gebhart/patrepeval huggingface dataset:
Photon dosimetry using plastic scintillators in pulsed radiation fields (2007)

Simulations and experiments have been carried out to explore using a plastic scintillator as a dosimetry probe in the vicinity of a pulsed bremsstrahlung source in the range 4 to 20 MeV. Taking advantage of the tissue-equivalent properties of this detector in conjunction with the use of a fast digital signal processor near real-time dosimetry was shown to be possible. The importance of accounting for a broad energy electron beam in bremsstrahlung production, and photon scattering and build-up, in correctly interpreting dosimetry results at long stand-off distances is highlighted by comparing real world experiments with ideal geometry simulations. Close agreement was found between absorbed energy calculations based upon spectroscopic techniques and calculations based upon signal integration, showing a ratio between 10 MeV absorbed dose to 12 MeV absorbed dose of 0.58 at a distance of 91.4 m from the accelerator. This is compared with an idealized model simulation with a monoenergetic electron beam and without scattering, where the ratio was 0.46.
Method and apparatus for preparation of spherical metal carbonates and lithium metal oxides for lithium rechargeable batteries (2023)

A number of materials with the composition Li.sub.1+xNi.sub..alpha.Mn.sub..beta.Co.sub..gamma.M'.sub..delta.O.sub.2-- zF.sub.z (M'=Mg,Zn,Al,Ga,B,Zr,Ti) for use with rechargeable batteries, wherein x is between about 0 and 0.3, .alpha. is between about 0.2 and 0.6, .beta. is between about 0.2 and 0.6, .gamma. is between about 0 and 0.3, .delta. is between about 0 and 0.15, and z is between about 0 and 0.2. Adding the above metal and fluorine dopants affects capacity, impedance, and stability of the layered oxide structure during electrochemical cycling. Another aspect of the invention includes materials with the composition Li.sub.1+xNi.sub..alpha.Co.sub..beta.Mn.sub..gamma.M'.sub..delta.O.sub.yF- .sub.z (M'=Mg,Zn,Al,Ga,B,Zr,Ti), where the x is between 0 and 0.2, the .alpha. between 0 and 1, the .beta. between 0 and 1, the .gamma. between 0 and 2, the .delta. between about 0 and about 0.2, the y is between 2 and 4, and the z is between 0 and 0.5.
Analysis of multimode point-defect cavities in three-dimensional photonic crystals using group theory in frequency and time domains (2004)

We present analysis of a multimode point-defect cavity in a three-dimensional (3D) photonic crystal belonging to the point group, utilizing group-theoretical classifications in both the plane-wave expansion (PWE) and 3D finite-difference time-domain (FDTD) methods. In the PWE method, application of the projection operator to the electromagnetic fields is proposed to classify the point-defect modes into a basis of the irreducible representation of the point group. This is a simple computational process. A group-theory formulation is developed for Maxwell's equations in the time domain, involving the electric and magnetic current densities. It is demonstrated that a temporal analysis can be made independently about each basis vector of the irreducible representation of the symmetry group and this fact establishes Bloch's theorem in the time domain. In the FDTD method, the number of the point-defect modes dealt with in each calculation becomes small so that analysis of the multimode point-defect cavity is much simplified. In practice, we investigate various properties of multimode point-defect cavities belonging to the point group ${C}_{2h}$, including resonant frequency, field distribution, quality factor, light-extraction efficiency, radiation pattern, and polarization.
Filling the Holes in Cystic Kidney Disease Research (2014)

