedance is tunable inside a range. Usually an antenna is designed to match a given source impedance, which can be too constraining. The new optimization problem formulation is introduced to answer a less strict query: which impedance is optimal for the behavior inside a frequency range of a given antenna? The formulation is used to investigate Archimedean spiral antennas.
Three-dimensional flexural-joint stiffness analysis of flexible manipulator arms

SUMMARY This paper presents a complete derivation of the combined flexural-joint stiffness matrix and the elastic deformation field of flexible manipulator arms treated in a three-dimensional fashion. The stiffness properties are derived directly from the differential equations used in the engineering beam theory. The expressions developed here can readily be used in the modeling, control and design of light weight flexible robot manipulators. A two-link arm is used to formulate these expressions and the results can be generalized to n–link manipulators. The stiffness matrix for a robotic link element in 3-D is of the order of 12 X 12, and for an n–link robotic arm the total elemental and system stiffness matrices will be of the order of the (12n X 12n) and 6(n + 1) X 6(n + 1), respectively.
Fixed-Nitrogen Loss Associated with Sinking Zooplankton Carcasses in a Coastal Oxygen Minimum Zone (Golfo Dulce, Costa Rica)

Oxygen minimum zones (OMZs) in the ocean are of key importance for pelagic fixed-nitrogen loss (N-loss) through microbial denitrification and anaerobic ammonium oxidation (anammox). Recent studies document that zooplankton is surprisingly abundant in and around OMZs and that the microbial community associated with carcasses of a large copepod species mediates denitrification. Here, we investigate the complex N-cycling associated with sinking zooplankton carcasses exposed to the steep O2 gradient in a coastal OMZ (Golfo Dulce, Costa Rica). 15N-stable-isotope enrichment experiments revealed that the carcasses of abundant copepods and ostracods provide anoxic microbial hotspots in the pelagic zone by hosting intense anaerobic N-cycle activities even in the presence of ambient O2. Carcass-associated anaerobic N-cycling was clearly dominated by dissimilatory nitrate reduction to ammonium (DNRA) at up to 30.8 nmol NH4+ individual-1 d-1, followed by denitrification (up to 10.8 nmol N2-N individual-1 d-1), anammox (up to 1.6 nmol N2-N individual-1 d-1), and N2O production (up to 1.2 nmol N2O-N individual-1 d-1). In contrast, anaerobic N-cycling mediated by free-living bacteria proceeded mainly through anammox and denitrification in the anoxic bottom water, which underpins the distinctive microbial metabolism associated with zooplankton carcasses. Pelagic N-loss is potentially enhanced by zooplankton carcasses both directly through N2 and N2O production, and indirectly through NH4+ production that may fuel free-living anammox bacteria. We estimate that in the hypoxic water layer of Golfo Dulce, carcass-associated N2 and N2O production enhance N-loss as much as 1.4-fold at a relative carcass abundance of 36%. In the anoxic bottom water, however, N-loss is likely enhanced only marginally due to high ambient rates and low zooplankton abundance. Thus, zooplankton carcasses may enhance N-loss mainly at the hypoxic boundaries of OMZs which are usually more extensive in open-ocean than in coastal settings. Notably, these contributions by zooplankton carcasses to pelagic N-loss remain undetected by conventional, incubation-based rate measurements.
Management of Alum-Treated Poultry Litter

