gebhart/patrepeval huggingface dataset:
Visual Evoked Potentials as an Early-Stage Biomarker in the rTg4510 Tauopathy Mouse Model (2023)

Our findings suggest that visual processing could be useful as a novel electrophysiological biomarker for early stages of tauopathy.
Atom‐Efficient Route for Converting Incineration Ashes into Heavy Metal Sorbents (2013)

Bottom ashes produced from municipal solid-waste incineration are suitable for sorbent synthesis because of their inherent composition, high alkalinity, metastable mineralogy, and residual heat. This work shows that bottom ashes can be atom-efficiently converted into valuable sorbents without the need for costly and hazardous chemicals. The ashes were hydrothermally treated in rotary autoclaves at autogenic pH conditions to promote the conversion of precursor mineral phases into zeolites and layered silicate hydrates. Two main mineral phases were formed: katoite and sodium aluminum phosphate silicate hydrate. These mineral alterations are accompanied by a tenfold increase in specific surface area and a twofold reduction in average particle size. Performance evaluation of the new sorbents for Cd(2+), Zn(2+), and Pb(2+) adsorption at pH5 indicates sorption capacities of 0.06, 0.08, and 0.22 mmol g(-1), respectively, which are similar to those of natural adsorbents and synthetic materials obtained from more demanding synthesis conditions.
No-Reference Image Quality Assessment Of T2-Weighted Magnetic Resonance Images In Prostate Cancer Patients (2021)

No-reference image quality assessment in magnetic resonance (MR) imaging is a challenging task due to the variable nature of these images and lack of standard quantification methods, which makes the interpretation to be almost always subjective. In this study, we propose an architecture where we: (i) extended the no-reference image quality assessment problem of MRI into a full-reference image quality assessment using unpaired generative adversarial network (GAN) and (ii) employed a weakly-supervised trained deep classifier to determine the quality of MR images by comparing each image with its synthetic higher quality reference image. Using this approach, we achieved 11.28% improvement in the accuracy of our MR image quality assessment algorithm on an independent data test with FPR in detecting low quality images, reduced from 13% to 9.6%.
Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H.pylori and P.falciparum (2005)

Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication-divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene duplications with immediate divergence alone may explain more than 60% of biological network data in both domains.
Genetic Code Expansion of the Silkworm Bombyx mori to Functionalize Silk Fiber (2018)

The genetic code in bacteria and animal cells has been expanded to incorporate novel amino acids into proteins. Recent efforts have enabled genetic code expansion in nematodes, flies, and mice, whereas such engineering is rare with industrially useful animals. In the present study, we engineered the silkworm Bombyx mori to synthesize silk fiber functionalized with azidophenylalanine. For this purpose, we developed a bacterial system to screen for B. mori phenylalanyl-tRNA synthetases with altered amino-acid specificity. We created four transgenic B. mori lines expressing the selected synthetase variants in silk glands, and found that two of them supported the efficient in vivo incorporation of azidophenylalanine into silk fiber. The obtained silk was bio-orthogonally reactive with fluorescent molecules. The results showed that genetic code expansion in an industrial animal can be facilitated by prior bacterial selection, to accelerate the development of silk fiber with novel properties.
A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer’s disease (2020)

Abstract We conducted a large multi-ethnic meta-analysis of genome-wide association studies for primary open-angle glaucoma (POAG) on a total of 34,179 cases vs 349,321 controls, and identified 127 independent risk loci, almost doubling the number of known loci for POAG. The majority of loci have broadly consistent effect across European, Asian and African ancestries. We identify a link, both genome-wide and at specific loci, between POAG and Alzheimer’s disease. Gene expression data and bioinformatic functional analyses provide further support for the functional relevance of the POAG risk genes. Several drug compounds target these risk genes and may be potential candidates for developing novel POAG treatments.
Development of computerised procedures for the characterization of the tableting properties with eccentric machines. High precision displacement instrumentation for eccentric tablet machines. (1998)

The paper deals with the instrumentation of displacement on an eccentric machine. Two instrumentation variants are evaluated. A displacement instrumentation consisting of two transducers attached to the frame was corrected for a slight non-linear calibration curve and corrected for machine deformation. A powder height signal was calculated from both signals. Upon dynamic punch to punch compression the powder height signal showed an oscillation of +/- 17 microns in amplitude due to tilting of the upper punch holder. A newly developed direct powder height instrumentation consisting of a set of special punches and a special die was also corrected for nonlinearities and punch deformation. The signal was free from any tilting effects and its accuracy is in the order of magnitude of the surface roughness of the punches. The machine deformation is discussed in detail. The instrumentation of the frame of the eccentric press in terms of force is possible but less sensitive by a factor of 5.4 than the use of the force sensors. The total machine deformation reaches nearly 0.5 mm under maximum load which is more than is often expected. The deformation was found to be non-linear for about 2% of the total deformation, the remaining 98% are linear deformation.
ChemInform Abstract: An Examination of the Scope and Stereochemistry of the Ireland—Claisen Rearrangement of Boron Ketene Acetals. (2014)

