gebhart/patrepeval huggingface dataset:
Photoinduced Electron Transfer from PbS Quantum Dots to Cobalt(III) Schiff Base Complexes: Light Activation of a Protein Inhibitor (2013)

This paper describes the activation of a biologically inert Co(III) Schiff base [Co(III)-SB] complex to its protein inhibitor form by photoinduced electron transfer (PET) from a colloidal PbS quantum dot (QD, radii of 1.5-1.7 nm) to the cobalt center, with a charge separation time constant of 125 ns. Reduction of the Co(III)-SB complex initiates release of the native axial ligands, promoting replacement with the histidine mimic 4-methylimidazole. The rate of ligand displacement increases by a factor of approximately 8 upon exposure of the PbS QD/Co(III)-SB mixture to light with an energy greater than the energy of the first excitonic state of the QDs, from which PET occurs. These results suggest an approach for the preparation of inorganic therapeutic agents that can be specifically coupled to a biologically active site by cooperative redox binding ligation.
Protoporphyrin IX delayed fluorescence imaging: a modality for hypoxia-based surgical guidance (2022)

PpIX DF provides a mechanism for tumor contrast that could easily be translated to human use as an intrinsic contrast mechanism for oncologic surgical guidance.
Genome-wide linkage scan for colorectal cancer susceptibility genes supports linkage to chromosome 3q (2008)

The strongest evidence of linkage was seen for the region on chromosome 3. Interestingly, the same region has recently been reported as the most significant finding in a genome-wide analysis performed with SNP arrays; thus our results independently support the finding on chromosome 3q.
Portability of Syntactic Structure for Language Modeling (2001)

The paper presents a study on the portability of statistical syntactic knowledge in the framework of the structured language model (SLM). We investigate the impact of porting SLM statistics from the Wall Street Journal (WSJ) to the Air Travel Information System (ATIS) domain. We compare this approach to applying the Microsoft rule-based parser (NLPwin) for the ATIS data and to using a small amount of data manually parsed at UPenn for gathering the intial SLM statistics. Surprisingly, despite the fact that it performs modestly in perplexity (PPL), the model initialized on WSJ parses outperforms the other initialization methods based on in-domain annotated data, achieving a significant 0.4% absolute and 7% relative reduction in word error rate (WER) over a baseline system whose word error rate is 5.8%; the improvement measured relative to the minimum WER achievable on the N-best lists we worked with is 12%.
Positive End Expiratory Pressure: Effects on Lung Mechanics of Premature Lambs (1978)

Pulmonary mechanics were determined at 0, 3, 6, and 10 cm H2O positive and expiratory pressure (PEEP) in premature lambs at a mean gestational age of 134 days. Functional residual capacity increased (p less than 0.005) by 7% (1.6 ml/kg) per cm H2O PEEP. Dynamic lung compliance and specific compliance significantly decreased by 10% (0.11 ml/cm H2O/kg) and 9% (0.0051 l/cm H2O) per cm H2O PEEP, respectively, for PEEP above 3 cm H2O level. Inspiratory lung resistance increased significantly (p less than 0.05) only between 0 and 6 cm H2O PEEP while expiratory lung resistance increased (p less than 0.05) between 0 cm H2O PEEP and all higher levels. The data suggest that PEEP in excess of 3 cm H2O produces undesirable effects on lung mechanics in premature lambs. These results may be important in predicting contraindications and potential complications of positive pressure breathing in the newborn.
The Chemistry of Metallacyclic Alkenylcarbene Complexes, 4. Unsaturated Metallacyclic Carbene Complexes as Flexible Tools in Organic Synthesis. Novel Rearrangement and Cascade Pathways to Functionalized Alkadienes, Carbo‐, and Heterocycles (1996)

