gebhart/patrepeval huggingface dataset:
Use of the transseptal puncture in transcatheter closure of long tunnel-type patent foramen ovale (2002)

Two patients with long tunnel-type patent foramen ovale presented for elective transcatheter closure following transient ischaemic attack and stroke. Right to left shunting was confirmed on transthoracic and transoesophageal echocardiography. A new technique that used a transseptal procedure was devised to enable closure of the tunnel-type patent foramen ovale using the CardioSEAL transseptal occluder to avoid "bunching up" of the device and residual transatrial shunting.
Cationic Lipid Formulations Alter the In Vivo Tropism of AAV2/9 Vector in Lung (2009)

Physicochemical properties of gene transfer vectors play an important role in both transduction efficiency and biodistribution following airway delivery. Adeno-associated virus (AAV) vectors are currently used in many gene transfer applications; however, the respiratory epithelium remains a challenging target. We synthesized two cationic sterol-based lipids, dexamethasone-spermine (DS) and disubstituted spermine (D(2)S) for pulmonary gene targeting. Scanning and transmission electron micrographs (TEM) confirmed that AAV/lipid formulations produced submicron-sized clusters. When AAV2/9 or AAV2/6.2 were formulated with these cationic lipids, the complexes had positive zeta potential (zeta) and the transduction efficiency in cultured A549 cells increased by sevenfold and sixfold, respectively. Transduction of cultured human airway epithelium with AAV2/6.2-lipid formulations also showed approximately twofold increase in green fluorescence protein (GFP) positive cells as quantified by flow cytometry. Intranasal administration of 10(11) genome copies (GC) of AAV2/9 and AAV2/6.2 coformulated with lipid formulations resulted in an average fourfold increase in transgene expression for both vectors. Formulation of AAV2/9 with DS changed the tropism of this vector for the alveolar epithelium, resulting in successful transduction of conducting airway epithelium. Our results suggest that formulating AAV2/9 and AAV2/6.2 with DS and D(2)S can lead to improved physicochemical characteristics for in vivo gene delivery to lung.
PipeAlign: a new toolkit for protein family analysis (2003)

PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated MACS (multiple alignment of complete sequences) in which sequences are clustered into potential functional subgroups. For the more experienced user, the PipeAlign server also provides numerous options to run only a part of the analysis, with the possibility to modify the default parameters of each software module. For example, the user can choose to enter an existing multiple sequence alignment for refinement, validation and subsequent clustering of the sequences. The aim is to provide an interactive workbench for the validation, integration and presentation of a protein family, not only at the sequence level, but also at the structural and functional levels. PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/.
Fabrication of Gd <sub>2</sub> O <sub>2</sub> S: Pr, Ce, F Scintillation Ceramics by Pressureless Sintering in Nitrogen Atmosphere (2015)

Gd 2 O 2 S: Pr, Ce, F ceramics with good scintillation properties were fabricated by pressureless sintering in nitrogen atmosphere. The effects of annealing temperature on the intensity of X‐ray excited luminescence and light output were investigated. The light output strongly depends on the thickness of Gd 2 O 2 S: Pr, Ce, F ceramics. Thermoluminescence properties of the samples were studied after X‐ray irradiation in the temperature range of 77–438 K.
Designing Non‐Native Iron‐Binding Site on a Protein Cage for Biological Synthesis of Nanoparticles (2014)

In biomineralization processes, a supramolecular organic structure is often used as a template for inorganic nanomaterial synthesis. The E2 protein cage derived from Geobacillus stearothermophilus pyruvate dehydrogenase and formed by the self-assembly of 60 subunits, has been functionalized with non-native iron-mineralization capability by incorporating two types of iron-binding peptides. The non-native peptides introduced at the interior surface do not affect the self-assembly of E2 protein subunits. In contrast to the wild-type, the engineered E2 protein cages can serve as size- and shape-constrained reactors for the synthesis of iron nanoparticles. Electrostatic interactions between anionic amino acids and cationic iron molecules drive the formation of iron oxide nanoparticles within the engineered E2 protein cages. The work expands the investigations on nanomaterial biosynthesis using engineered host-guest encapsulation properties of protein cages.
High-frequency SiPM readout advances measured coincidence time resolution limits in TOF-PET (2019)

