gebhart/patrepeval huggingface dataset:
Synergistic Effects of Stereochemistry and Appendages on the Performance Diversity of a Collection of Synthetic Compounds (2018)

Target- and phenotype-agnostic assessments of biological activity have emerged as viable strategies for prioritizing scaffolds, structural features, and synthetic pathways in screening sets, with the goal of increasing performance diversity. Here, we describe the synthesis of a small library of functionalized stereoisomeric azetidines and its biological annotation by "cell painting," a multiplexed, high-content imaging assay capable of measuring many hundreds of compound-induced changes in cell morphology in a quantitative and unbiased fashion. Using this approach, we systematically compare the degrees to which a core scaffold's biological activity, inferred from its effects on cell morphology, is affected by variations in stereochemistry and appendages. We show that stereoisomerism and appendage diversification can produce effects of similar magnitude, and that the concurrent use of these strategies results in a broader sampling of biological activity.
Extracorporeal CO<sub>2</sub> Removal – A Way to Achieve Ultraprotective Mechanical Ventilation and Lung Support: The Missing Piece of Multiple Organ Support Therapy (2010)

Extracorporeal therapies are able to sustain life through different mechanisms. This approach, called multiple organ support therapy, can in fact obtain blood purification by hemodialysis/hemofiltration to replace kidney function, temperature control, electrolyte and acid-base control to mimic homeostatic regulation of the kidney and circulation, fluid balance control to support the right hydration and cardiac performance, cardiac support removing cardiodepressant substances and equilibrating potassium levels, blood detoxification and liver support by coupled plasma filtration and adsorption or direct adsorption on blood (hemoperfusion), immunomodulation and endothelial support in the presence of sepsis by cutting the peaks of pro- and anti-inflammatory mediators, and immunoadsorption or adsorption of specific substances such as endotoxin. A missing piece of this group of therapies was the protective lung support. Today this is made possible by removal of CO(2) either by complete extracorporeal membrane oxygenation or by using decapneization in conjunction with hemofiltration in a system called DECAP/DECAPSMART. In conclusion, circulating blood outside the body and treating it with different filters or cartridges in a multiple organ support therapy may represent an important support for multiple organ dysfunction conditions induced by sepsis, acute respiratory distress syndrome and in recent times by complicated H1N1-related infections.
Location Aware Training Scheme for D2D networks (2013)

We consider the problem of acquiring Channel State Information (CSI) in base-station (BS) controlled Device To Device (D2D) networks. Obtaining high-quality CSI requires a trade-off between interference, outdatedness of CSI, and noise. Thus, the goal is to find an efficient pilot scheduling scheme that minimizes errors in the estimates. In this paper we present the Location Aware Training Scheme (LATS) as simple yet efficient training technique. Assuming that users know their location, LATS distributes the users onto segments and assigns a frequency reuse pattern to them. To identify the parameters of this scheme (size of segments and guard spaces), we numerically minimize the Mean Square Error (MSE) as a metric that combines the outdatedness, noise, and interference. Simulations shows that LATS outperforms other existing schemes.
Silicon-photonics-based optical transceivers for high-speed interconnect applications (2016)

In this paper we discuss design and characterization of silicon-photonics-based 100 Gbps (4&times;26 Gbps) transceivers for parallel single mode fiber communication. We also address some key underlying technologies including silicon photonics wafer processing, photonic device libraries, light source integration and packaging technologies.
Large Effective χ(2) Nonlinearity via Coherent Photon Conversion on a Si3N4 Chip (2017)

We generate large effective χ(2) nonlinearities in a purely χ(3)-nonlinear Si3N4 microring-resonator using the coherent photon conversion scheme and measure a normalized effective second harmonic generation efficiency above 77%/mW.
Learning from computations and experiments simultaneously: Multi-agent consensus equlibrium (MACE) for improving chemical structure determination (2020)

A framework for integration of empirically measured molecular structure, as inferred by moment of inertia, and <i>ab initio</i> structure prediction is presented to enable recovery of molecular structure representative of empirical conditions. Structural elucidation is a ubiquitous endeavor in chemistry, from crystal structure determination to molecular structure and conformational
<title>Progress toward implantable fluorescence-based sensors for monitoring glucose levels in interstitial fluid</title> (2000)