Abstract Isopropylacetates, tert‐butylacetates and acetates as well as esters of secondary alcohols fail to rearrange.
A sensitive x-ray phase contrast technique for rapid imaging using a single phase grid analyzer (2013)

Phase contrast x-ray imaging (PCXI) is a promising imaging modality, capable of sensitively differentiating soft tissue structures at high spatial resolution. However, high sensitivity often comes at the cost of a long exposure time or multiple exposures per image, limiting the imaging speed and possibly increasing the radiation dose. Here, we demonstrate a PCXI method that uses a single short exposure to sensitively capture sample phase information, permitting high speed x-ray movies and live animal imaging. The method illuminates a checkerboard phase grid to produce a fine grid-like intensity reference pattern at the detector, then spatially maps sample-induced distortions of this pattern to recover differential phase images of the sample. The use of a phase grid is an improvement on our previous absorption grid work in two ways. There is minimal loss in x-ray flux, permitting faster imaging, and, a very fine pattern is produced for homogenous high spatial resolution. We describe how this pattern permits retrieval of five images from a single exposure; the sample phase gradient images in the horizontal and vertical directions, a projected phase depth image, an edge-enhanced image, and a type of scattering image. Finally, we describe how the reconstruction technique can achieve subpixel distortion retrieval and study the behavior of the technique in regard to analysis technique, Talbot distance, and exposure time.
Experimental study of parameters affecting the sound transmission of stapes piston prosthesis using an artificial inner ear model (2019)

Since the first stapesplasty was introduced in 1956, the optimal diameter of the stapes piston was discussed controversially. Several retrospective clinical studies led to partly contradictory results which, moreover, were not in agreement with simulation results.
Optical Trapping Forces on Non-Spherical Particles in Fluid Flows (2012)

The optical stability of particles above a waveguide surface depends on the forces induced by fluid drag and the electromagnetic field. The optical trapping forces on non-spherical particles were examined for various flow conditions. A three-dimensional finite element method was employed to calculate the electromagnetic field and the fluid flow. It was found that the stability of non-spherical particles is significantly affected by the fluid velocity and the orientation of the particles. The downward trapping force meant that non-spherical particles are more stable at higher Reynolds numbers. The length of the particle in the transverse direction also had a significant impact on particle stability. The present model was tested against previously reported results.
Reviews (1996)

Wave Propagation in Petroleum Engineering by Wilson Chin, ISBN O-88415-169-7. Gulf, Houston, TX, 1994.396 p. Ocean Processes in Climate Dynamics: Global and Mediterranean Examples, edited by P. Malanotte-Rizzoli and A.R. Robinson, ISBN O-7923-2624-5. Kluwer Academic Publishers Group, The Netherlands, 1994.437 p. $176. Theory of Seismic Imaging, by John A. Scales, ISBN 3-540-59051 -X, Springer-Verlag, Berlin, and in electronic form via Samizdat Press, Colorado School of Mines. 291 p. River Geomorphology edited by E.J. Hickin, ISBN 0-471-95531-O. J Wiley &amp; Sons, New York, 1995. 255 p. $89.95. River, Coastal and Shoreline Proctection: Erosion Control Using Riprap and Armourstone, edited by C. Thome, S. Abt, F. Barends, S. Maynord, and K. Plarczyk, ISBN O-471-94235-9. J. Wiley and Sons, New York, 1995. 766 p. To Interpret the Earth - Ten Ways to be Wrong, by Stanley A. Schumm, ISBN o-521-39507-0, Cambridge University Press, Cambridge, UK, 199 1. 133 p.
Ash Plasma Exposure of Hybrid Material (SiOCH and porogen): Comparisaon with Porous SiOCH (2007)

International audience
Classification Of Material Surfaces Using The Polarization Of Specular Highlights (1989)