Kidney disease is a significant medical and public health problem. The National Institute of Diabetes and Digestive and Kidney Diseases recently asked the community to identify research objectives, which, if addressed, could improve understanding of basic kidney function and aid in prevention, treatment, and reversal of kidney disease. The Kidney Research National Dialogue invited interested parties to submit, discuss, and prioritize ideas using an interactive website; 1600 participants posted more than 300 ideas covering all areas of kidney disease, including the cystic kidney diseases. Although much is known about the genetics and pathogenesis of cystic diseases, there remain challenges to our understanding of the fundamental mechanisms of cyst formation, what genes act as modifiers to cause variable responses in different people, and how to detect and monitor disease progression. This article summarizes key research questions for cystic kidney diseases.
Synthesis and Characterization of Vanadyl Hydrogen Phosphite Hydrate. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Targeting the methyltransferase SETD8 impairs tumor cell survival and overcomes drug resistance independently of p53 status in multiple myeloma (2021)

Altogether, our data indicate that the up-regulation of the epigenetic enzyme SETD8 is associated with a poor outcome and the deregulation of major signaling pathways in MM. Moreover, we provide evidences that myeloma cells are dependent on SETD8 activity and its pharmacological inhibition synergizes with melphalan, which could be beneficial to improve MM treatment in high-risk patients whatever their status for p53.
Cluster method for the Ashkin-Teller model (1993)

A cluster Monte Carlo algorithm for the Ashkin-Teller (AT) model is constructed according to the guidelines of a general scheme for such algorithms. Its dynamical behavior is tested for the square-lattice AT model. We perform simulations on the line of critical points along which the exponents vary continuously, and find that critical slowing down is significantly reduced. We find continuous variation of the dynamical exponent z along the line, following the variation of the ratio of specific-heat and correlation-length exponents \ensuremath{\alpha}/\ensuremath{\nu}, in a manner which satisfies the Li-Sokal bound ${\mathit{z}}_{\mathrm{cluster}}$\ensuremath{\ge}\ensuremath{\alpha}/\ensuremath{\nu}, that was so far proved only for Potts models.
Object-based services with optimization in layered multi-source video delivery (2006)

We investigate the authoring, streaming and playback of object-based presentations. We also address optimization problems for adapting multimedia content in a scenario with multiple video sources encoded in multiple scalable layers. 
We first present the design and implementation of an MPEG-4 software toolkit. The modular design of the components in the toolkit is an advantage over existing MPEG-4 software as it allows components to be reused separately for developing parts of an MPEG-4 application. 
We also implement a new MPEG-4 node and a proposed client-server streaming framework; both were adopted by the MPEG-4 Systems specification. The node allows external applications (PDF reader or web browser) to be embedded with other objects within a scene while the framework supports more sophisticated two-way communication between the client and the server. 
We then investigate object-based content authoring issues and present a comparative analysis between MPEG-4 and the Synchronized Multimedia Integration Language (SMIL). Using SMIL, we create a PDA-based application and compare its capability with Macromedia Flash for supporting mobile applications. In view of the several limitations of MPEG-4, we co-developed the eXtensible MPEG-4 Textual Format (XMT), which was adopted by the MPEG-4 Systems specification. The goal of XMT is to improve the ease of content authoring and to support interoperability among existing standards. 
In the area of media adaptation, we address the problem of rate scaling of multiple video sources with sequences encoded in multiple layers. The scenario of multisource video streaming evolves naturally from a multi-object streaming application where resources are allocated among the various objects. Our work uses a combinatorial optimization technique---Multiple-Choice Knapsack Problem (MCKP). We develop several heuristics including one suitable for applications where a different priority is assigned to each source. In addition, we design a message passing protocol for synchronizing transmission of state information in a multi-camera video surveillance system and investigate the communications complexity of both centralized and distributed network configurations. 
Finally, we introduce the first genetic algorithm for solving MCKP. Our algorithm consists of several components designed utilizing problem-specific knowledge based on the characteristics of MCKP and yields performance improvement over existing heuristics.
Ultrabroadband microwave radiation from near- and mid-infrared laser-produced plasmas in air (2021)

