gebhart/patrepeval huggingface dataset:
How to determine the permeability for cement infiltration of osteoporotic cancellous bone (2003)

Cement augmentation is an emerging surgical procedure in which bone cement is used to infiltrate and reinforce osteoporotic vertebrae. Although this infiltration procedure has been widely applied, it is performed empirically and little is known about the flow characteristics of cement during the injection process. We present a theoretical and experimental approach to investigate the intertrabecular bone permeability during the infiltration procedure. The cement permeability was considered to be dependent on time, bone porosity, and cement viscosity in our analysis. In order to determine the time-dependent permeability, ten cancellous bone cores were harvested from osteoporotic vertebrae, infiltrated with acrylic cement at a constant flow rate, and the pressure drop across the cores during the infiltration was measured. The viscosity dependence of the permeability was determined based on published experimental data. The theoretical model for the permeability as a function of bone porosity and time was then fit to the testing data. Our findings suggest that the intertrabecular bone permeability depends strongly on time. For instance, the initial permeability (60.89 mm(4)/N(*)s) reduced to approximately 63% of its original value within 18 seconds. This study is the first to analyze cement flow through osteoporotic bone. The theoretical and experimental models provided in this paper are generic. Thus, they can be used to systematically study and optimize the infiltration process for clinical practice.
Functionalized Mesoporous Silicas Direct Structural Polymorphism of Amyloid-β Fibrils (2020)

Abstract The aggregation of Amyloid-β (Aβ) is associated with the onset of Alzheimer’s Disease (AD) and involves a complex kinetic pathway as monomers self-assemble into fibrils. A central feature of amyloid fibrils is the existence of multiple structural polymorphs, which complicates the development of disease-relevant structure-function relationships. Developing these relationships requires new methods to control fibril structure. In this work, we demonstrate that mesoporous silicas (SBA-15) functionalized with hydrophobic (SBA-PFDTS) and hydrophilic groups (SBA-PEG) direct the aggregation kinetics and resulting structure of Aβ 1-40 fibrils. The hydrophilic SBA-PEG had little effect on amyloid kinetics while as-synthesized and hydrophobic SBA-PFDTS accelerated aggregation kinetics. Subsequently, we quantified the relative population of fibril structures formed in the presence of each material using electron microscopy. Fibrils formed from Aβ 1-40 exposed to SBA-PEG were structurally similar to control fibrils. In contrast, Aβ 1-40 incubated with SBA-15 or SBA-PFDTS formed fibrils with shorter cross-over distances that were more structurally representative of fibrils found in AD patient-derived samples. Overall, these results suggest that mesoporous silicas and other exogenous materials are promising scaffolds for the de novo production of specific fibril polymorphs of Aβ 1-40 and other amyloidogenic proteins. Significance Statement A major challenge in understanding the progression of Alzheimer’s Disease lies in the various fibril structures, or polymorphs, adopted by Amyloid-β (Aβ). Heterogenous fibril populations may be responsible for different disease phenotypes and growing evidence suggests that Aβ fibrils formed in vitro are structurally distinct from patient-derived fibrils. To help bridge this gap, we used surface-functionalized mesoporous silicas to influence the formation of Aβ 1-40 fibrils and evaluated the distribution of resulting fibril polymorphs using electron microscopy (EM). We found that silicas modified with hydrophobic surfaces resulted in fibril populations with shorter cross-over distances that are more representative of Aβ fibrils observed ex vivo . Overall, our results indicate that mesoporous silicas may be leveraged for the production of specific Aβ polymorphs.
Organic wavelength selective mirrors for luminescent solar concentrators (2012)

Organic polymeric chiral nematic liquid crystalline (cholesteric) wavelength selective mirrors can increase the efficiency of luminescent solar concentrators (LSCs) when they are illuminated with direct sunlight normal to the device. However, due to the angular dependence of the reflection band, at larger incidence angles the cholesterics reflect away some incoming sunlight that could have been absorbed by the luminophore. As a result, the increase in LSC efficiency after application of a cholesteric reflector drops if the light incident to the device is at angles larger than 30 degrees. The cholesteric reflectors still have a positive impact on device performance for light incident up to 45-50 degrees but at larger angles efficiency decreases when a cholesteric reflector is added. This affects the performance of the LSC device when illuminated with indirect incident light, especially when the incident light has a large contribution of photons above 45 degrees.
On the behavior of several fitness functions for genetically optimized microstrip antennas (2015)

