gebhart/patrepeval huggingface dataset:
Statistical wavelet analysis of functional images of the brain (2002)

Functional magnetic resonance imaging (fMRI) is a recent, non-invasive technique that allows the measurement of brain metabolism while a subject is performing specific motor or cognitive tasks. The practical difficulty is that the signal changes are very small and the noise is relatively high. To enhance the activation signal, conventional methods, such as SPM, apply a Gaussian filter to the data and perform a statistical analysis at the pixel-level. Gaussian filtering obviously suppresses high frequency information. To avoid this loss of resolution, we propose instead to apply a wavelet transform and to perform the statistical analysis in the wavelet domain. Our statistical analysis relies on a conservative decision strategy which ensures that the false detection rate is kept well under control. In the first chapter, we introduce the fMRI technique and compare it with other modalities. We then characterize the noise of fMRI data and introduce the statistical tools for our analysis. Next, we describe different types of wavelet transforms and show how those can be applied to the analysis of fMRI data. Different wavelet bases offer different compromises. To determine the wavelet properties that are the most beneficial for the detection of activation patterns in fMRI data, we develop a test procedure for the objective evaluation of analysis methods. This procedure allows us to compare various brands of wavelet transforms, including Daubechies wavelets (real and complex) and the newly-defined fractional splines. We observe that one of the transforms—dual fractional spline of degree 1.2—usually outperforms the others. We establish an interesting theoretical connection between this particular wavelet transform and the Gaussian filter recommended by SPM. Traditional, separable wavelets are constrained to dyadic scale progressions (powers of two). To allow for finer scale progressions, we define new 2D and 3D fractional wavelets which use quincunx sampling. We propose an FFT-based implementation that turns out to be surprisingly fast. We also present some experimental examples where these quincunx wavelets offer some benefits.
Position Statement from the German Biobank Alliance on the Cooperation Between Academic Biobanks and Industry Partners (2019)

Under the umbrella of the German Biobank Node (GBN), 11 biobanks and two IT development centers are funded by the Federal Ministry of Education and Research (BMBF) to work together in the German Biobank Alliance (GBA). Their common aim is to make existing biomaterials hosted by different biobanks nationally and internationally available for biomedical research. This position article reflects and summarizes contributions and comments made during a GBA workshop, on the cooperation between academic biobanks and pharmaceutical and diagnostics companies that took place in Leipzig on the 21st of June 2018. It documents key points agreed on by all participating biobanks during the workshop thereby addressing several of the challenges identified. Although there are various possibilities for cooperation between academic biobanks and industry, this position article focuses exclusively on projects where academic biobanks give access to their biosamples and related data to industry partners. In doing so it considers the general conditions/framework and procedures in the German biobanking environment and raises ethical, legal, and procedural issues to be addressed when initiating such collaborations. It intends to furnish a basis for further activities to foster cooperation with industry and to push an overarching national coordination process. The final aim is to develop GBN-recommendations. Of course, many hospitals already have clear regulations on collaboration(s) with industry partners. These naturally take precedence for the GBA biobanks. However, where interest exists, GBN/GBA recommendations could help to induce changes to existing local policies nonetheless.
Abstract 3446: Therapeutic Neovascularization by Catheter-Based, Intramyocardial Gene Transfer of Naked DNA Encoding Human Placental Growth Factor in Swine Chronic Myocardial Ischemia (2008)

Background: We have reported that intramyocardial transfer of plasmid encoding human placental growth factor (phPlGF) augments myocardial angiogenesis, inhibits myocardial apoptosis and left ventri...
Oxygénothérapie hyperbare et infirmité motrice cérébrale (2001)

