gebhart/patrepeval huggingface dataset:
Diabetic retinopathy and ultrawide field imaging (2020)

The introduction of ultrawide field imaging has allowed the visualization of approximately 82% of the total retinal area compared to only 30% using 7-standard field Early Treatment Diabetic Retinopathy (ETDRS) photography. This substantially wider field of view, while useful in many retinal vascular diseases, is particularly important in diabetic retinopathy where eyes with predominantly peripheral lesions or PPL have been shown to have significantly greater progression rates compared to eyes without PPL. In telemedicine settings, ultrawide field imaging has substantially reduced image ungradable rates and increased rate of disease identification allowing care to be delivered more effectively. Furthermore, the use of ultrawide field fluorescein angiography allows the visualization of significantly more diabetic retinal lesions and allows more accurate quantification of total retinal nonperfusion, with potential implications in the management of diabetic retinopathy and diabetic macular edema. The focus of this paper is to review the current role of ultrawide field imaging in diabetic retinopathy and its possible future role in innovations for retinal image analysis such as artificial intelligence and vessel caliber measurements.
UWB-aided GNSS/INS Fusion for Resilient Positioning in GNSS Challenged Environments (2023)

The fusion of Inertial Navigation System (INS) and Global Navigation Satellite System (GNSS) is a well established technique to provide resilient positioning even in GNSS chal-lenged environments. However, when GNSS reception conditions are persistently degraded, the inherent drift of inertial navigation can result in insufficient accuracy (e.g. greater than 1m), especially when using industrial or tactical grade Inertial Measurement Unit (IMU). This study introduces the tightly coupled integration of Ultra-Wideband (UWB) ranging measurements with fixed beacons to a loosely coupled GNSS/INS fusion. The algorithm uses an Error-State Kalman Filter (ES-KF) that supports Velocity Constraints (VC) and Zero-Angular Rate Updates (ZARU)/Zero Velocity Updates (ZVU). It details the necessary pre-processing of UWB measurements to correct for clock drift, velocity and latency errors, and provides two calibration techniques suitable for guided and generic use cases, resulting in ranging accuracy of better than 3cm and 11cm, respectively, based on 28 field tests. The benefits of UWB measurements in fusion are demonstrated through a field trial with severely degraded GNSS conditions, resulting in horizontal accuracy better than 40cm (compared to 2.1m without UWB) and improved rejection of poor GNSS measurements.
The importance of the magnesium transporter MgtB for virulence of Yersinia pseudotuberculosis and Yersinia pestis (2014)

Mg(2+) has been shown to be an important signal controlling gene regulation via the PhoPQ two-component regulatory system for a range of Gram-negative bacteria, including Yersinia pestis and Yersinia pseudotuberculosis. The magnesium ion transporter MgtB is part of the complex PhoPQ regulon, being upregulated in response to low Mg(2+). Despite the presence of other Mg(2+) transport systems in Yersinia, inactivation of mgtB had a significant effect on the ability of the bacteria to scavenge this crucial ion. Whereas inactivation of PhoPQ is reported to adversely affect intracellular survival, we show that Y. pestis and Y. pseudotuberculosis ΔmgtB mutants survived equally as well as the respective parent strain within macrophages, although they were more sensitive to killing in the Galleria model of infection. Surprisingly, despite MgtB being only one member of the Mg(2+) stimulon and PhoPQ controlling the expression levels of a range of genes including mgtB, the Yersinia ΔmgtB mutants were more highly attenuated than the equivalent Yersinia ΔphoP mutants in mouse models of infection. MgtB may be a suitable target for development of novel antimicrobials, and investigation of its role may help elucidate the contribution of this component of the PhoPQ regulon to pathogenesis.
Lactobacillus paracasei CBA L74 Metabolic Products and Fermented Milk for Infant Formula Have Anti-Inflammatory Activity on Dendritic Cells In Vitro and Protective Effects against Colitis and an Enteric Pathogen In Vivo (2014)