A painless monitoring procedure for diabetics has proven to be an elusive goal. While completely noninvasive measurements are the desired technique, minimally invasive procedures using implanted fluorescence sensor chemistry offer significant advantages in specificity over current noninvasive approaches. The goal was to evaluate the potential for transdermal glucose sensing using intensity measurements from implanted microspheres. A fiber-optic probe and spectrometer were custom-built for collection of in vivo data. Comparisons with commercial fluorometers show the constructed device is adequate for this project.
Impact of anti-Zeno Effect on a Coupled Nanocavity-Quantum-Dot System (2009)

A comprehensive theory of couplings between a cavity and different charge configurations in a quantum dot is developed. It is shown that the quantum anti-Zeno effect is essential for the results obtained by QED experiments.
ChemInform Abstract: A Convenient Synthesis of (S)‐3‐Methyladipic Acid. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Discovery, synthesis and biological evaluation of a series of N-(phenylcarbamothioyl)-2-napthamides as inhibitors of Claudin-1 (2023)

Colorectal cancer (CRC) remains a leading cause of cancer-related deaths worldwide, despite advancements in diagnosis. The main reason for this is that many newly diagnosed CRC patients will suffer from metastasis to other organs. Thus, the development of new therapies is of critical importance. Claudin-1 protein is a component of tight junctions in epithelial cells, including those found in the lining of the colon. It plays a critical role in the formation and maintenance of tight junctions, which are essential for regulating the passage of molecules between cells. In CRC, claudin-1 is often overexpressed, leading to an increase in cell adhesion, which can contribute to the development and progression of the disease. Studies show that high levels of claudin-1 are associated with poor prognosis in CRC patients and targeting claudin-1 may have therapeutic potential for the treatment of CRC. Previously, we have identified a small molecule that inhibits claudin-1 dependent CRC progression. Reported herein are our lead optimization efforts around this scaffold to identify the key SAR components and the discovery of a key new compound that exhibits enhanced potency in SW620 cells.
Adaptive search for sparse targets with informative priors (2010)

This works considers the problem of energy constrained adaptive search for sparse targets given probabilistic prior knowledge of target locations. An Adaptive Resource Allocation Policy (ARAP) was introduced by Bashan (2008), showing significant gains over standard methods can be achieved without prior knowledge on the targets' locations. This work extends ARAP to account for nonuniform prior knowledge. It is shown that potential gains exist as compared to ARAP. Moreover, we show that by overestimating the true region of interest, the proposed search policy can always outperform ARAP in terms of worst-case gain. Lastly, results from an application involving estimating the approach of airplanes at an airport suggest that bi-level piecewise uniform priors are adequate approximations.
DNA Methylation Is Involved in the Expression of miR-142-3p in Fibroblasts and Induced Pluripotent Stem Cells (2014)

MicroRNAs are differentially expressed in cells and regulate multiple biological processes. We have been analyzing comprehensive expression patterns of microRNA in human and mouse embryonic stem and induced pluripotent stem cells. We determined microRNAs specifically expressed in these pluripotent stem cells, and miR-142-3p is one of such microRNAs. miR-142-3p is expressed at higher levels in induced pluripotent stem cells relative to fibroblasts in mice. Level of expression of miR142-3p decreased during embryoid body formation from induced pluripotent stem cells. Loss-of-function analyses of miR-142-3p suggested that miR-142-3p plays roles in the proliferation and differentiation of induced pluripotent stem cells. CpG motifs were found in the 5' genomic region of the miR-142-3p; they were highly methylated in fibroblasts, but not in undifferentiated induced pluripotent stem cells. Treating fibroblasts with 5-aza-2'-deoxycytidine increased the expression of miR-142-3p significantly and reduced methylation at the CpG sites, suggesting that the expression of miR-142-3p is suppressed by DNA methylation in fibroblasts. Luciferase analysis using various lengths of the 5' genomic region of miR142-3p indicated that CpGs in the proximal enhancer region may play roles in suppressing the expression of miR-142-3p in fibroblasts.
Assessment of side-effects by Ludox TMA silica nanoparticles following a dietary exposure on the bumblebeeBombus terrestris (2011)