Scintillator based radiation detectors readout by SiPMs successively break records in their reached time resolution. Nevertheless, new challenges in time of flight positron emission tomography (TOF-PET) and high energy physics are setting unmatched goals in the 10 ps range. Recently it was shown that high frequency (HF) readout of SiPMs significantly improves the measured single photon time resolution (SPTR), allowing to evaluate the intrinsic performance of large area devices; e.g. FBK NUV-HD SiPMs of [Formula: see text] mm<sup>2</sup> area and 40 [Formula: see text]m single photon avalanche diode (SPAD) size achieve 90 ps FWHM. In TOF-PET such readout allows to lower the leading edge detection threshold, so that the fastest photons produced in the crystal can be utilized. This is of utmost importance if a high SPTR and prompt Cherenkov light generated by the hot-recoil electron upon 511 keV photo-absorption should improve timing. This paper shows that high-frequency bipolar transistor readout of state-of-the-art SiPMs coupled to high-performance scintillators can substantially improve the best achievable coincidence time resolution (CTR) in TOF-PET. In this context a CTR of 158 [Formula: see text] 3 ps FWHM with [Formula: see text] mm<sup>3</sup> BGO crystals coupled to FBK SiPMs is achieved. This faint Cherenkov signal is as well present in standard LSO scintillators, which together with low SPTR values (<90 ps FWHM) improves the CTR of [Formula: see text] mm<sup>3</sup> LSO:Ce:Ca coupled to FBK NUV-HD [Formula: see text] mm<sup>2</sup> with 25 [Formula: see text]m SPAD size to 61 [Formula: see text] 2 ps FWHM using HF-electronics, as compared to 73 [Formula: see text] 2 ps when readout by the NINO front-end ASIC. When coupling the LSO:Ce:Ca crystals to FBK NUV-HD SiPMs of [Formula: see text] mm<sup>2</sup> and 40 [Formula: see text]m SPAD size, using HF-electronics, a CTR of even 58 [Formula: see text] 3 ps for [Formula: see text] mm<sup>3</sup> and 98 [Formula: see text] 3 ps for [Formula: see text] mm<sup>3</sup> is achieved. This new experimental data will allow to further discuss the timing limits in scintillator-based detectors.
Multiphysics and multiscale modelling, data–model fusion and integration of organ physiology in the clinic: ventricular cardiac mechanics (2016)

With heart and cardiovascular diseases continually challenging healthcare systems worldwide, translating basic research on cardiac (patho)physiology into clinical care is essential. Exacerbating this already extensive challenge is the complexity of the heart, relying on its hierarchical structure and function to maintain cardiovascular flow. Computational modelling has been proposed and actively pursued as a tool for accelerating research and translation. Allowing exploration of the relationships between physics, multiscale mechanisms and function, computational modelling provides a platform for improving our understanding of the heart. Further integration of experimental and clinical data through data assimilation and parameter estimation techniques is bringing computational models closer to use in routine clinical practice. This article reviews developments in computational cardiac modelling and how their integration with medical imaging data is providing new pathways for translational cardiac modelling.
High-Throughput Screening for Bioactive Molecules Using Primary Cell Culture of Transgenic Zebrafish Embryos (2012)