An ultrashort laser pulse focused in air creates a plasma that radiates broadband electromagnetic waves. We experimentally compare the generation of microwaves from plasmas produced with two different laser systems that operate in the near- and mid-infrared regimes. Changing the laser wavelength increases the microwave power by 100 times and changing the input pulse energy allows for tuning of the microwave frequency spectrum, which we absolutely calibrate over a range of 2--70 GHz. The variation of the spectrum with laser pulse energy confirms the existence of a distinct mechanism that generates microwave radiation from laser-produced plasmas in gases. We propose that a radial diffusive expansion wave of the plasma electrons drives a longitudinal current along the plasma surface whose amplitude varies with the total residual electron energy imparted by the laser field and this longitudinal current produces the detected radiation.
Conversation Modeling to Predict Derailment (2023)

Conversations among online users sometimes derail, i.e., break down into personal attacks. Derailment interferes with the healthy growth of communities in cyberspace. The ability to predict whether an ongoing conversation will derail could provide valuable advance, even real-time, insight to both interlocutors and moderators. Prior approaches predict conversation derailment retrospectively without the ability to forestall the derailment proactively. Some existing works attempt to make dynamic predictions as the conversation develops, but fail to incorporate multisource information, such as conversational structure and distance to derailment. We propose a hierarchical transformer-based framework that combines utterance-level and conversation-level information to capture fine-grained contextual semantics. We propose a domain-adaptive pretraining objective to unite conversational structure information and a multitask learning scheme to leverage the distance from each utterance to derailment. An evaluation of our framework on two conversation derailment datasets shows an improvement in F1 score for the prediction of derailment. These results demonstrate the effectiveness of incorporating multisource information for predicting the derailment of a conversation.
Selection of Quantum Dot Wavelengths for Biomedical Assays and Imaging (2003)

Fluorescent semiconductor nanocrystals (quantum dots [QDs]) are hypothesized to be excellent contrast agents for biomedical assays and imaging. A unique property of QDs is that their absorbance increases with increasing separation between excitation and emission wavelengths. Much of the enthusiasm for using QDs in vivo stems from this property, since photon yield should be proportional to the integral of the broadband absorption. In this study, we demonstrate that tissue scatter and absorbance can sometimes offset increasing QD absorption at bluer wavelengths, and counteract this potential advantage. By using a previously validated mathematical model, we explored the effects of tissue absorbance, tissue scatter, wavelength dependence of the scatter, water-to- hemoglobin ratio, and tissue thickness on QD performance. We conclude that when embedded in biological fluids and tissues, QD excitation wavelengths will often be quite constrained, and that excitation and emission wavelengths should be selected carefully based on the particular application. Based on our results, we produced near-infrared QDs optimized for imaging surface vasculature with white light excitation and a silicon CCD camera, and used them to image the coronary vasculature in vivo. Taken together, our data should prove useful in designing fluorescent QD contrast agents optimized for specific biomedical applications.
Ligand‐Stabilized and Atomically Precise Gold Nanocluster Catalysis: A Case Study for Correlating Fundamental Electronic Properties with Catalysis (2013)

We present results from our investigations into correlating the styrene-oxidation catalysis of atomically precise mixed-ligand biicosahedral-structure [Au25(PPh3)10(SC12H25)5Cl2](2+) (Au25-bi) and thiol-stabilized icosahedral core-shell-structure [Au25(SCH2CH2Ph)18](-) (Au25-i) clusters with their electronic and atomic structure by using a combination of synchrotron radiation-based X-ray absorption fine-structure spectroscopy (XAFS) and ultraviolet photoemission spectroscopy (UPS). Compared to bulk Au, XAFS revealed low Au-Au coordination, Au-Au bond contraction and higher d-band vacancies in both the ligand-stabilized Au clusters. The ligands were found not only to act as colloidal stabilizers, but also as d-band electron acceptor for Au atoms. Au25-bi clusters have a higher first-shell Au coordination number than Au25-i, whereas Au25-bi and Au25-i clusters have the same number of Au atoms. The UPS revealed a trend of narrower d-band width, with apparent d-band spin-orbit splitting and higher binding energy of d-band center position for Au25-bi and Au25-i. We propose that the differences in their d-band unoccupied state population are likely to be responsible for differences in their catalytic activity and selectivity. The findings reported herein help to understand the catalysis of atomically precise ligand-stabilized metal clusters by correlating their atomic or electronic properties with catalytic activity.
PD42-09 URINE CELL IMAGE ANALYSIS USING A DEEP LEARNING MODEL (2020)