Genetic algorithm (GA) is a popular optimization technique used in the design of performance improved microstrip patch antennas (MPAs). The fitness function plays a vital role in the successful application of GA in MPAs.Â This paper investigates the performance of several fitness functions for achieving bandwidth improved MPAs.
A toxic friend: Genotoxic and mutagenic activity of the probiotic strain Escherichia coli Nissle 1917 (2021)

Abstract The probiotic Escherichia coli strain Nissle 1917 (DSM 6601, Mutaflor), generally considered as beneficial and safe, has been used for a century to treat various intestinal diseases. However, Nissle 1917 hosts in its genome the pks pathogenicity island that codes for the biosynthesis of the genotoxin colibactin. Colibactin is a potent DNA alkylator, suspected to play a role in colorectal cancer development. We show in this study that Nissle 1917 is functionally capable of producing colibactin and inducing interstrand crosslinks in the genomic DNA of epithelial cells exposed to the probiotic. This toxicity was even exacerbated with lower doses of the probiotic, when the exposed cells started to divide again but exhibited aberrant anaphases and increased gene mutation frequency. DNA damage was confirmed in vivo in mouse models of intestinal colonization, demonstrating that Nissle 1917 produces the genotoxin in the gut lumen. Although it is possible that daily treatment of adult humans with their microbiota does not produce the same effects, administration of Nissle 1917 as a probiotic or as a chassis to deliver therapeutics might exert long term adverse effects and thus should be considered in a risk versus benefit evaluation. Importance Nissle 1917 is sold as a probiotic and considered safe even though it is known since 2006 that it encodes the genes for colibactin synthesis. Colibactin is a potent genotoxin that is now linked to causative mutations found in human colorectal cancer. Many papers concerning the use of this strain in clinical applications ignore or elude this fact, or misleadingly suggest that Nissle 1917 does not induce DNA damage. Here, we demonstrate that Nissle 1917 produces colibactin in vitro and in vivo and induces mutagenic DNA damage. This is a serious safety concern that must not be ignored, for the interests of patients, the general public, health care professionals and ethical probiotic manufacturers.
Supplementary Figure 2 from The OPCML Tumor Suppressor Functions as a Cell Surface Repressor–Adaptor, Negatively Regulating Receptor Tyrosine Kinases in Epithelial Ovarian Cancer (2023)

&lt;p&gt;PDF file - 93K&lt;/p&gt;
deepCEST: 9.4 T spectral super resolution from 3 T CEST MRI data: optimization of network architectures (2019)

Different neural network architectures for predicting 9T CEST contrasts from 3T spectral data are investigated as well as the influence of different training data sets on the quality of resulting predictions. Although optimized convolutional neural network (CNN) architectures perform well, the best results were reached with a simpler feedforward neural network (FFNN). As CNNs have many hyperparameters to tune, this work forms a basis for CNN architecture optimization for the proposed super-resolution CEST application.
A Power Optimized Transconductance Amplifier and its Application to a LowPass 6th order GmC Filter (2009)

International audience
Removal of Contaminant DNA by Combined UV-EMA Treatment Allows Low Copy Number Detection of Clinically Relevant Bacteria Using Pan-Bacterial Real-Time PCR (2015)

We investigated the efficacy of ethidium monoazide (EMA) and propidium monoazide (PMA) treatment as emerging methods for the decontamination of PCR reagents. Both treatments were able to inactivate contaminating microbial DNA but only at concentrations that considerably affected assay sensitivity. Increasing amplicon length improved EMA/PMA decontamination efficiency but at the cost of assay sensitivity. The same was true for UV exposure as an alternative decontamination strategy, likely due to damage sustained by oligonucleotide primers which were a significant source of contamination. However, a simple combination strategy with UV-treated PCR reagents paired with EMA-treated primers produced an assay capable of two genome copy detection and a <5% contamination rate. This decontamination strategy could have important utility in developing improved pan-bacterial assays for rapid diagnosis of low pathogen burden conditions such as in the blood of patients with suspected blood stream infection.
Improving the power, bandwidth, and latency performance of UAV-based imaging systems by structural computation methods (2007)