Transgenic zebrafish embryos expressing tissue-specific green fluorescent protein (GFP) can provide an unlimited supply of primary embryonic cells. Agents that promote the differentiation of these cells may be beneficial for therapeutics. We report a high-throughput approach for screening small molecules that regulate cell differentiation using lineage-specific GFP transgenic zebrafish embryonic cells. After validating several known regulators of the differentiation of endothelial and other cell types, we performed a screen for proangiogenic molecules using undifferentiated primary cells from flk1-GFP transgenic zebrafish embryos. Cells were grown in 384-well plates with 12,128 individual small molecules, and GFP expression was analyzed by means of an automated imaging system, which allowed us to screen thousands of compounds weekly. As a result, 23 molecules were confirmed to enhance angiogenesis, and 11 of them were validated to promote the proliferation of mammalian human umbilical vascular endothelial cells and induce Flk1+ cells from murine embryonic stem cells. We demonstrated the general applicability of this strategy by analyzing additional cell lineages using zebrafish expressing GFP in pancreatic, cardiac, and dopaminergic cells.
MMP-9 and MMP-2 Contribute to Neuronal Cell Death in iPSC Models of Frontotemporal Dementia with MAPT Mutations (2016)

How mutations in the microtubule-associated protein tau (MAPT) gene cause frontotemporal dementia (FTD) remains poorly understood. We generated and characterized multiple induced pluripotent stem cell (iPSC) lines from patients with MAPT IVS10+16 and tau-A152T mutations and a control subject. In cortical neurons differentiated from these and other published iPSC lines, we found that MAPT mutations do not affect neuronal differentiation but increase the 4R/3R tau ratio. Patient neurons had significantly higher levels of MMP-9 and MMP-2 and were more sensitive to stress-induced cell death. Inhibitors of MMP-9/MMP-2 protected patient neurons from stress-induced cell death and recombinant MMP-9/MMP-2 were sufficient to decrease neuronal survival. In tau-A152T neurons, inhibition of the ERK pathway decreased MMP-9 expression. Moreover, ectopic expression of 4R but not 3R tau-A152T in HEK293 cells increased MMP-9 expression and ERK phosphorylation. These findings provide insights into the molecular pathogenesis of FTD and suggest a potential therapeutic target for FTD with MAPT mutations.
Expansion of the Web Space (2011)

Current Web space does not provide standard integrated environment. This, especially in case of large task, can be a cause of low performance of task processing. We proposed an integrated space(called SB space) in this paper through which various actors can share their mutual process in processing a task together. SB space can be installed as a Web site and can be used effectively with Web space. This actually means the expansion of the Web space, which allows us to improve the productivity of the Web space notably. In this paper, this is proved through a concrete case study.
Parvovirus Infections in Humans (2003)

Abstract Parvoviruses are small, species‐specific DNA‐containing viruses that infect several animal species. The human parvoviruses include two agents, B19 virus and adeno‐associated virus; B19 virus causes several disease syndromes and is a medically important pathogen.
Design of Unapodized Surface-Wave Transducers with Spectral Weighting (1974)

The technique commonly employed to provide a wide-band surface-wave transducer with a specific conversion loss as a function of frequency uses the linear frequency-modulation (LFM) (quadratic-phase) design. This provides the necessary dispersion, and anodization is then employed to obtain the required conversion loss. In some applications the anodization presents complications in that the beam generated has nonuniform width, and diffraction and phase-front problems can result. An alternate technique is described that relies on varying the number of effective transducer elements as a function of frequency to provide the conversion-loss variation. As examples of this technique, a flat bandpass filter for a nonlinear convolver and a very large fractional-bandwidth transducer (with spectral weighting to provide sidelobe control) for a memory application are described.
Omega: a language and system for on-line monitoring of software processes (2000)

International audience
Investigating the Role of Histidine 157 in the Catalytic Activity of Human Cytomegalovirus Protease (2001)