Quelques histoires de traitements par oxygenotherapie hyperbare couronnes de succes ayant circule entre familles d'enfants atteints d'infirmite motrice cerebrale, les parents se sont mis a reclamer ce type de traitement malgre le peu d'arguments scientifiques en faveur de son efficacite. Collet et al. ont conduit une etude randomisee et en double aveugle au cours de laquelle 57 enfants atteints d'une infirmite motrice cerebrale ont recu une oxygenotherapie hyperbare (100 % d'oxygene a une pression de 1,75 atmospheres) et 54 autres un air legerement pressurise (air ambiant a 1,3 atmospheres). Les resultats n'indiquent pas d'avantage de l'oxygene hyperbare sur l'air pressurise, mais, de facon surprenante, on observait une amelioration clinique reelle dans les deux groupes d'enfants, que ce soit au niveau du langage, de l'attention, de la memoire, ou des fonctions motrices. Le degre d'amelioration etait le meme que celui que l'on a observe lors d'etudes faisant appel a une kinesitherapie intensive. On peut en deduire que soit les deux traitements ont ete egalement efficaces, ce qui parait assez peu probable, soit le seul fait de participer a l'etude a favorise des rencontres entre familles enthousiastes, ce qui aurait eu un effet benefique sur tous.Collet J.P., et al. 2001. Hyperbaric oxygen for children with cerebral palsy : a randomised multicentre trial. Lancet 357 : 582-586.
Breaking C–C Bonds via Electrochemically Mediated Hydrogen Atom Transfer Reactions (2021)

Cleaving inert sp&lt;sup&gt;3&lt;/sup&gt;-sp&lt;sup&gt;3&lt;/sup&gt; carbon-carbon (C-C) bonds selectively remains a major challenge in organic chemistry and a main bottleneck in the chemical upcycling of recalcitrant polyolefin waste. Here, we present an electrochemical strategy using redox mediators to activate and break C-C bonds at room temperature and ambient pressure. Specifically, we use &lt;i&gt;N&lt;/i&gt;-hydroxyphthalimide (NHPI) as a redox mediator that undergoes electrochemical oxidation to form the &lt;a&gt;phthalimide-&lt;i&gt;N&lt;/i&gt;-oxyl (PINO) radical &lt;/a&gt;to initiate hydrogen atom transfer (HAT) reactions with benzylic C-H bonds. The resulting benzylic carbon radical is readily captured by molecular oxygen to form a peroxy radical that decomposes into oxygenated C-C bond-scission fragments. This indirect, mediated approach for C&lt;sub&gt;sp3&lt;/sub&gt;-C&lt;sub&gt;sp3&lt;/sub&gt; bond cleavage reduces the oxidation potential by &gt; 1.2 V compared to the direct oxidation of the substrate, thereby eliminating deleterious side reactions, such as solvent oxidation, that may occur at high potentials. Studies with a bibenzyl model compound revealed a bifurcated reaction pathway following the initial HAT step. At a bibenzyl conversion of 61.0%, the C-C bond cleavage pathway generates benzaldehyde and benzoic acid products at 38.4% selectivity, and the C-H bond oxygenation pathway leads to 1,2-diphenylethanone and benzil products at 39.2% selectivity. Changes in reaction selectivity were investigated with various model compounds, including bibenzyl, 1,3-diphenylpropane, 1,4-diphenylbutane, and their derivatives. Product selectivity is correlated with the C-C bond strength of the reactant, with weaker C-C bonds favoring the C-C bond cleavage pathway. We also evaluated the mediated oxidation of oligomeric styrene (&lt;i&gt;M&lt;/i&gt;&lt;sub&gt;n&lt;/sub&gt; = 510 Da, OS&lt;sub&gt;510&lt;/sub&gt;) which were converted into oxygenated products. Lastly, proof-of-concept depolymerization of polystyrene (PS, ~10,000 Da) into oxygenated monomers, dimers, and oligomers was demonstrated using NHPI-mediated oxidation.
A Review of Phased Array Steering for Narrow-Band Electrooptical Systems Rapid, accurate, non-mechanical techniques for steering optical beams can provide the kind of efficient random access pointing offered by microwave radars. (2009)