In this paper we present a new method of compressing and decompressing video streams directly on video sensors and display panels, without the use of on-board or independent DSP processors. This eliminates compression/decompression processing delays, minimizes power use, reduces the physical size of the system, and significantly reduces the bandwidth required for the live transmission of images. The method enhances the capabilities of small size surveillance systems, UAVs as well as battery powered mobile entertainment equipment (digital cameras, iPODs, camcorders, camera cell phones...). To achieve these goals we make structural changes to the camera and display sub-system architectures so they can directly process the compressed streams. In particular, we geometrically distribute the light detection and generation elements to correspond to the DCT and ICT coefficients of the JPEG/MPEG algorithm. This eliminates many system redundancies which in turn deliver the aforementioned performance improvements.
ChemInform Abstract: N‐Heterocyclic Carbene Catalyzed Oxidative Stannylation of Aldehydes: A Facile Entry to Organotin(IV) Carboxylates. (2013)

Abstract Aerobic oxidation followed by stannylation of the resulting carboxylic acids allows the preparation of the target compounds.
Mucoromycotina fine root endophyte fungi form nutritional mutualisms with vascular plants (2019)

Abstract Fungi and plants have engaged in intimate symbioses that are globally widespread and have driven terrestrial biogeochemical processes since plant terrestrialisation &gt;500 Mya. Recently, hitherto unknown nutritional mutualisms involving ancient lineages of fungi and non-vascular plants have been discovered. However, their extent and functional significance in vascular plants remains uncertain. Here, we provide first evidence of abundant carbon-for-nitrogen exchange between an early-diverging vascular plant (Lycopodiaceae) and Mucoromycotina (Endogonales) fine root endophyte regardless of changes in atmospheric CO 2 concentration. Furthermore, we provide evidence that the same fungi also colonize neighbouring non-vascular and flowering plants. These findings fundamentally change our understanding of the evolution, physiology, interrelationships and ecology of underground plant-fungal symbioses in terrestrial ecosystems by revealing an unprecedented nutritional role of Mucoromycotina fungal symbionts in vascular plants.
Ellipsometric studies of sputtered silicon nitride on n-GaAs (1982)

Ellipsometry, which is the study of optical systems through their effect on polarized light, is a nondestructive technique offering extremely high sensitivity and in situ operation. One of the intriguing possibilities is to make use of the high sensitivity of ellipsometry for studying the very thin interface between an insulating film and a semiconductor substrate. Researchers have been especially interested in native or anodic oxides. In a recent study, Aspnes and Theeten used ellipsometry to study the interface between silicon and its thermally grown oxide, SiO2. These authors were able to conclude that the interface consisted of a 7 +/- 2 A graded region of atomically mixed silicon and oxygen. In this paper we report both analysis and experimental results for the system: sputtered silicon nitride on (100) n-type gallium arsenide.
NeFSAC: Neurally Filtered Minimal Samples (2022)

Since RANSAC, a great deal of research has been devoted to improving both its accuracy and run-time. Still, only a few methods aim at recognizing invalid minimal samples early, before the often expensive model estimation and quality calculation are done. To this end, we propose NeFSAC, an efficient algorithm for neural filtering of motion-inconsistent and poorly-conditioned minimal samples. We train NeFSAC to predict the probability of a minimal sample leading to an accurate relative pose, only based on the pixel coordinates of the image correspondences. Our neural filtering model learns typical motion patterns of samples which lead to unstable poses, and regularities in the possible motions to favour well-conditioned and likely-correct samples. The novel lightweight architecture implements the main invariants of minimal samples for pose estimation, and a novel training scheme addresses the problem of extreme class imbalance. NeFSAC can be plugged into any existing RANSAC-based pipeline. We integrate it into USAC and show that it consistently provides strong speed-ups even under extreme train-test domain gaps - for example, the model trained for the autonomous driving scenario works on PhotoTourism too. We tested NeFSAC on more than 100k image pairs from three publicly available real-world datasets and found that it leads to one order of magnitude speed-up, while often finding more accurate results than USAC alone. The source code is available at https://github.com/cavalli1234/NeFSAC.
Regulation of Cell-Specific Inositol Metabolism and Transport in Plant Salinity Tolerance (1998)