The rapid expansion of commercially available fermented food products raises important safety issues particularly when infant food is concerned. In many cases, the activity of the microorganisms used for fermentation as well as what will be the immunological outcome of fermented food intake is not known. In this manuscript we used complex in vitro, ex-vivo and in vivo systems to study the immunomodulatory properties of probiotic-fermented products (culture supernatant and fermented milk without live bacteria to be used in infant formula). We found in vitro and ex-vivo that fermented products of Lactobacillus paracasei CBA L74 act via the inhibition of proinflammatory cytokine release leaving anti-inflammatory cytokines either unaffected or even increased in response to Salmonella typhimurium. These activities are not dependent on the inactivated bacteria but to metabolic products released during the fermentation process. We also show that our in vitro systems are predictive of an in vivo efficacy by the fermented products. Indeed CBA L74 fermented products (both culture medium and fermented milk) could protect against colitis and against an enteric pathogen infection (Salmonella typhimurium). Hence we found that fermented products can act via the inhibition of immune cell inflammation and can protect the host from pathobionts and enteric pathogens. These results open new perspectives in infant nutrition and suggest that L. paracasei CBA L74 fermented formula can provide immune benefits to formula-fed infants, without carrying live bacteria that may be potentially dangerous to an immature infant immune system.
PUNS (Haas Chances Emulation) (2018)

And now what next? A pun?
General description of the wireless miniature NanoWalker robot designed for atomic-scale operations (2001)

The NanoWalker is a miniature wireless instrumented robot designed for high-speed autonomous operations down to the atomic scale. As such, it requires very advanced electro-mechanical specifications and complex embedded sub-systems. The locomotion is based on three piezo-ceramic legs that are modulated at high frequencies to achieve several thousand steps per second with computer-controlled step sizes ranging from a few tenths of nanometers to a few micrometers. Each robot has an onboard 48 MIPS computer based on a digital signal processor (DSP) and 4 Mb/s half-duplex infrared communication system. A special instrument interface has been embedded in order to allow positioning capability at the atomic scale and sub-atomic operations within a 200 nanometer surface area using a scanning tunneling microscope (STM) tip. The design allows 200,000 STM-based measurements per second. In this paper, we describe the many sub-systems and the approaches used to successfully integrate them onto such a miniature robot.
IMPACT OF OBESITY ON THE CLINICAL OUTCOMES OF SPINAL SURGERY BY TRANSPSOAS LATERAL FUSION (2022)

ABSTRACT Introduction: Obesity is a global phenomenon that affects the quality of life of the population. In addition to being a factor that can lead to cases of degeneration in the spine, it can also influence the clinical outcomes of spine surgeries. However, with the development of minimally invasive techniques, the impact of obesity has become uncertain. Methods: A single-center, non-randomized, comparative, observational study, here clinical and surgical outcomes and postoperative complications were analyzed between obese and non-obese patients undergoing LLIF surgery. Results: There was no difference between surgical times and blood loss between the groups; the number of postoperative complications was similar. Both groups showed significant improvement in clinical parameters, but there was no difference between the amount of improvement between the obese and non-obese groups. Conclusion: The present study demonstrated that LLIF is a safe and effective technique regardless of the patient’s degree of obesity. Level of Evidence III; Retrospective study.
CCDC 1587130: Experimental Crystal Structure Determination (2017)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Transition from poor ductility to room-temperature superplasticity in a nanostructured aluminum alloy (2018)