Nonmechanical steering of optical beams will enable revolutionary systems with random access pointing, similar to microwave radar phased arrays. An early approach was birefringent liquid crystals writing a sawtooth phase profile in one polarization, using 2� resets. Liquid crystals were used because of high birefringence. Fringing fields associated with voltage control required to implement the 2� resets have limited the efficiency and steering angle of this beam steering approach. Because of steering angle limitations, this conventional liquid crystal steering approach is usually combined with a large angle step-steering approach. Volume holograms, birefringent prisms orsawtooth-profile birefringentphase gratings, andcircular-type polarizationgratingsarethelargeanglestepsteeringapproaches that will be reviewed in this paper. Alternate steering approaches to the combined liquid crystal and step-steering approach exist. Microelectromechanical system mirrors, lenslet arrays, electro- wetting, and a variable birefringent grating approach will be reviewed and compared against the conventional liquid crystal and step-steering approaches. Step-steering approaches can also be combined with these approaches. Multiple nonmechan- ical steering approaches are developing that will allow high- efficiency steering, excellent steering accuracy, and wide fields of view.
Design and analysis of a highly efficient coupler between a micro/nano optical fiber and an SOI waveguide (2012)

A compact coupling structure is proposed for highly efficient coupling between a micro/nano fiber and a silicon-on-insulator waveguide. The proposed structure is characterized by high coupling efficiency, wavelength insensitivity, large misalignment tolerance, and easy fabrication. Theoretical analysis and numerical simulation results show that coupling efficiency of >90% can be achieved with a taper length of ∼4.5 μm.
An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease (2022)

Celiac disease (CeD) is an autoimmune disorder induced by consuming gluten proteins from wheat, barley, and rye. Glutens resist gastrointestinal proteolysis, resulting in peptides that elicit inflammation in patients with CeD. Despite well-established connections between glutens and CeD, chemically defined, bioavailable peptides produced from dietary proteins have never been identified from humans in an unbiased manner. This is largely attributable to technical challenges, impeding our knowledge of potentially diverse peptide species that encounter the immune system. Here, we develop a liquid chromatographic-mass spectrometric workflow for untargeted sequence analysis of the urinary peptidome. We detect over 600 distinct dietary peptides, of which ~35% have a CeD-relevant T cell epitope and ~5% are known to stimulate innate immune responses. Remarkably, gluten peptides from patients with CeD qualitatively and quantitatively differ from controls. Our results provide a new foundation for understanding gluten immunogenicity, improving CeD management, and characterizing the dietary and urinary peptidomes.
Abstract LB-164: Ran Binding Protein 9 (RanBP9) is a novel mediator of cellular DNA damage response in lung cancer cells (2015)

Abstract Currently, most of the anti-neoplastic treatments for lung cancer patients are based on DNA-damaging cytotoxic therapies such as platinum-containing compounds and radiotherapy. Therefore, a better understanding of the molecular mechanisms involved in the cellular response to genotoxic stresses is required in order to improve the clinical management of lung cancer. Ran Binding Protein 9 (RanBP9, also known as RanBP-M) is a ubiquitous and evolutionary conserved scaffold protein that shuttles between the nucleus and the cytoplasm, and interacts with many major players in tumor biology. However, its biological functions are not well studied and still debated. Here, we show that RanBP9 interacts with and is phosphorylated by ATM, one of the apical activators of the DNA damage response (DDR) following DNA Double-Strand Breaks (DSBs). Following ATM-dependent phosphorylation, RanBP9 rapidly accumulates into the nucleus of lung cancer cells. By using three different lung cancer cell lines (A549, H460, and H1299), we found that stable silencing of RanBP9 (ShRanBP9) significantly affects the DDR. In fact, stable ShRanBP9 clones display a delayed and/or reduced activation of key components of the cellular response to Ionizing Radiation (IR), including ATM, Chk2, H2AX-γ and p53. Accordingly, abrogation of RanBP9 expression significantly affected Homology-Directed repair of damaged DNA. On the other hand, stable silencing of RanBP9 results in increased IR-induced senescence and apoptosis. In summary, here we present evidence that RanBP9 is a novel mediator of the cellular DDR, whose recruitment into the nucleus upon IR is dependent on ATM kinase activity. In turn, nuclear RanBP9 participates to the efficient activation of cellular DDR. On the contrary, its absence hampers the repair of damaged DNA following DSBs, resulting in enhanced lung cancer sensitivity to genotoxic stresses. Taken together, our findings suggest that targeting RanBP9 might represent a new potential approach to increase sensitivity of lung cancer cells to genotoxic anti-neoplastic treatments. Citation Format: Dario Palmieri, Mario Scarpa, Anna Tessari, Rexhep Uka, Foued Amari, Cindy Lee, Timothy Richmond, Tyler Sheetz, Jeffrey Parvin, Thomas Ludwig, Carlo M. Croce, Vincenzo Coppola. Ran Binding Protein 9 (RanBP9) is a novel mediator of cellular DNA damage response in lung cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-164. doi:10.1158/1538-7445.AM2015-LB-164
An automated microfluidic assay for the detection of cancer biomarkers in serum using photonic crystal enhanced fluorescence (2016)