Recently there has been interest, in computer vision research, in the segmentation of images based upon the actual material makeup of the objects or object parts that constitute image regions. The idea is to identify image characteristics which can be used to predict the material properties of objects that are being imaged. A majority of object surfaces can be simply classified according to their basic electrical properties; metal objects (e.g. Aluminum, Copper) conduct electricity rather well while dielectric objects (e.g. Rubber, Plastic, Ceramic) conduct electricity poorly. Distinguishing image regions according to whether they correspond to metal or dielectric material can provide important information for scene understanding especially in industrial machine vision. One such major application is circuit board inspection where the presence of dielectric or metal material in the wrong place can cause trouble. A previous approach to the problem of identifying metal or dielectric material in images is based upon careful spectral (i.e. color) analysis of reflected light from material objects. This paper presents a technique for identifying the material properties of objects in an image using a polarizing lens (i.e. Polaroid filter). Two images of the same scene are taken with a polarizing lens placed in front of a camera in two different respective orientations. Effectively these two images represent two linearly independent polarization components of the reflected light. It is shown that when the linearly independent components of polarization are taken parallel and perpendicular with respect to the plane in which specular rays travel that dielectric objects can be distinguished from metallic objects when specular highlights are present. In particular the two polarization components are very similar at specular highlights on metals while the two polarization components for specular highlights on dielectrics are very different, the perpendicular component having much larger magnitude than the parallel component. This is shown to hold regardless of whether the surface is polished or rough. Results for coated surfaces will be presented at a future date.
Knowledge Extraction From Neural Networks Using the All-Permutations Fuzzy Rule Base: The LED Display Recognition Problem (2007)

A major drawback of artificial neural networks (ANNs) is their black-box character. Even when the trained network performs adequately, it is very difficult to understand its operation. In this letter, we use the mathematical equivalence between ANNs and a specific fuzzy rule base to extract the knowledge embedded in the network. We demonstrate this using a benchmark problem: the recognition of digits produced by a light emitting diode (LED) device. The method provides a symbolic and comprehensible description of the knowledge learned by the network during its training.
Unrelated partially matched lymphocyte infusions in a patient with complete DiGeorge/CHARGE syndrome (2007)

We present an infant with cDGS overlapping with CHARGE syndrome, who suffered from T-cell deficiency treated with screened healthy DLI from an unrelated donor (8/10 match). The first dose of DLI (1.1 x 10(6) CD3+/kg) was administered at the age of six months, the second one (0.9 x 10(6) CD3+/kg) 36 days later. No conditioning was employed, GvHD prophylaxis consisting of CsA was used only during the second infusion. Since day+10 after the first DLI, split chimerism showing T-cell engraftment has been documented. Proliferative response to PHA was detected on day+145. The treatment was complicated by severe acute GvHD (grade II-III) after the first DLI and prolonged chronic liver cholestatic GvHD developing after the second DLI. Vigorous EBV proliferation four wk after the second DLI was accompanied by peripheral expansion of CD8+ donor cells. The patient, 26-months old, is clinically well and has slowly started to gain his developmental milestones. We believe that infusions of small doses of DLI from an unrelated donor represent a potentially helpful therapeutic option in patients with cDGS/CHARGE phenotype.
Microstructure/property relations in YBa2Cu3O7-x powders (1989)

We have studied several samples of YBa 2 Cu 3 O 7-x superconductor with substantially differing electromagnetic characteristics in an effort to relate microstructure with superconducting properties. It is has been shown that the bulk oxygen content of the material can be related to the difference in the a and b lattice parameters which has a linear relationship with the bulk T c value. Bulk measurements of electronic properties may be misleading as they are complicated by the presence of weak-links in the forms of inter- or intra- granular phases or even oxygen poor regions within a single grain. The samples used were all prepared with the same starting materials but subject to heat treatments which varied the 950°C sintering time and the partial pressure of oxygen in the furnace atmosphere. All of the samples had nominally identical x-ray diffraction patterns (e.g., equivalent bulk Δa/a values as measured by the (103)-(013)/(110) peak splitting) but showed markedly different superconducting properties as measured by the inductance-flux exclusion technique.
32.1 Gbit/s InverseRZ-ASK-DQPSK Modulation with Low Implementation Penalty (2006)

32.1 Gbit/s InverseRZ-ASK-DQPSK is experimentally investigated using a new InverseRZ generation method. We demonstrate <1 dB upgrade penalty from 21.4 Gbit/s RZ-DQPSK, and <2 dB transmission penalty after one 75 km fibre span
Sex ratio and adult behaviour of the Antarctic midge Belgica antarctica (Diptera, Chironomklae) (1981)

Abstract. 1. The sex ratio in populations of the Antarctic chironomid Belgica antarctica approximates 1:1 at eclosion. 2. Male predominance in surface populations of the short‐lived adult persists throughout the summer. The mean ratio, based on data from surface aggregations (austral summer 1977–78) and from sticky traps (1978–79) is about 6:1, with a steady seasonal decline from 10–20:1 to 2–5:1. 3. Males live slightly longer than females but the difference does not account for observed ratios. 4. Samples of adult populations taken from subsurface sites have sex ratios nearer to equality than surface populations. 5. It is concluded that the male‐dominated surface populations are equivalent to the male swarms typical of winged Chironomidae. 6. Capture of airborne adults shows that aerial transport as well as water‐surface rafting may play a role in dispersal of adults.
Clinical experience with microdialysis catheters in pediatric liver transplants (2013)