Donald E. Nelson, Gerald Rammesmayer, Hans J. Bohnert, Regulation of Cell-Specific Inositol Metabolism and Transport in Plant Salinity Tolerance, The Plant Cell, Vol. 10, No. 5 (May, 1998), pp. 753-764
Immunity to bacterial infection (excluding mycobacteria) (WS-060) (2010)

Although it is suggested that nature of memory CTL changes over immune responses, molecular characteristics of memory CTLs distinguished by the number of antigen experiences are largely unknown. In this study, we analyzed genome wide transcriptome of primary and secondary memory CTL using a next-generation DNA sequencer. Ly5.2+ C57/B6 WT mice were injected with na ve Ly5.1+ OT-I cells and intravenously challenged with OVA-expressing Listeria Monocytogenes (LM-OVA). Splenic Ly5.1+ OT-I cells (primary memory) were recovered around 60-70 days after LM-OVA infection and again adoptively transferred into Ly5.2+ mice, followed by LM-OVA challenge to generate secondary memory. Primary and secondary memory OT-I cells were sorted from spleen cells 60 days after LM-OVA infection. Na ve population was directly obtained from na ve OT-I mice. Total RNA from these three populations were sequenced using the newly developed 5 -end mRNA collection method and Illumina/Solexa system. The mRNA expression levels were confirmed by real-time PCR. Comparison of primary and secondary memory CTL showed that inhibitory receptors such as PD-1, CTLA-4 and 2B4, that were reported to be induced in exhausted CTL, were not over-expressed in secondary memory. On the other hand, senescence related molecules such as p21 and KLRG-1 were over expressed in secondary memory. In addition, secondary memory showed effector memory phenotype (CCR7lo, CD62Llo). These results suggest that memory CTL changes molecular signature as they experience the responses and also memory CTL senescence differs from exhaustion.
Clofarabine/cyclophosphamide for debulking before stem cell transplantation (2014)

Clofarabine/cyclophosphamide is a novel effective treatment approach for pts with chemotherapy-refractory acute leukaemia prior to HSCT. Whether this novel debulking protocol leads to improved long-term outcome in pts with refractory leukaemias remains to be determined in forthcoming clinical studies.
High-frequency isolated ac-dc converter with stacked architecture (2017)

This paper presents a new isolated ac-dc power converter achieving both high power factor and converter miniaturization suitable for many low power ac-dc applications. The proposed ac-dc converter architecture comprises a line-frequency rectifier, a stack of capacitors, a set of regulating converters, and a multi-input isolated bus converter. Among many suitable circuit implementations, the prototype system utilizes the resonant-transition buck converter as a regulating converter, and the capacitively-aided isolated bus converter for the isolated bus converter. The converter is miniaturized by operating at high frequency (1-10 MHz range), and it buffers the ac-line frequency energy with a pair of stacked ceramic capacitors (1 μF and 150 μF, 100 V rating) without a requirement for electrolytic capacitors. The prototype converter is implemented to operate from 120 Vac to 12 V, and up to 50 W output as an example isolated ac-dc converter for power supply applications. The prototype converter demonstrates with 88 % efficiency and 0.86 power factor, and provides 50 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> power density, which is five times higher than the power density of typical conventional designs.
META-ANALYSIS OF CONTINUOUS PHENOTYPES IDENTIFIES A GENE SIGNATURE THAT CORRELATES WITH COPD DISEASE STATUS (2016)

The utility of multi-cohort two-class meta-analysis to identify robust differentially expressed gene signatures has been well established. However, many biomedical applications, such as gene signatures of disease progression, require one-class analysis. Here we describe an R package, MetaCorrelator, that can identify a reproducible transcriptional signature that is correlated with a continuous disease phenotype across multiple datasets. We successfully applied this framework to extract a pattern of gene expression that can predict lung function in patients with chronic obstructive pulmonary disease (COPD) in both peripheral blood mononuclear cells (PBMCs) and tissue. Our results point to a disregulation in the oxidation state of the lungs of patients with COPD, as well as underscore the classically recognized inammatory state that underlies this disease.
Protective Effect of Taurine in the Induction of Genotoxicity by Mutagenic Drugs (2018)