We assessed lethal and sublethal side-effects of Ludox TMA silica nanoparticles on a terrestrial pollinator, Bombus terrestris (Linnaeus), via a dietary exposure. Dynamic light scattering analysis confirmed that silica Ludox TMA nanoparticles remained in suspension in the drinking sugar water. Exposure of bumblebee microcolonies during 7 weeks to the different nanoparticle concentrations (high: 34, 170 and 340 mg/l and low: 34 and 340 μg/l) did not cause worker mortality compared to the controls. Also no effect on the worker foraging behavior was observed after exposure to nanoparticles concentrations up to 340 μg/l. In contrast, the high concentrations (≥34 mg/l) resulted in a total loss of reproduction. Using histological analysis we confirmed severe midgut epithelial injury in intoxicated workers (≥34 mg/l). Despite the fact that these concentrations are much higher than the predicted environmental concentrations, precaution is still needed as information regarding their fate in the terrestrial environment and their potency to bioaccumulate and biomagnificate is lacking.
Large‐signal microwave transistor modeling using multiharmonic load‐pull measurements (1992)

Abstract This article presents a method of transistor parameter extraction using multiharmonic Load‐Pull (MHLP) measurements completed with modified harmonic balance calculations. An advantage of this approach is that the parameters of the nonlinear elements of the transistor are obtained solely from large‐signal measurements at the fundamental and the generated harmonic frequencies. The calculated parameters of the nonlinear model of a commercial MESFET (NE 71083), are found suitable for large‐signal operating mode at different impedance loading. © 1992 John Wiley &amp; Sons. Inc.
Improving Handwritten OCR with Training Samples Generated by Glyph Conditional Denoising Diffusion Probabilistic Model (2023)

Constructing a highly accurate handwritten OCR system requires large amounts of representative training data, which is both time-consuming and expensive to collect. To mitigate the issue, we propose a denoising diffusion probabilistic model (DDPM) to generate training samples. This model conditions on a printed glyph image and creates mappings between printed characters and handwritten images, thus enabling the generation of photo-realistic handwritten samples with diverse styles and unseen text contents. However, the text contents in synthetic images are not always consistent with the glyph conditional images, leading to unreliable labels of synthetic samples. To address this issue, we further propose a progressive data filtering strategy to add those samples with a high confidence of correctness to the training set. Experimental results on IAM benchmark task show that OCR model trained with augmented DDPM-synthesized training samples can achieve about 45% relative word error rate reduction compared with the one trained on real data only.
Evaluating the Performance of Models for Matrix Permeability Estimation from Complex Resistivity Measurements at Two Sedimentary Rock Sites (2015)

Spatially extensive estimates of permeability remain challenging to acquire using conventional borehole hydraulic tests at a scale to resolve matrix permeability values. Geophysical measurements are sensitive to the pore geometry controlling fluid flow and provide opportunities for indirect estimation of permeability from continuous measurements acquired in boreholes. The spectral induced polarization (SIP) or complex resistivity (CR) geophysical method provides information on a length-scale related to pore or grain diameter and the tortuosity of the interconnected porosity of the matrix, representing matrix permeability values. We tested a model for permeability prediction using CR on intact core samples obtained from two sedimentary rock sites. We acquired surface area measurements by nitrogen gas adsorption using the Brunauer–Emmett–Teller (BET) method, pore size distributions from mercury injection capillary pressure (MICP) porosimetry and gas permeability following ASTM D4525. The results demonstrate the sensitivity of CR to the pore geometric properties controlling fluid flow but show that the model requires calibration of fitting parameters that vary depending on site lithology conditions. The findings indicate the need for further studies of the control of mineralogy and fluid chemistry on the interfacial polarization generating the CR response.
Human iPSC-derived astrocytes transplanted into the mouse brain display three morphological responses to amyloid-β plaques (2020)