An automated microfluidic photonic crystal enhanced fluorescence (PCEF) assay platform was recently reported for the multiplexed detection of cytokines spiked into phosphate buffered saline. In this work, we apply the aforementioned platform for cancer biomarker detection in human serum. Detection and control proteins were printed in a microarray format onto the surface of a photonic crystal designed to enhance the signal of fluorophores in the excitation and emission range of Cyanine 5 dye and similar alternatives. Fluorescence-linked immunosorbent assays (FLISAs) were performed, and a dose-response curve was obtained for human serum spiked with anti-E7 antibody, a known biomarker for human papillomavirus (HPV)-associated oropharyngeal cancer (OPC). Further, clinical samples of 20 OPC patients and 20 healthy controls were also tested using the PCEF platform, and the results were compared to those of the gold standard enzyme-linked immunosorbent assay (ELISA). Based on the results of a single trial of forty clinical samples, the sensitivity and specificity of the automated PCEF assay for anti-E7 is 75% and 65%, respectively, compared to 56% and 95% for ELISA.
Sunlight-driven atmospheric water capture capacity is enhanced by nano-enabled photothermal desiccants (2020)

Atmospheric water capture (AWC) is an alternative method of localized water production whereby water vapor is removed from air to produce drinking water.
Rankine cycle waste heat recovery system (2023)

A waste heat recovery (WHR) system connects a working fluid to fluid passages formed in an engine block and/or a cylinder head of an internal combustion engine, forming an engine heat exchanger. The fluid passages are formed near high temperature areas of the engine, subjecting the working fluid to sufficient heat energy to vaporize the working fluid while the working fluid advantageously cools the engine block and/or cylinder head, improving fuel efficiency. The location of the engine heat exchanger downstream from an EGR boiler and upstream from an exhaust heat exchanger provides an optimal position of the engine heat exchanger with respect to the thermodynamic cycle of the WHR system, giving priority to cooling of EGR gas. The configuration of valves in the WHR system provides the ability to select a plurality of parallel flow paths for optimal operation.
Stratégie de la conversion d’énergie de la Toyota Prius (2008)

International audience
Fair queueing for input-buffered switches with back pressure (2002)

The output-buffered switching architecture with its ability to offer high throughput, guaranteed delay and fairness, is not practical owing to its lack of scalability, i.e., the memory size, speed, and control logic have to be scaled up proportionally to the number of input links, thus becoming infeasible for large switches. The commercial and research trend is to adopt an architecture with input buffering which is scalable, but yields lower throughput and lacks the quality-of-service features such as delay bound and fairness. Although the problem of low throughput owing to head of line blocking in input-buffered switches can be resolved by adopting per-output-port queueing in each input port, the contention among input ports still limits the throughput. Existing schedulers designed for input-buffered switches attempt to improve throughput by imposing back pressure to the contending cells, and scheduling cells free of contention for transmission, at the expense of delay and fairness. In this paper, we have modeled and analyzed the back pressure with an independent Bernoulli traffic load, and we have shown that there is a high probability of back pressure occurring under loaded traffic. We have also derived the average queue length at the input buffer. To address the above issues in input-buffered switches, we proposed a new algorithm, referred to as min-max fair input queueing (MFIQ), which minimizes the additional delay caused by back pressure and at the same time provides fair service among competing sessions.
Quantitative analysis of magnetic spin and orbital moments from an oxidized iron (1 1 0) surface using electron magnetic circular dichroism (2015)