Genotoxicity is a toxic action of several drugs, such as anti-neoplastic and nitro-related compounds. TAU (Taurine, 2-aminoetano sulfonic acid) is an important and potent antioxidant amino acid involved in the maintenance of homeostasis in many systems like leukocytes, skeletal muscle, the heart, the kidney, the liver, the bowel, the brain and the retina. The aim of this work was evaluated by the protective effect of TAU co-administered with mutagenic drugs such as benznidazole, cyclophosphamide, hydroxyurea, metronidazole, and nitrofurazone in an in vivo model using a micronucleus assay, evaluatation for the ability of different substances to promote DNA injury. The results showed that TAU decreased genotoxic activity of all drugs suggesting that the protective action of TAU supplementation can be beneficial to reduce genotoxicity of drugs. In this context, we propose one possible mechanism for how TAU blocks the chromosomal aberrations caused by the action of genotoxic substances.
Stereospecific Synthesis and Assignment of Absolute Configuration at Phosphorus in Nucleoside 3′- and 5′-O-Arylphosphorothioates and Nucleoside Cyclic 3′,5′-Phosphorothioates (1981)

The new class of phosphorylating reagents, asymmetric O,N-diarylphosphoramidochloridates and O,N-diarylphosphoramidochloridothioates, has been reported from this Laboratory /1,2/. By virtue of the asymmetric phosphorus atom, nucleoside 5'_ and 3'-O,N-diarylphosphoramidates (diarylphosphoramidothioates) consist of a mixture of diastereomers which can be separated into individual P-enantiomeric species. These, by the method established in this laboratory /3/, can be stereospecifically converted by means of NaH/CY2 (Y=O,S,Se) to the desired nucleoside O-arylphosphates, -phosphorothioates and -phosphoroselenoates /2,4/, which may be further utilized for the synthesis of oligonucleotides /5/. Nucleoside 3'- and 5'-O,N-diarylphosphoramidates can be also used for preparation of nucleoside cyclic 3',5'-phosphoranilidates, the key intermediates in the stereospecific synthesis of nucleoside cyclic 3',5'-phosphorothioates /6,7,8/ and -|18O|phosphates /9,10/. Since the absolute configuration at the P-atom in deoxyadenosine cyclic 3',5'-|Rp|-phosphoranilidate was assigned by means of X-ray crystallography /11/ and this assessment has confirmed the earlier determination made by means of 31P-NMR spectroscopy /7/, the knowledge of the absolute configuration
Detecting Correlations Using Phase-Change Neurons and Synapses (2016)

As the conventional von Neumann-based computational architectures reach their scalability and performance limits, alternative computational frameworks inspired by biological neuronal networks hold promise to revolutionize the way we process information. Here, we present a bioinspired computational primitive that utilizes an artificial spiking neuron equipped with plastic synapses to detect temporal correlations in data streams in an unsupervised manner. We demonstrate that the internal states of the neuron and of the synapses can be efficiently stored in nanoscale phase-change memory devices and show computations with collocated storage in an experimental setting.
Prevalence of Rift Valley Fever among Ruminants, Mayotte (2012)

Rift Valley fever threatens human and animal health. After a human case was confi rmed in Comoros in 2007, 4 serosurveys among ruminants in Mayotte suggested that Rift Valley fever virus had been circulating at low levels since 2004, although no clinical cases occurred in animals. Entomologic and ecologic studies will help determine outbreak potential.
Design optimization of 40 Gb/s RZ-DQPSK transceiver for high OSNR and PMD tolerance under fast polarization changes (2007)

Full-band tunable, multi-rate (43 and 44.6 Gb/s) RZ-DQPSK transceiver with excellent balance of OSNR and PMD tolerances under fast (1.6 rad/ms) SOP change was realized and its manufacturability was confirmed through measurement on 100 modules. (2 pages)