ABSTRACT Background Increasing evidence for a direct contribution of astrocytes to neuroinflammatory and neurodegenerative processes causing Alzheimer’s disease comes from molecular studies in rodent models. However, these models may not fully recapitulate human disease as human and rodent astrocytes differ considerably in morphology, functionality, and gene expression. Methods To address these challenges, we established an approach to study human astroglia within the context of the mouse brain by transplanting human induced pluripotent stem cell (hiPSC)-derived glia progenitors into neonatal brains of immunodeficient mice. Results Xenografted (hiPSC)-derived glia progenitors differentiate into astrocytes that integrate functionally within the mouse host brain and mature in a cell-autonomous way retaining human-specific morphologies, unique features and physiological properties. In Alzheimer’s chimeric brains, transplanted hiPSC-derived astrocytes respond to the presence of amyloid plaques with various morphological changes that seem independent of the APOE allelic background. Conclusion In sum, this chimeric model has great potential to analyze the role of patient-derived and genetically modified astroglia in Alzheimer’s disease.
Bulk Heterojunction Solar Cells – Tuning of the HOMO and LUMO Energy Levels of Pyrrolic Squaraine Dyes (2011)

Abstract The optimization of organic photovoltaic (OPV) devices requires, amongst several factors mainly related to thin‐film blend morphology, the capability to finely tune the characteristic energy levels of both the donor and the acceptor materials constituting the active layer. Squaraine compounds represent one of the most promising small molecule materials to be employed as the donor in the bulk heterojunction (BHJ) OPV configuration. In this study a series of arylhydrazone end‐capped symmetric squaraine compounds bearing electron‐withdrawing substituents on the aryl ring has been synthesized with the aim of increasing the device open circuit voltage by shifting the highest occupied molecular orbital (HOMO) energy level. These new semiconductors have been characterized by optical spectroscopy (UV/Vis absorption and IR transmittance) and electrochemical measurements (cyclic voltammetry and differential pulsed voltammetry). Our data enable the establishment of interesting structure–property relationships relating the nature, position and number of electron‐withdrawing substituents to the position of the donor HOMO and lowest unocupied molecular orbital (LUMO) levels. The low energy shift effect on the HOMO level with respect to the parent unsubstituted squaraine can be as high as 0.3 eV. The effect is so strong that the derivative bearing the strongest acceptor no longer behaves as a donor semiconductor. Preliminary results on OPV device preparation and characterization are also discussed.
A NOTE ON A SYMPTOMATIC TREATMENT OF ASTHMA (1929)

1. Ephedrinie hhas a definiite beneficial effect oni moderate attacks of asthma, tlieir iiinumber and severity being diminiislhed( or1 even comp)letely aborted.
Highly Linear and Highly Efficient Dual-Carrier Power Amplifier Based on Low-Loss RF Carrier Combiner (2014)

This paper presents a novel power amplifier (PA) architecture for amplifying dual-carrier signals with simultaneous high efficiency and high linearity. This dual-carrier PA is based on two high-efficiency PAs and an innovative RF carrier combiner, which is a diplexer implemented with bandstop filters (BSFs). This special BSF diplexer is capable of combining two carriers with ultra-narrow frequency spacings, e.g., down to 0.25% fractional bandwidth, while maintaining a low combining loss of 1 dB. Compared to conventional diplexers implemented with bandpass filters, this new technology leads to minimized resource usage for achieving the same combining performance. The integrated PA exhibits excellent performance when amplifying dual-carrier signals in terms of linearity and efficiency. Specifically, third-order intermodulations of 40 dBc were measured with 70.2% (60.8%) power-added efficiency for carrier spacing of 10 MHz (5 MHz).
Admixture and Ethno-Specific Alleles: Missing Links for Global Pharmacogenomics (2016)

Admixture is deemed a potential confounder that may give rise to spurious associations in genetic studies due to varying degree of parental backgrounds among individuals in the population.
Design of a Navigational Aid for Colonoscopy (2008)