Previous research has shown that treatment of poultry litter with alum is an effective management strategy to reduce phosphorus (P) solubility in litter thereby reducing potential P losses to surface runoff after surface applications. However, limited data are available evaluating alum-treated poultry litter (ATPL) environmental impact in cultivated systems and how its application will affect crop production. In addition little is known as to how its application affects various P fractions or exchangeable Aluminum (Al) content in treated soils. Two, 3-yr field trials with corn (Zea mays L.) were used to show that, when applied at rates based on current litter management strategies, ATPL resulted in yields similar to those achieved through applications of non-treated poultry litter (NPL). These trials also showed that ATPL applications resulted in lower soil P status and decreased P losses in surface water runoff compared to application of NPL. A 4-yr field trial with fescue (Festuca arudinacea) also showed no significant differences in productivity when comparing ATPL and NPL. This trial was utilized to evaluate the distribution of P in soils receiving ATPL. Soil analysis data showed that ATPL applications result in decreased water-extractable P (H2O-P) and that this decrease was associated with an elevation in NaOH extractable organic soil P. A laboratory incubation was utilized to evaluate the short and long-term impact of ATPL application on soil pH, exchangeable soil Al and H2O-P. Data from this incubation confirmed that the relationship between soil pH and exchangeable Al is not adversely affected by ATPL applications. Also, variations in the H2O-P content of soils treated with two different ATPL sources could not be associated with differences in Al:P ratio or soluble P content of the two litters, providing evidence that additional characteristics also control P availability after incorporation in soil.
Automated spectral analysis for pediatric cardiac auscultation

Early recognition of heart disease is an important goal in pediatrics. Developing countries have a large population of children living with undiagnosed heart murmurs. As a result of an accompanying skills shortage, most of these children will not get the necessary treatment. We designed a system for automatically detecting systolic murmurs due to a variety of conditions. This could enable health care providers in developing countries with tools to screen large amounts of children without the need for expensive equipment or specialist skills. For this purpose an algorithm was designed and tested to detect heart murmurs in digitally recorded signals. A specificity of 100% and a sensitivity of 90.57% were achieved using signal processing techniques and a k-nn as classifier.
Computational models for the prediction of intestinal membrane permeability.

Lead compounds generated in high-throughput drug discovery programs often have unfavorable biopharmaceutical properties, resulting in a low success rate for such drug candidates in clinical development. Efficient and reliable methods that predict biopharmaceutical properties, such as intestinal permeability and solubility are therefore required in order to reduce the attrition rate during development of these compounds.One aim of this thesis was to identify molecular properties that are important for intestinal drug permeability using a wide range of drugs and model compounds. A second aim was to develop computational models for predicting intestinal drug permeability based on these properties.The calculated molecular descriptors ranged from the simple counting of atoms and fragments to more complex descriptors derived from molecular mechanics and quantum mechanics calculations. Particular attention was given to descriptors associated with molecular surface areas. Descriptors calculated by the various methods were used to establish structure-permeability relationships for conventional drugs, peptide derivatives and large, lipophilic compounds generated by high-throughput pharmacological screening. Caco-2 cell monolayer permeabilities were determined for a structurally diverse set of compounds and were used to predict human intestinal membrane permeability and to develop computational models.From these investigations, several new models for the computational prediction of intestinal membrane permeability were developed. Models were developed that are suitable for the prediction of membrane permeability to specific types of drugs, as well as models that are more generally applicable. One of these general models is based on partitioned total molecular surface areas, and this model can be used to predict intestinal membrane permeability to structurally diverse compounds. It was also demonstrated how these models can be applied in a manner that increases both the accuracy of the prediction and the throughput. In addition, a simplified protocol based on Caco-2 cells for the experimental prediction of intestinal permeability was developed. These improvements can be used to construct highly effective experimental and computational filters for use in drug discovery and development.
Title : A new class of bifunctional major histocompatibility class I antibody fusion molecules to redirect CD 8 T cells

Title: A new class of bifunctional major histocompatibility class I antibody fusion molecules to redirect CD8 T cells Authors: Martina Schmittnaegel, Eike Hoffmann, Sabine Imhof-Jung, Cornelia Fischer, Georg Drabner, Guy Georges, Christian Klein, Hendrik Knoetgen Authors' Affiliations: ROCHE Pharma Research and Early Development: 1 Large Molecule Research, ROCHE Innovation Center Munich, Germany; 2 Discovery Oncology, ROCHE Innovation Center Zurich, Switzerland; 3 Therapeutic Modalities, ROCHE Innovation Center Basel, Switzerland; 4 Current Affiliation: Swiss Federal Institute of Technology Lausanne (EPFL), The Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland Corresponding Author: Hendrik Knoetgen, ROCHE Pharma Research and Early Development: Therapeutic Modalities, ROCHE Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland Phone: +41 616821959, mailto:hendrik.knoetgen@roche.com Disclosure of Potential Conflicts of Interest: All authors are or have been employees of the F. Hoffmann-La Roche AG, Switzerland or Roche Diagnostics GmbH, Germany. H. Knoetgen, S. Imhof-Jung and M. Schmittnaegel have ownership interest (including patents). Running Title: Bifunctional MHC I antibody fusions
Statistique bayésienne et applications en génétique des populations. (Bayesian statistics and applications to populations genetics)