Recent developments of nanostructured materials with grain sizes in the nanometer to submicrometer range have provided ground for numerous functional properties and new applications. However, in terms of mechanical properties, bulk nanostructured materials typically show poor ductility despite their high strength, which limits their use for structural applications. The present article shows that the poor ductility of nanostructured alloys can be changed to room-temperature superplastisity by a transition in the deformation mechanism from dislocation activity to grain-boundary sliding. We report the first observation of room-temperature superplasticity (over 400% tensile elongations) in a nanostructured Al alloy by enhanced grain-boundary sliding. The room-temperature grain-boundary sliding and superplasticity was realized by engineering the Zn segregation along the Al/Al boundaries through severe plastic deformation. This work introduces a new boundary-based strategy to improve the mechanical properties of nanostructured materials for structural applications, where high deformability is a requirement.
Kinetic Control in Assembly of Plasmid DNA/Polycation Complex Nanoparticles (2019)

Polyelectrolyte complex (PEC) nanoparticles assembled from plasmid DNA (<i>p</i>DNA) and polycations such as linear polyethylenimine (<i>l</i>PEI) represent a major nonviral delivery vehicle for gene therapy tested thus far. Efforts to control the size, shape, and surface properties of <i>p</i>DNA/polycation nanoparticles have been primarily focused on fine-tuning the molecular structures of the polycationic carriers and on assembly conditions such as medium polarity, pH, and temperature. However, reproducible production of these nanoparticles hinges on the ability to control the assembly kinetics, given the nonequilibrium nature of the assembly process and nanoparticle composition. Here we adopt a kinetically controlled mixing process, termed flash nanocomplexation (FNC), that accelerates the mixing of <i>p</i>DNA solution with polycation <i>l</i>PEI solution to match the PEC assembly kinetics through turbulent mixing in a microchamber. This achieves explicit control of the kinetic conditions for <i>p</i>DNA/<i>l</i>PEI nanoparticle assembly, as demonstrated by the tunability of nanoparticle size, composition, and <i>p</i>DNA payload. Through a combined experimental and simulation approach, we prepared <i>p</i>DNA/<i>l</i>PEI nanoparticles having an average of 1.3 to 21.8 copies of <i>p</i>DNA per nanoparticle and average size of 35 to 130 nm in a more uniform and scalable manner than bulk mixing methods. Using these nanoparticles with defined compositions and sizes, we showed the correlation of <i>p</i>DNA payload and nanoparticle formulation composition with the transfection efficiencies and toxicity <i>in vivo</i>. These nanoparticles exhibited long-term stability at -20 °C for at least 9 months in a lyophilized formulation, validating scalable manufacture of an off-the-shelf nanoparticle product with well-defined characteristics as a gene medicine.
A Unified Bayesian Framework for Sparse Non-negative Matrix Factorization (2016)

In this work, we study the sparse non-negative matrix factorization (Sparse NMF or S-NMF) problem. NMF and S-NMF are popular machine learning tools which decompose a given non-negative dataset into a dictionary and an activation matrix, where both are constrained to be non-negative. We review how common concave sparsity measures from the compressed sensing literature can be extended to the S-NMF problem. Furthermore, we show that these sparsity measures have a Bayesian interpretation and each one corresponds to a specific prior on the activations. We present a comprehensive Sparse Bayesian Learning (SBL) framework for modeling non-negative data and provide details for Type I and Type II inference procedures. We show that efficient multiplicative update rules can be employed to solve the S-NMF problem for the penalty functions discussed and present experimental results validating our assertions.
Biochemical analysis of the immune B cell defect in xid mice (1991)