Abstract Cationic metallacyclic carbene complexes of iron and cobalt bearing a terminal η 3 ‐allyl ligand are susceptible to nucleophilic attack at different sites depending on the particular set of substituents, the central metal fragment, and the nucleophile. Attack of enolates, cuprates, acetylides, or heteroatom nucleophiles like phosphanes at the metallacyclic perimeter of the iron complexes 18 provides an easy access to unsaturated organic products like 1,2‐ or 1,3‐dienes, δ‐lactones, and functionalized cyclopentenones through novel rearrangement or cascade pathways. Synthetic applications are described; factors governing reactivity/selectivity are discussed; X‐ray analytical structures of novel metallacycles are provided.
Intestinal Epigenetic Reprogramming Relates to Glycemic Improvement after Roux-en-Y Gastric Bypass Surgery (2018)

Despite the remarkable, early remission of T2D after RYGB, the surgery’s key mechanisms have yet to be defined in a way that can be translated to less invasive therapies. Recently, we demonstrated that improved glucose homeostasis after RYGB in rodents is associated with intestinal metabolic reprogramming: the Roux Limb (RL) exhibits dramatic morphologic and metabolic remodeling, leading to augmented utilization of metabolic fuels to support the increased bioenergetic demand. To address whether this phenomenon is important for T2D remission in human patients after RYGB, RL biopsies were obtained at the time of surgery and at 1 and 6 months postoperatively. Differentially expressed genes (DEG) were determined using Affymetrix HTA 2.0 microarrays; morphology was examined via electron microscopy, revealing a significant increase in microvillus length over time (P&amp;lt;0.01). Enrichment analysis showed robust changes cellular proliferation, cell cycle regulation, and cytoskeletal remodeling pathways at both timepoints. DEG suggest a metabolic shift away from fatty acid oxidation, toward utilization of glucose and amino acids. Common DEG (FDR&amp;lt;0.05) at 1 and 6 months were strongly correlated (R2=0.899, P&amp;lt;0.0001), suggesting that RL signatures are established early and persist. Interestingly, 91% of the top 100 DEG at 6 months were downregulated; GSEA revealed significant enrichment of genes regulating epigenetic reprogramming (P&amp;lt;0.01), e.g., DNMT1 and DNMT3B at 1 and 6 months. Remarkably, change in DNMT1 expression at 1 month, controlling for baseline body weight, predicted 6-month HbA1c change (R2=0.744, P=0.002). This suggests a mechanistic role for methylation to underlie glycemic improvement, and points to a potential predictive role for early RL DEG. We hypothesize that post-RYGB T2D improvement may relate to RL remodeling including increased energy utilization, and that the stimulus may be epigenetic reprogramming as a result of altered intestinal nutrient flow. Disclosure M.A. Stefater: None. C. Panciotti: None. H.A. Feldman: None. W.F. Gourash: Research Support; Self; Coviden, Ethicon US, LLC., National Institute of Diabetes and Digestive and Kidney Diseases. E. Shirley: None. A. Courcoulas: Research Support; Self; National Institute of Diabetes and Digestive and Kidney Diseases, Patient-Centered Outcomes Research Institute, National Institutes of Health, Coviden. N. Stylopoulos: None.
Kleister: A novel task for Information Extraction involving Long Documents with Complex Layout (2020)

State-of-the-art solutions for Natural Language Processing (NLP) are able to capture a broad range of contexts, like the sentence-level context or document-level context for short documents. But these solutions are still struggling when it comes to longer, real-world documents with the information encoded in the spatial structure of the document, such as page elements like tables, forms, headers, openings or footers; complex page layout or presence of multiple pages. To encourage progress on deeper and more complex Information Extraction (IE) we introduce a new task (named Kleister) with two new datasets. Utilizing both textual and structural layout features, an NLP system must find the most important information, about various types of entities, in long formal documents. We propose Pipeline method as a text-only baseline with different Named Entity Recognition architectures (Flair, BERT, RoBERTa). Moreover, we checked the most popular PDF processing tools for text extraction (pdf2djvu, Tesseract and Textract) in order to analyze behavior of IE system in presence of errors introduced by these tools.
Atomic layer diffusion and electronic structure at In0.53Ga0.47As/InP interfaces (2004)