Understanding the ramifications of reduced crystalline symmetry on magnetic behavior is a critical step in improving our understanding of nanoscale and interfacial magnetism. However, investigations of such effects are often controversial largely due to the challenges inherent in directly correlating nanoscale stoichiometry and structure to magnetic behavior. Here, we describe how to use Transmission Electron Microscope (TEM) to obtain Electron Magnetic Circular Dichroism (EMCD) signals as a function of scattering angle to locally probe the magnetic behavior of thin oxide layers grown on an Fe (1 1 0) surface. Experiments and simulations both reveal a strong dependence of the magnetic orbital to spin ratio on its scattering vector in reciprocal space. We exploit this variation to extract the magnetic properties of the oxide cladding layer, showing that it locally may exhibit an enhanced orbital to spin moment ratio. This finding is supported here by both spatially and angularly resolved EMCD measurements, opening up the way for compelling investigations into how magnetic properties are affected by nanoscale features.
Patient-Specific Computer Simulation of Transcatheter Aortic Valve Replacement in Bicuspid Aortic Valve Morphology (2019)

Patient-specific computer simulation of TAVR in bicuspid aortic valve may predict the development of important clinical outcomes, such as paravalvular regurgitation and conduction abnormalities. Patient-specific THV sizing and positioning may improve clinical outcomes of TAVR in bicuspid aortic valve.
Human inhalable antibody fragments neutralizing SARS-CoV-2 variants for COVID-19 therapy (2022)

As of December 2021, coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global emergency, and novel therapeutics are urgently needed. Here we describe human single-chain variable fragment (scFv) antibodies (76clAbs) that block an epitope of the SARS-CoV-2 spike protein essential for ACE2-mediated entry into cells. 76clAbs neutralize the Delta variant and other variants being monitored (VBMs) and inhibit spike-mediated pulmonary cell-cell fusion, a critical feature of COVID-19 pathology. In two independent animal models, intranasal administration counteracted the infection. Because of their high efficiency, remarkable stability, resilience to nebulization, and low cost of production, 76clAbs may become a relevant tool for rapid, self-administrable early intervention in SARS-CoV-2-infected subjects independently of their immune status.
Pheochromocytomas: Fabulous, Fascinating, and First (in everything)! (2019)

"<i>Patients that sweat over their whole bodies from the beginning…that have burning heat, are cooled without a crisis and then quickly become burning hot again…</i>" 1 Was Hippocrates talking about patients with pheochromocytomas and their classic triad of paroxysmal symptomatology of palpitations, diaphoresis, and headaches? We will never know….
Streaming Computations with Precise Control (2014)

Streaming computing is a paradigm of distributed computing that features networked nodes connected by first-in-first-out data channels.Communication between nodes may include not only high-volume data tokens but also infrequent and unpredictable control messages carrying control information, such as data set boundaries, exceptions, or reconfiguration requests.In many applications, it is necessary to order delivery of control messages precisely relative to data tokens, which can be especially challenging when nodes can filter data tokens.Existing approaches, mainly data serialization protocols, do not exploit the low-volume nature of control messages and may not guarantee that synchronization of these messages with data will be free of deadlock.In this paper, we propose an efficient messaging system for adding precisely ordered control messages to streaming applications.We use a credit-based protocol to avoid the need to tag data tokens and control messages.For potential deadlocks caused by filtering behavior and global synchronization, we propose deadlock avoidance solutions and prove their correctness.Experimental results show that with our messaging system, we can substantially improve the performance of a sparse-data streaming application by filtering unnecessary data tokens.