Les approches statistiques en genetique des populations visent deux objectifs distincts qui sont la description des donnees et la possibilite d'inferer les processus evolutifs qui ont genere les patrons observes. Le premier chapitre de ce manuscrit decrit nos apports theoriques et methodologiques concernant le calcul bayesien approche (Approximate Bayesian Computation) qui permet de realiser l'objectif d'inference des processus evolutifs. Je decris des resultats asymptotiques qui permettent de decrire des proprietes statistiques du calcul bayesien approche. Ces resultats mettent en evidence a la fois l'interet des methodes dites avec ajustement qui reposent sur des equations de regression et aussi l'interet de reduire la dimension des descripteurs statistiques utilises dans le calcul bayesien approche. Je presente ensuite une methode originale de calcul bayesien approche qui permet de maniere conjointe d'effectuer des ajustements et de reduire la dimension des descripteurs statistiques. Une comparaison des differentes methodes de reduction de dimension clos le premier chapitre. Le deuxieme chapitre est consacre a l'objectif de description des donnees et se place plus particulierement dans un cadre spatial. Les methodes statistiques proposees reposent sur le concept d'isolement par la distance qui est une forme particuliere de l'autocorrelation spatiale ou la correlation entre individus decroit avec la distance. Une approche originale de krigeage nous permet de caracteriser des patrons d'isolement par la distance non-stationnaire ou la maniere avec laquelle la correlation entre individus decroit avec la distance depend de l'espace. Une deuxieme extension que nous proposons est celle d'isolement par la distance anisotrope que nous caracterisons et testons a partir d'une equation de regression. La conclusion de ce manuscrit met l'accent sur les problemes d'interpretation des resultats statistiques, l'importance de l'echantillonnage et la necessite de tester l'adequation des modeles aux donnees. Je conclus par des perspectives qui se proposent de faire passer l'analyse statistique bayesienne a l'echelle des donnees massives produites en genetique.
To Claim or Not to Claim: Estimating Non-Take-Up of Social Assistance in Germany and the Role of Measurement Error

Using representative micro data from the German Socio-Economic Panel Study (SOEP) for the year 2002, we analyse non-take-up behaviour of Social Assistance (SA) in Germany. According to our simulation as much as 67 percent of the eligible population did not claim SA in that year which is slightly higher than reported in previous work. We particularly emphasize the role of measurement error in estimating non-take-up. First, we consider misspecifications of the simulation model due, e.g., to households claiming to have received SA although not simulated as eligible ("beta-error"). Second, we employ sensitivity analyses revealing the impact of measurement errors in reported household income and wealth as well as in simulated needs. Misreported household incomes appear to have the greatest impact on the estimated non-take-up rates, as shown in Monte-Carlo-type simulations. Regression analysis of the potential determinants of non-take-up behaviour confirm that rational motives - i.e., the expected net utility from claiming - as well as stigma and other barriers play a crucial role in explaining the puzzle of large non-take-up rates of SA.
Power-law spin correlations in pyrochlore antiferromagnets

The ground state ensemble of the highly frustrated pyrochlore-lattice antiferromagnet can be mapped to a coarse-grained ``polarization'' field satisfying a zero-divergence condition From this it follows that the correlations of this field, as well as the actual spin correlations, decay with separation like a dipole-dipole interaction ($1/|R|^3$). Furthermore, a lattice version of the derivation gives an approximate formula for spin correlations, with several features that agree well with simulations and neutron-diffraction measurements of diffuse scattering, in particular the pinch-point (pseudo-dipolar) singularities at reciprocal lattice vectors. This system is compared to others in which constraints also imply diffraction singularities, and other possible applications of the coarse-grained polarization are discussed.