We have used secondary ion mass spectrometry and cathodoluminescence spectroscopy to determine the effects that growth and postgrowth conditions have on interdiffusion and near band edge emissions in In0.53Ga0.47As/InP heterojunctions grown by molecular beam epitaxy. This lattice-matched interface represents a model system for the study of atomic movements and electronic changes with controlled anion overlap during growth. Structures subjected to anneals ranging from 440 to 495 °C provide a quantitative measure of concentration-driven cross diffusion of group-III and group-V atoms. By measuring anneal-induced broadening at the InGaAs-on-InP interface we have determined an activation energy for As diffusion into InP of ∼2.44±0.40 eV. An interface layer with Ga–P bonds indicates Ga competes favorably versus As for bonding in the preannealed InP near-surface region. In addition, we present evidence that interface chemical effects manifest themselves electronically as variations of the InGaAs band gap energy.
Low temperature transport of Al into and through copper starting with Cu/Al/SiO2 bilayers (1999)

The transport of Al into Cu is studied by annealing Cu/Al/SiO2 bilayers. In order to minimize the effects of contaminants, samples were prepared and annealed in all-metal ultrahigh vacuum systems. In situ resistivity was used to continuously monitor the transport of Al into the bulk of the copper films. It is observed: that Al begins to move into the copper at low temperature (100–150 °C); that during an isothermal anneal, there is an initial rapid increase in Al concentration in the copper followed by a very slow increase; the equivalent of about 45 A of Al remains bound at the SiO2 interface or at the surface of the copper and is not free to dissolve in the copper. These data are not consistent with simple one-dimensional bulk diffusion but are in good agreement with a model of three-dimensional copper grains in which there is rapid transport to saturate the grain boundaries followed by diffusion of Al from the grain boundaries into the copper grains. One important observation is that because of the role of grain boundaries, it is possible to transport Al through copper films without a significant increase in the resistivity of the copper films. The potential application of this system for microelectronic interconnects in modern microelectronics is discussed.
Abstract 5538A: Cell size-specific intracellular delivery (2015)

Abstract Among the many methods of intracellular delivery, cell size-selective delivery is particularly applicable to cancer research and therapeutics where tumor cells tend to be larger than blood cells and selective manipulation of a single cell-type while minimally affecting the other cells in a heterogeneous mixture is important. In this study, cell size-selective delivery is achieved using a novel microfluidic device with 75 parallel channels through which cells are pushed under nitrogen pressure. The cells undergo deformation as they transit through the channels, which results in temporary disruption of the cell membrane to facilitate delivery of material into the cytoplasm. For each cell size, there is a specific channel width for which optimal cell viability and fluorophore delivery is achieved, with smaller cells requiring narrower channels. When two cells of different sizes are mixed in solution, the channel width for optimal cell viability and fluorophore delivery for each cell type remains the same, and larger cells can achieve fluorophore delivery at a significantly higher percentage than smaller cells at the former's optimal channel width. One possible application for this technology is tagging circulating tumor cells, and we have been able to selectively deliver fluorophores into tumor cells when spiked into whole human blood with 91% specificity. We were also able to isolate pancreatic tumors cells from a patient's blood sample that matched the genotype of the patient's primary pancreatic tumor. Intracellular delivery of materials has become increasingly important as we delve deeper into understanding cellular processes and developing targeted therapies, and with this device, selective delivery can be achieved in a vector-free environment and without dependence on cell-surface receptors. Citation Format: May Tun Saung, Armon Sharei, Viktor Adalsteinsson, Andrew Liss, Nahyun Cho, Tushar Kamath, Camilo Ruiz, Jesse Kirkpatrick, Robert Langer, Christopher Love, Klavs Jensen. Cell size-specific intracellular delivery. [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 5538A. doi:10.1158/1538-7445.AM2015-5538A
Maximin Analysis of Message Passing Algorithms for Recovering Block Sparse Signals (2013)