Ischemic vascular complications and rejection occur more frequently with pediatric liver transplants versus adult liver transplants. Using intrahepatic microdialysis catheters, we measured lactate, pyruvate, glucose, and glycerol values at the bedside for a median of 10 days in 20 pediatric liver grafts. Ischemia (n = 6), which was defined as a lactate level > 3.0 mM and a lactate/pyruvate ratio > 20, was detected without a measurable time delay with 100% sensitivity and 86% specificity. Rejection (n = 8), which was defined as a lactate level > 2.0 mM and a lactate/pyruvate ratio < 20 lasting for 6 or more hours, was detected with 88% sensitivity and 45% specificity. With additional clinical criteria, the specificity was 83% without a decrease in the sensitivity. Rejection was detected at a median of 4 days (range = 1-7 days) before alanine aminotransferase increased (n = 5, P = 0.11), at a median of 4 days (range = 2-9 days) before total bilirubin increased 25% or more (n = 7, P = 0.04), and at a median of 6 days (range = 4-11 days) before biopsy was performed (n = 8, P = 0.05). In conclusion, microdialysis catheters can be used to detect episodes of ischemia and rejection before current standard methods in pediatric liver transplants with clinically acceptable levels of sensitivity and specificity. The catheters were well tolerated by the children, and no major complications related to the catheters were observed.
Immunotherapy for HCV infection: next steps (2008)

With more than 170 million individuals currently infected, HCV is a global pandemic, effecting approximately 3% of the entire world's population. HCV infection is a growing infectious disease pandemic with approximately 3-4 million new cases reported each year. Due to the persistent nature of the virus, 70-90% of infected individuals will develop chronic infection, which can lead to progressive liver disease including cirrhosis and hepatocellular carcinoma. Current standard treatment with a combination of IFN-alpha and ribavirin has improved the prognosis for many HCV sufferers; however, infection is very difficult to treat successfully and the protocol for treatment is neither simple, well tolerated nor economically favorable. Standard treatment can cost an average of US$22,000, and depending on genotype, as few as 42% of treated individuals will clear the infection. This collection of treatment issues combined with new concepts in immune therapy serve to underscore an urgent need for the development of improved immunotherapies, such as novel interferons, and support the possible development of therapeutic vaccines for the treatment of chronic HCV infection.
Prevalence and Risk Factors for Diabetic Retinopathy in the Multiethnic Population of Mauritius (1998)

This study examines the prevalence of, and risk factors for, diabetic retinopathy in Asian Indian, Chinese, and Creole Mauritians in whom there is an increasing prevalence of non-insulin-dependent diabetes mellitus (NIDDM). As part of a population-based survey on the Indian Ocean island of Mauritius in 1992, glucose tolerance was classified using a 75-g oral glucose tolerance test on 6,553 persons. Subjects with newly diagnosed (n = 358) or known diabetes (n = 388), and a random sample of one in four subjects with impaired glucose tolerance (n = 165), had stereoscopic 45 degrees retinal photographs taken of three fields in the right eye after mydriasis. Photographs were graded according to a modified version of the Airlie House criteria. The prevalence of nonproliferative and proliferative retinopathy was: 14.5% and 0.3%, respectively, in newly diagnosed diabetic subjects; 42.0% and 2.3%, respectively, in known diabetic subjects; and 9.1% and 0%, respectively, in persons with impaired glucose tolerance. Muslim Indians had the lowest prevalence of retinopathy (10.8% and 34.0% for new and known diabetes, respectively), but after adjusting for other factors, this was significantly different only to Creoles (18.8% and 53.8%, respectively). Univariate analysis revealed significant differences between diabetic subjects with and without retinopathy in mean age, body mass index, fasting and 2-hour plasma glucose levels, systolic and diastolic blood pressure, fasting triglycerides, serum creatinine, and urinary albumin levels. For known diabetes, mean duration of diabetes and the proportion using insulin were also greater in those with retinopathy. Multivariate analysis using logistic regression confirmed that increasing duration of diabetes, fasting plasma glucose, systolic blood pressure, and urinary albumin concentration, and decreasing body mass index, were independently associated with retinopathy. The high prevalence of diabetic retinopathy observed in all major ethnic groups in Mauritius portends a serious public health problem, given the relative recency of the NIDDM epidemic in that country and the limited resources for laser photocoagulation. Strategies to minimize this problem among those already known to have diabetes should include strict control of plasma glucose and blood pressure.