Herpesvirus proteases belong to a new class of serine proteases and contain a novel Ser-His-His catalytic triad, while classical serine proteases have an acidic residue as the third member. To gain a better understanding of the molecular basis for the functional role of the third-member His residue, we have carried out structural and biochemical investigations of human cytomegalovirus (HCMV) protease that bears mutations of the His157 third member. Kinetic studies showed that all the mutants have reduced catalytic activity. Structural studies revealed that a solvent molecule is hydrogen-bonded to the His63 second member and Ser134 in the H157A mutant, partly rescuing the activity of this mutant. This is confirmed by our kinetic and structural observations on the S134A/H157A double mutant, which showed further reductions in the catalytic activity. The structure of the H157A mutant is also in complex with the PMSF inhibitor. The H157E mutant has the best catalytic activity among the mutants; its structure, however, showed conformational readjustments of the His63 and Ser132 residues. The Ser132-His63 diad of HCMV protease has similar activity as the diads in classical serine proteases, whereas the contribution of the His157 third member to the catalysis is much smaller. Finally, structural comparisons revealed the presence of two conserved structural water molecules at the bottom of the S(1) pocket, suggesting a possible new direction for the design of HCMV protease inhibitors.
Secure Data Provenance for the Internet of Things (2017)

The vision of smart environments, systems, and services is driven by the development of the Internet of Things (IoT). IoT devices produce large amounts of data and this data is used to make critical decisions in many systems. The data produced by these devices has to satisfy various security related requirements in order to be useful in practical scenarios. One of these requirements is data provenance which allows a user to trust the data regarding its origin and location. The low cost of many IoT devices and the fact that they may be deployed in unprotected spaces requires security protocols to be efficient and secure against physical attacks. This paper proposes a light-weight protocol for data provenance in the IoT. The proposed protocol uses physical unclonable functions (PUFs) to provide physical security and uniquely identify an IoT device. Moreover, wireless channel characteristics are used to uniquely identify a wireless link between an IoT device and a server/user. A brief security and performance analysis are presented to give a preliminary validation of the protocol.
Determination of the thermal conductivity of gases under flow conditions (2013)

This contribution presents a calorimetric flow sensor that is capable of determining the thermal conductivity (k) regardless of the flow conditions. The sensor can also measure the flow rate (Q) provided that the volumetric heat capacity (ρc <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> ) or the thermal diffusivity (α=k/(ρc <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> )) of the flowing gas is known. No additional sensors or bypass channels are needed. The measuring principle relies on using high frequency heat generation (200 Hz). The thermal conductivity of several common gases is measured.
Photoirradiation-generated radicals in two-component supramolecular gel for polymerization (2018)

While supramolecular gels have been attracting great interest due to their easy design and fabrication, development of new applications based on these gels is always a challenging topic. Here, we report a two-component supramolecular gel that can generate and stabilize radicals through photo-irradiation, which can be subsequently used for polymerization. It has been found that the electrostatic interactions between a cationic amphiphile and anionic sulfonate could afford co-assembly into a two-component supramolecular gel. Upon photo-irradiation, the gel changed colour and produced the radicals, as verified from the EPR measurements. The radical thus formed in the supramolecular gel is relatively stable and could be used to polymerize acrylic acid directly without deoxygenation. In contrast, acrylic acid could not be polymerized in solution under the same conditions. This work expands the application scope of supramolecular gels.
Identification of hypoxanthine as a urine marker for non-Hodgkin lymphoma by low-mass-ion profiling (2010)

The present study represents a good example of low-mass-ion profiling in the setting of disease screening using urine. This technique can be a powerful non-invasive diagnostic tool with high sensitivity and specificity for NHL screening. Furthermore, HX identified in the study may be a useful single urine marker for NHL screening.
Molecular Basis of Purinergic Signal Metabolism by Ectonucleotide Pyrophosphatase/Phosphodiesterases 4 and 1 and Implications in Stroke* (2013)

NPP4 is a type I extracellular membrane protein on brain vascular endothelium inducing platelet aggregation via the hydrolysis of Ap3A, whereas NPP1 is a type II extracellular membrane protein principally present on the surface of chondrocytes that regulates tissue mineralization. To understand the metabolism of purinergic signals resulting in the physiologic activities of the two enzymes, we report the high resolution crystal structure of human NPP4 and explore the molecular basis of its substrate specificity with NPP1. Both enzymes cleave Ap3A, but only NPP1 can hydrolyze ATP. Comparative structural analysis reveals a tripartite lysine claw in NPP1 that stabilizes the terminal phosphate of ATP, whereas the corresponding region of NPP4 contains features that hinder this binding orientation, thereby inhibiting ATP hydrolysis. Furthermore, we show that NPP1 is unable to induce platelet aggregation at physiologic concentrations reported in human blood, but it could stimulate platelet aggregation if localized at low nanomolar concentrations on vascular endothelium. The combined studies expand our understanding of NPP1 and NPP4 substrate specificity and range and provide a rational mechanism by which polymorphisms in NPP1 confer stroke resistance.
Common customer complaint: “My hot water stinks” (1981)