We consider the problem of recovering a block (or group) sparse signal from an underdetermined set of random linear measurements, which appear in compressed sensing applications such as radar and imaging. Recent results of Donoho, Johnstone, and Montanari have shown that approximate message passing (AMP) in combination with Stein's shrinkage outperforms group LASSO for large block sizes. In this paper, we prove that, for a fixed block size and in the strong undersampling regime (i.e., having very few measurements compared to the ambient dimension), AMP cannot improve upon group LASSO, thereby complementing the results of Donoho et al.
A simple transmission line de-embedding method for accurate RF CMOS noise modeling (2004)

We propose a simple method to de-embed the transmission line and pad parasitics from the measured RF noise of multi-finger MOSFETs with aggressive gate length scaling down to 80 nm and 65 nm respectively. Good agreement has been realized between measurement and simulation in terms of S-parameters and NF/sub min/ (minimum noise figure) for RF CMOS devices with various finger numbers by using this novel de-embedding method. The extracted NF/sub min/ after de-embedding matches well with the published noise correlation matrix method but is relatively simple without resort to complicated matrices calculation.
A silicon nitride microphone diaphragm inspired by the ears of the parasitoid fly Ormia ochracea (2001)

A differential microphone is described that has been designed to employ similar operating principles to that of the ears of the parasitoid fly, Ormia ochracea. The ears of this fly have been shown to be highly directional even though they are only about 1 mm across [R. N. Miles, D. Robert, and R. R. Hoy, J. Acoust. Soc. Am. 98, 3059–3070 (1995)]. Analyses of the mechanics of this biological system suggest novel approaches to the design of miniature directional microphones. Finite element analysis results for the acoustic resonse of a 1 mm by 2 mm silicon nitride microphone diaphragm are presented. The diaphragm responds to pressure gradients in a manner that is inspired by Ormia’s ears. Predicted results for the natural frequencies, mode shapes, frequency response and directivity of our design are shown to compare closely with measured data obtained for a prototype silicon nitride diaphragm. [Work supported by NIH and DARPA.]
Transmission and Amplification of Information and Properties in Nanostructured Liquid Crystals (2008)

Abstract In recent years the design of chemical structures of liquid‐crystalline materials has developed rapidly, and in many cases changed radically. Since Reinitzer's days, liquid crystals have either been classed as rodlike or disclike, with combinations of the two leading to phasmidic liquid crystals. The discovery that materials with bent molecular structures exhibited whole new families of mesophases inspired investigations into the liquid‐crystal properties of materials with widely varying molecular topologies—from pyramids to crosses to dendritic molecules. As a result of conformational change, supermolecular materials can have deformable molecular structures, which can stabilize mesophase formation, and some materials that are non‐mesogenic, on complexation form supramolecular liquid crystals. The formation of mesophases by individual molecular systems is a process of self‐organization, whereas the mesophases of supramolecular systems are formed by self‐assembly and self‐organization. Herein we show 1) deformable molecular shapes and topologies of supermolecular and self‐assembled supramolecular systems; 2) surface recognition processes of superstructures; and 3) that the transmission of those structures and their amplification can lead to unusual mesomorphic behavior where conventional continuum theory is not suitable for their description.
Continuous Wavelength Conversion of 40-Gb/s Data Over 100 nm Using a Dispersion-Engineered (2011)

We demonstrate broadband continuous wavelength conversion based on four-wave mixing in silicon waveguides, operating with data rates up to 40 Gb/s, validating signal integrity using bit-error-rate measurements. The dispersion-engineered silicon waveguide provides broad phase-matching bandwidth, enabling complete wavelength-conversion coverage of the -, -, and -bands of the International Telecommunication Union (ITU) grid. We experimentally show this with wavelength conversion of high-speed data exceeding 100 nm, and characterize the resulting power penalty induced by the wavelength conversion process. We then validate the bit-rate transparency of the all-optical process by scaling the data rate from 5 Gb/s up to 40 Gb/s at the 100-nm wavelength conversion configuration, showing consistent low power penalties, validating the robustness of the four-wave mixing process in the silicon platform for all-optical processing.
FAST FLUID REGISTRATION WITH DIRICHLET BOUNDARY CONDITIONS: A TRANSFORM-BASED APPROACH (2007)