Previous studies have shown that B cells from xid immune defective CBA/N mice that are unresponsive do not proliferate after stimulation with unconjugated anti-Ig. The experiments in this manuscript demonstrate that dextran-anti-Ig conjugates, which induce extensive and prolonged sIg cross-linking, are able to stimulate proliferation of xid B cells. The ability of these conjugates to stimulate proliferation of xid B cells is not related to their ability to stimulate higher levels of PIP2 breakdown. Thus, high concentrations of unconjugated anti-Ig antibody, which are nonmitogenic for xid B cells, stimulate higher levels of PIP2 breakdown and of calcium transients than lower concentrations of dextran-conjugated anti-Ig, which are mitogenic. Although unconjugated anti-Ig does not provide a fully competent signal to stimulate proliferation of xid B cells, it induces a sufficiently stimulatory signal to enable them to enter DNA synthesis in the presence of the protein kinase C activator, indolactam. This suggests that the extent or duration of activation of protein kinase C by anti-Ig may be limiting in xid B cells. To examine whether another recently described pathway of B cell activation is defective in these mice, we studied the induction of early anti-Ig-mediated tyrosine kinase activity in xid B cells. Both unconjugated and dextran-conjugated anti-Ig antibody stimulated comparable but not identical patterns of tyrosine phosphorylation. These data taken together with other findings that the combination of phorbol ester and calcium ionophore stimulates high levels of proliferation in xid B cells suggests that the immune defect of xid B cells may be distal to surface Ig-mediated activation of tyrosine kinase and of PIP2 breakdown but proximal to PKC activation. Alternatively, the xid immune defect may not result from abnormalities in the early signal transduction pathways, but rather from more distal and/or as yet undefined pathways leading to B cell activation.
Histone deacetylase 6 inhibition improves memory and reduces total tau levels in a mouse model of tau deposition (2014)

Potential mechanisms by which HDAC6 inhibitors might benefit the rTg4510 mouse include stabilization of microtubules secondary to increased tubulin acetylation, increased degradation of tau secondary to increased acetylation of HSP90 or both. These data support the use of HDAC6 inhibitors as potential therapeutic agents against tau pathology.
The Molecular and Microbial Microenvironments in Chronically Diseased Lungs (2019)

Abstract To visualize the personalized distributions of pathogens, chemical environments including microbial metabolites, pharmaceuticals, and their metabolic products within and between human lungs afflicted with cystic fibrosis, we generated 3D microbiome and metabolome maps of six explanted lungs from three cystic fibrosis patients. These 3D spatial maps revealed that the chemical environments are variable between patients and within the lungs of each patient. Although the patients’ microbial ecosystems were defined by the dominant pathogen, their chemical diversity was not. Additionally, the chemical diversity between locales in lungs of the same individual sometimes exceeded inter-individual variation. Thus, the chemistry and microbiome of the explanted lungs appear to be not only personalized but also regiospecific. Previously undescribed analogs of microbial quinolones and antibiotic metabolites were also detected. Furthermore, mapping the chemical and microbial distributions allowed visualization of microbial community interactions, such as increased production of quorum sensing quinolones in locations where Pseudomonas was in contact with Staphylococcus and Granulicatella , consistent with in vitro observations of bacteria isolated from these patients. Visualization of microbe-metabolite associations within a host organ in early-stage CF disease in animal models will help elucidate a complex interplay between the presence of a given microbial structure, antibiotics, metabolism of antibiotics, microbial virulence factors, and host responses. Importance Microbial infections are now recognized to be polymicrobial and personalized in nature. A comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remains limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we describe how different the chemical environments are between hosts that are dominated by the same pathogen and how community interactions shape the chemical environment, or vice versa. We highlight that three-dimensional organ mapping are hypothesis building tools that allow us to design mechanistic studies aimed at addressing microbial responses to other microbes, the host, and pharmaceutical drugs.
Fiducial-Less Compensation of Breathing Motion in Extracranial Radiosurgery (2006)