Non‐pathogenic anaerobic bacteria, such as Desulfuvibrio desulfuricans, form enzymes as a metabolic function that accelerate the sulfate‐reduction reaction. The subsequent production of hydrogen sulfide gas creates a distinctive rotten egg odor which causes many customer complaints. Oxidation by chlorination, maintenance of chlorine residuals in the distribution system, cathodic protection, and ion exchange water softeners are discussed. Remedies for rotten egg odor include maintaining chlorine residuals, flushing distribution lines, killing bacteria with heat, replacing magnesium anode rods, and removing cathodic‐protection anodes.
A Low Phase Noise Quadrature LC-VCO in0.1 8-gm (2008)

A 5.2-GHzquadrature LC voltage controlled oscillator (VCO)hasbeendesigned inastandard 0.18-gm CMOS process. Digitally controlled switch arrayisusedinthis design to achieve sufricient frequency tuning rangeandlowphasenoise. Theoscillation frequency canbetunedfrom5.03GHz to5.32 GHz through the2-bit switch array. Withtheselection ofan optimal on-chip inductor, thequadrature VCO achieves a single-sideband phasenoiseof-116dBc/Hz at1.0MHz offset frequency consuming total 9.8mAofcurrent froma1.5V power supply. IndexTermsCMOS, PhaseNoise, LC-VCO,Quadrature VCO,Wireless Local AreaNetwork (WLAN).
<scp>pH</scp> dependency of sclerotial development and pathogenicity revealed by using genetically defined oxalate‐minus mutants of <scp> <i>S</i> </scp> <i>clerotinia sclerotiorum</i> (2015)

The devastating plant pathogen Sclerotinia sclerotiorum produces copious (up to 50 mM) amounts of oxalic acid, which, for over a quarter century, has been claimed as the pathogenicity determinant based on UV-induced mutants that concomitantly lost oxalate production and pathogenicity. Such a claim was made without fulfilling the molecular Koch's postulates because the UV mutants are genetically undefined and harbour a developmental defect in sclerotial production. Here, we generated oxalate-minus mutants of S. sclerotiorum using two independent mutagenesis techniques, and tested the resulting mutants for growth at different pHs and for pathogenicity on four host plants. The oxalate-minus mutants accumulated fumaric acid, produced functional sclerotia and have reduced ability to acidify the environment. The oxalate-minus mutants retained pathogenicity on plants, but their virulence varied depending on the pH and buffering capacity of host tissue. Acidifying the host tissue enhanced virulence of the oxalate-minus mutants, whereas supplementing with oxalate did not. These results suggest that it is low pH, not oxalic acid itself, that establishes the optimum conditions for growth, reproduction, pathogenicity and virulence expression of S. sclerotiorum. Exonerating oxalic acid as the primary pathogenicity determinant will stimulate research into identifying additional candidates as pathogenicity factors towards better understanding and managing Sclerotinia diseases.
A fragment calculus-towards a model of separate compilation, linking and binary compatibility (2003)

We propose a calculus describing compilation and linking in terms of operations on fragments, i.e. compilation units, without reference to their specific contents. We believe this calculus faithfully reflects the situation within modern programming systems. Binary compatibility in Java prescribes conditions under which modification of fragments does not necessitate recompilation of importing fragments. We apply our calculus to formalize binary compatibility, and demonstrate that several interpretations of the language specification are possible, each with different ramifications. We choose a particular interpretation, justify our choice, formulate and prove properties important for language designers and code library developers.