Fluid registration is an example of a nonrigid image registration algorithm that uses a deformation field to define the transformation between two images. The velocity of the deformation field is governed by the Navier-Lame equations, which can be discretized and solved numerically via fixed-point iteration. The fixed-point iteration generates a succession of linear PDE systems, which can be solved quickly via discrete Fourier transform (DFT) techniques, as shown in the prior art. The major drawback of this approach is that it is only applicable when the boundary conditions of the velocity field are assumed to be periodic. This paper shows that by considering the adjoint of the Navier-Lame operator, the succession of linear PDE systems can be solved quickly via discrete sine transform (DST) techniques, generating velocity fields that satisfy Dirichlet boundary conditions (where the velocities are zero on the boundaries)
Mathematical Modeling of an Anode - Supported Solid Oxide Fuel Cell (2009)

International audience
Design of surface patterns with optimized thermodynamic driving forces for the directed self-assembly of block copolymers in lithographic applications (2017)

A theoretical method for developing design rules for the directed self-assembly of block copolymers for lithographic applications.
An Expedient Synthesis of Highly Functionalized Naphthyridones and Quinolines from a Common N‐Aryl Pyridinone Template. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Etrasimod as induction and maintenance therapy for ulcerative colitis (ELEVATE): two randomised, double-blind, placebo-controlled, phase 3 studies (2023)

Arena Pharmaceuticals.
2D Frequency Selective Extrapolation for Spatial Error Concealment in H.264/AVC Video Coding (2006)

The frequency selective extrapolation extends an image signal beyond a limited number of known samples. This problem arises in image and video communication in error prone environments where transmission errors may lead to data losses. In order to estimate the lost image areas, the missing pixels are extrapolated from the available correctly received surrounding area which is approximated by a weighted linear combination of basis functions. In this contribution, we integrate the frequency selective extrapolation into the H.264/AVC coder as spatial concealment method. The decoder reference software uses spatial concealment only for I frames. Therefore, we investigate the performance of our concealment scheme for I frames and its impact on following P frames caused by error propagation due to predictive coding. Further, we compare the performance for coded video sequences in TV quality against the non-normative concealment feature of the decoder reference software. The investigations are done for slice patterns causing chequerboard and raster scan losses enabled by flexible macroblock ordering (FMO).
Fan in loss in electrical and optical circuits and systems (2002)

Analogies between the fan-in limitations of linear electrical circuits and linear optical circuits are explored. In both cases, the second law of thermodynamics sets the limits as to the amount of power that can be coupled from multiple inputs into a single output. The limitation applies to the power coupled into a single (properly defined) output "mode" from a set of input modes. While fan-in limitations of optics have generally been stated in terms of power coupled into a single outgoing spatial mode from incoming spatial modes, a more general view makes use of temporal and polarization modes as well. It is then possible to show that the usual fan-in restrictions stated with respect to only spatial modes can be violated, while the more general restriction in terms of space-time-polarization modes remains satisfied. The results have direct application to wavelength multiplexed optical interconnects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Targeted therapies for the systemic treatment of advanced hepatocellular carcinoma (2009)

The prognosis for advanced hepatocellular carcinoma is poor and systemic therapy has historically been of limited benefit. However, novel targeted agents offer promise in improving patient outcomes. In a recent phase III study the oral multi-tyrosine kinase inhibitor sorafenib was demonstrated to have a survival advantage over a placebo in advanced hepatocellular carcinoma. Similar efficacy was demonstrated in a phase III trial limited to an Asian‐Pacific group of patients. While these results are encouraging, it is vital to make further progress. In this review we examine current knowledge of targeted agents in advanced hepatocellular carcinoma. We also address some of the key issues that require exploration regarding the use of targeted agents in advanced hepatocellular carcinoma.