Tumors located in the chest and abdomen are often treated by using percutaneous radiation therapy. When radiosurgical methods are applied to these tumors, it is necessary to take into account respiratory motion, which may cause the tumor to shift its position by 1 cm or more. Without compensation of this motion, it is unavoidable to enlarge the target volume by a safety margin. Thus, healthy tissue is also affected by radiation and therefore lower doses must be used to spare healthy tissue. This thesis describes a new concept, enabling a prediction of the position of the tumor at a certain time without using fiducial markers. The implantation of these markers means an encumbering operation for the patient and the medical staff. By matching periodically taken X-ray images to a computed volumetric deformation model, the respiratory state and thus the position of the target can be determined. As this registration cannot be performed in real-time, infrared emitters are attached to the patient's chest and abdomen to report information on the current state of respiration. The information of the sensor is correlated to the target location computed by the comparison between the X-ray image and the model. Thus, a complete correlation model between external and internal motion is acquired, without using any implanted fiducials. The main focus of this work lies on the process of creating the volumetric deformation model, which is based on corresponding anatomical landmarks selected in two volume scans, one taken during maximal inhalation one taken during maximal exhalation. A method for fully automatic detection of corresponding anatomical landmarks in volume scans taken at the two different respiratory states was developed. Furthermore, new techniques for labeling computed tomography images with respiratory states are introduced, enabling evaluation of the computed models. The suggested method for computing volumetric deformation models was evaluated on six patient data sets, five concerning the lung and one the liver. Surface distance measurements of the particular segmented organ of the scan to be deformed and the reference scan, as well as visual inspections on corresponding image slices, yielded high accuracy. Moreover, the feasibility of determining the respiratory state by comparison of an X-ray image to the model was successfully demonstrated by using digitally reconstructed radiographs.
Preparation and characterization of long-lived molecular Rydberg states: Application to HD (1996)

The decay dynamics by predissociation and rotational autoionization of high Rydberg states of HD close to the first few rotational levels of the ground vibronic state of the HD+ cation have been studied by delayed pulsed field ionization following resonant (1+1′) two-photon absorption via the B state. Although predissociation and autoionization both contribute to the rapid decay of Rydberg states with principal quantum number n≪100, the highest Rydberg states (n≳100) are stable for more than 20 μs. In contrast to H2, channels associated with an HD+ (v+=0, N+=even) ion core are coupled to channels associated with an HD+ (v+=0, N+=odd) ion core. We demonstrate that complex resonances that arise from rotational channel interactions between low (n∼25) Rydberg states characterized by a core with rotational angular momentum quantum number N++2 and the pseudocontinuum of very high Rydberg states characterized by an N+ core can be used with high efficiency to produce long-lived high Rydberg states. An investigation of the pulsed field ionization characteristics of these complex resonances enables us to measure the branching between diabatic and adiabatic field ionization and to determine the optimal conditions required to extend the method of H-photofragment Rydberg translational spectroscopy pioneered by Schnieder et al. [J. Chem. Phys. 92, 7027 (1990)] to molecular species.
Determination of chromium in catalysts by ultraviolet/visible spectrophotometry (1991)

Instrumental neutron-activation analysis (INAA), atomic absorption spectrometry (AAS) and ultraviolet/visible (UV/VIS) spectrophotometry were applied as independent methods to the determination of chromium in Phillips-type polymerization catalysts. Catalysts were prepared in the gas phase, using chromium oxychloride vapour as the adsorbate and silica as the support. From freshly prepared catalysts, chromium was quantitatively brought into solution with de-ionized water, enabling its rapid determination as chromate by UV/VIS spectrophotometry. The use of INAA and AAS in addition to UV/VIS spectrophotometry allowed the quantitative nature of the release of chromium from silica with de-ionized water to be verified, the accuracy of the chromium determination to be checked and the speciation of chromium between the oxidation states +3 and +6 to be determined.
Accurate analysis of whispering gallery modes in dielectric resonators with BoR FDTD method (2018)

This paper presents an accurate approach to FDTD analysis of whispering gallery modes in dielectric resonators. In those problems resonant frequencies are supposed to be extracted with relative errors below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> . It is widely believed that only custom - made software codes, based on mode matching methods, can meet such stringent accuracy requirements. Herein, we demonstrate how the required accuracy can be obtained with a general - purpose FDTD code, run within a new three - step procedure. Advantages of the FDTD approach include more flexibility in modelling scenarios with unusual shapes or / and lossy materials.