Colonoscopy is currently the gold standard for diagnosing colorectal cancer and inflammatory bowel disease. During a colonoscopy, a flexible endoscope is inserted into the patient’s colon to inspect the inner wall of the large intestine, from the rectum to the caecum. This procedure is very important for cancer screening and can yield early diagnosis. Colon cancer is 85–95% successfully treated if detected early; however, there is only a 30% compliance rate for the procedure in the United States. This low compliance rate for the examination is largely due to its uncomfortable nature, caused by difficulties in blind scope manipulation, and “looping” of the endoscope which can lead to stretching and perforation of the bowel [1] (Figure 1).
Long QT syndrome-associated mutations in the S4-S5 linker of KvLQT1 potassium channels modify gating and interaction with minK subunits. (1999)

The author list was incorrect. Dr. Shen should appear as noted above.
A new procedure for the Juliá–Colonna stereoselective epoxidation reaction under non-aqueous conditions: the development of a catalyst comprising polyamino acid on silica (PaaSiCat) (1999)

T. Geller and S. M. Roberts, J. Chem. Soc., Perkin Trans. 1, 1999, 1397 DOI: 10.1039/A903219C
A Robust Adjacent Track Servo System with Linear Positioning Method (2011)

A multi-layer disk without guide groove enables a large capacity and price competitive optical disk. We propose a novel tracking servo system which is robust and accurate for disks without groove, and confirm its performance with simulation.
Neural Network-supported Fast Online-Customized (FOCUS) parallel transmit (pTx) pulses for slice-selective, large flip angle excitation (2023)

Slice-selective, two-spoke parallel transmit (pTx) pulses for exciting large flip angles can be designed quickly and show robust performance for MRI at 7 Tesla using an 8Tx/32Rx coil. Firstly, clusters of B 1 + /B 0 maps are defined and corresponding pulses are optimized prior to the scan. These serve as initialization for a fast, gradient-descent based online-optimization. For each slice, the best cluster-specific initialization is chosen online via neural networks, which predict their respective spatial distribution of the longitudinal magnetization. This approach outperforms other strategies to initialize the pTx RF pulses such as offline-optimized slab-specific and circularly polarized RF pulses as initializations.
Pharmacogenetic approach to losartan in Marfan patients: a starting point to improve dosing regimen? (2016)

The optimal dose of angiotensin receptor blocker is not known, and no data are available about losartan pharmacogenetic profile in Marfan syndrome; we have proposed a strategy to tackle this issue based on evaluating the major genetic polymorphisms involved in the losartan conversion into active carboxylic acid metabolite. Further studies are needed to support the use of genetic polymorphisms as predictors of the right dose of losartan.
TGF-β modulates cell fate in human ES cell-derived foregut endoderm by inhibiting multiple endogenous signaling pathways (2021)

Summary Genetic differences between pluripotent stem cell lines causes variable activity of extra-cellular signaling pathways, which limits the reproducibility of directed differentiation protocols. Here we used human embryonic stem cells (hESCs) to interrogate how exogenously provided factors modulate endogenous signaling events during specification of foregut endoderm lineages. We find that TGF-β1 activates an OTX2 / LHX1 gene regulatory network that promotes anterior fate by antagonizing endogenous Wnt signaling. In contrast to Porcupine inhibition, the effects of TGF-β1 cannot be reversed by exogenous Wnt ligands, suggesting that induction of SHISA proteins and intracellular accumulation of Fzd receptors make TGF-β1 treated cells refractory to Wnt signaling. Subsequently, TGF-β1-mediated inhibition of Bmp- and Wnt-signaling suppresses liver- and promotes pancreas fate. However, pancreas differentiation is delayed by TGF-β1-induced CYP26A1 expression and inhibition of RA signaling. Our study thus identifies multiple mechanisms of crosstalk between major developmental signaling pathways during foregut patterning.
Survivability Using Controlled Security Services (2005)

Abstract : This document represents the final report on the SUCSES project funded by DARPA/ITO under the Dynamic Coalitions (DC) program. SUCSES' period of performance spanned roughly four years between August 1999 and September 2003. The document is organized as follows: First part contains the overview of the project's setting and its goals. We then present a summary of year-by-year technical achievements and activities. Next, we list all external results, including publications, presentations, dissertations and technology transfer efforts. The bulk of the report is contained in the appendix that includes the copies of all publications produced under the aegis of the SUCSES project.