In silico analysis (TCGA) compared disease-free survival (DFS) between ARID1A mutant (ARID1Amut) and wildtype (wt) tumors. Western blot compared EZH2, ARID1A, and H3K27me3 protein levels between matched pairs of BCa and normal urothelium from cystectomy specimens. Cell proliferation assays were performed with/without EZH2 inhibitor GSK-126. Stable ARID1A knockdown cell lines were also tested. Murine xenograft experiments were performed using ARID1Amut and wt BCa cell lines to compare tumor growth inhibition by GSK-126. RNA microarray evaluated differentially expressed genes in ARID1Amut and wt BCa cell lines with/without GSK-126. Western blot and chromatin-immunopreciptation (ChIP) analysis confirmed the microarray findings.
SenseCode (2013)

Designing a communication protocol for sensor networks often involves obtaining the right trade-off between energy efficiency and end-to-end packet error rate. In this article, we show that network coding provides a means to elegantly balance these two goals. We present the design and implementation of SenseCode, a collection protocol for sensor networks—and, to the best of our knowledge, the first such implemented protocol to employ network coding. SenseCode provides a way to gracefully introduce a configurable amount of redundant information into the network, thereby decreasing end-to-end packet error rate in the face of packet loss. We compare SenseCode to the best (to our knowledge) existing alternative and show that it reduces end-to-end packet error rate in highly dynamic environments, while consuming a comparable amount of network resources. We have implemented SenseCode as a TinyOS module and evaluate it through extensive TOSSIM simulations.
Regioselective glycosylation: What's new? (2017)

International audience
The human cationic host defense peptide LL-37 mediates contrasting effects on apoptotic pathways in different primary cells of the innate immune system (2006)

The human cathelicidin LL-37 is a cationic host defense peptide (antimicrobial peptide) expressed primarily by neutrophils and epithelial cells. This peptide, up-regulated under conditions of inflammation, has immunomodulatory and antimicrobial functions. We demonstrate that LL-37 is a potent inhibitor of human neutrophil apoptosis, signaling through P2X(7) receptors and G-protein-coupled receptors other than the formyl peptide receptor-like-1 molecule. This process involved modulation of Mcl-1 expression, inhibition of BID and procaspase-3 cleavage, and the activation of phosphatidylinositol-3 kinase but not the extracellular signal-regulated kinase 1/2 mitogen-activated protein kinase pathway. In contrast to the inhibition of neutrophil apoptosis, LL-37 induced apoptosis in primary airway epithelial cells, demonstrating alternate consequences of LL-37-mediated modulation of apoptotic pathways in different human primary cells. We propose that these novel immunomodulatory properties of LL-37 contribute to peptide-mediated enhancement of innate host defenses against acute infection and are of considerable significance in the development of such peptides and their synthetic analogs as potential therapeutics for use against multiple antibiotic-resistant infectious diseases.
A DNA–porphyrin minor-groove complex at atomic resolution: The structural consequences of porphyrin ruffling (2000)

The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-N-methyl-pyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an R factor of 11.5% at a resolution of 0.9 A. The structure has been solved and refined as two crystallographically independent duplexes, stacked end to end. Contrary to expectation, the porphyrin molecule is not intercalated into the duplex but is stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly buckled as a consequence of the nickel coordination, which produces large changes in local DNA structure. A second mode of porphyrin binding is apparent as a consequence of crystal packing, which places the ligand in the minor groove of an adjacent duplex. This structure thus provides, to our knowledge, the first atomic visualization of minor-groove binding for a porphyrin molecule. The geometry of groove binding provides a ready explanation for porphyrin-induced DNA strand cleavage at deoxyribose residues.
Controlled Chainlike Agglomeration of Charged Gold Nanoparticles via a Deliberate Interaction Balance (2008)

Chain-like agglomeration (one-dimensional self-assembly) of aqueous gold nanoparticles (NPs) has been experimentally and theoretically studied. It is demonstrated that the chain growth of aqueous gold NPs is mainly triggered by the anisotropic dipolar interaction due to the Au−S bonding originating from the thiol-ligand capping, plus van der Waals interaction. This anisotropic self-assembly can be endorsed by the isotropic electrostatic repulsion between the gold NPs, which can be finely tuned by the dielectric constant of the surrounding media of the NPs that is dependent on the volume ratio of water to a polar organic solvent. Adding more thiol-ligands or NaCl brings a similar effect of increasing the ionic strength of the NP suspensions, thus lowering the electrostatic repulsion between and, at a certain range, accelerating chain-like agglomeration of the NPs. The use of various thiol-ligands with different terminal groups allow involvement of other interactions, including hydrophobic interaction and hydrogen bonding, between charged gold NPs, which gives rise to a faster kinetic of chain-like agglomeration.
Functionalized 4-(Dialkylamino)-4‘-nitrostilbenes as Reactive Fluorescent Probes for Monitoring the Photoinitiated Polymerization of MMA (1999)

A series of reactive (2, 4) and nonreactive (3, 5) fluorescent probes based on 4-(dimethylamino)-4‘-nitrostilbene (1) have been synthesized. Substitution of a methyl on the dimethylamino group results in blue shifts in emission and increases in Φf, and corresponding reactive and nonreactive probes are indistinguishable. Emission spectra of 1−5 were recorded during the photoinitiated polymerization of methyl methacrylate (MMA). For nonreactive probes, only minor changes in emission are observed during the first 40% of the reaction, while at conversions between 50 and 90% λmax is proportional to the conversion. For reactive probes shifts of λmax during the early stages of the process are observed, enabling them to monitor the full polymerization process. It was proven that the shift in emission during the first stage of the reaction is due to covalent attachment of the reactive probes to the PMMA backbone.
Vertical integration of array-type miniature interferometers at wafer level by using multistack anodic bonding (2016)

In this work, vertical integration of miniaturized array-type Mirau interferometers at wafer level by using multi-stack anodic bonding is presented. Mirau interferometer is suitable for MEMS metrology and for medical imaging according to its vertical-, lateral- resolutions and working distances. Miniaturized Mirau interferometer can be a promising candidate as a key component of an optical coherence tomography (OCT) system. The miniaturized array-type interferometer consists of a microlens doublet, a Si-based MEMS Z scanner, a spacer for focus-adjustment and a beam splitter. Therefore, bonding technologies which are suitable for heterogeneous substrates are of high interest and necessary for the integration of MEMS/MOEMS devices. Multi-stack anodic bonding, which meets the optical and mechanical requirements of the MOEMS device, is adopted to integrate the array-type interferometers. First, the spacer and the beam splitter are bonded, followed by bonding of the MEMS Z scanner. In the meanwhile, two microlenses, which are composed of Si and glass wafers, are anodically bonded to form a microlens doublet. Then, the microlens doublet is aligned and bonded with the scanner/spacer/beam splitter stack. The bonded array-type interferometer is a 7- wafer stack and the thickness is approximately 5mm. To separate such a thick wafer stack with various substrates, 2-step laser cutting is used to dice the bonded stack into Mirau chips. To simplify fabrication process of each component, electrical connections are created at the last step by mounting a Mirau chip onto a flip chip PCB instead of through wafer vias. Stability of Au/Ti films on the MEMS Z scanner after anodic bonding, laser cutting and flip chip bonding are discussed as well.