gebhart/patrepeval huggingface dataset:
Metabolic Networks (2006)

The function of cells is based on complex networks of interacting chemical reactions carefully organized in space and time. These biochemical reaction networks produce observable cellular functions. Network reconstruction is the process of identifying all the reactions that comprise a network. The reconstruction process for metabolic networks has been developed and implemented for a number of organisms. The main features of metabolic network reconstruction are described in this chapter. We briefly review the key properties of metabolic networks and introduce the hierarchical thinking that goes into the interpretation of complex network functions. Further details can be found in authoritative sources.
Contrasts in Copper Deposition on Pt(111) Modified by 1-Mercaptopropionic and 1-Mercaptoacetic Acids as Probed by Voltammetry and STM (2018)

Copper deposition on metal electrodes modified by organosulfur compounds has been extensively studied, from which some fundamental insights of this indispensable process used for semiconductor packaging have been obtained. This study employs voltammetry and scanning tunneling microscopy (STM) to examine Cu deposition on Pt(111) electrode modified with mercaptoacetic (MAA) and mercaptopropionic acids (MPA) in 0.1 M sulfuric acid containing 10−5 M CuSO4. The slight difference in the molecular structures of these organic surfactants leads to stark differences in Cu deposition. Both electrochemical and STM results show that Cu deposition proceeds much faster at the MAA- than MPA-modified Pt(111) electrode. Bulk Cu deposit grows in layers and 3D crystallites on the MAA- and MPA-modified Pt(111) electrodes, respectively. STM imaging shows that MAA and MPA modifiers segregate from the Pt(111) electrode to the Cu deposit, arranging in (√3 × √3)R30° like structures after Cu UPD, and transforming to Moire and striped patterns for bulk Cu deposition. Although MAA and MPA adsorbed on Pt(111) are both hydrogen-bonded to their neighbors, the latter has a higher degree of freedom to orient on the electrode for more intermolecular hydrogen bonds, which decreases the interaction between –COOH and Cu2+ and finally causes slower Cu deposition.
The Discharge and Charge Characteristics of FeOCl Modified by Aniline in Water (1991)

Many layered compounds, e.g. TiS 2 , MoS 2 , and FeOCl, have been investigated in order to improve the cathodic discharge and charge characteristics of secondary lithium batteries. In this study, FeOCl was modified by using an ion exchange reaction of the intercalation compound of FeOCl and aniline in order to improve the rechargeability of FeOCl
Ultrasonic transducers for navigation (2013)

Free space ultrasonic ranging is attractive for applications such as gesture recognition and robotic navigation. Unlike optical ranging technologies, ultrasound based solutions are insensitive to ambient illumination and can therefore be used in- and outdoors. Using time-of-flight, ultrasound rangers work over distances of up to a few meters and achieve sub-mm resolution. Using arrays, objects can be localized in three dimensions. Transducers consist of 400μm aluminum-nitride membranes sandwiched between actuation electrodes batch fabricated on silicon wafers. Unlike capacitive transducers, which require actuation voltages in excess of 100 V, piezoelectric devices are compatible with low-voltage actuation. At the 200 kHz resonance frequency, the wavelength at atmospheric pressure is 2 mm, ideal for compact arrays. The transducers do not dissipate static power and are therefore ideal for battery powered applications. Energy consumption is dominated by the low-noise readout amplifier and is on the order of 1μJ per channel including analog-digital conversion and signal processing, enabling video-rate object tacking at less than 1 mW power dissipation. A prototype system consisting of seven transducers on a 1 mm grid operates up to a 750 mm range and ±35o angle span with ±3.5mm accuracy and ±3o worst case angle error.
Hydroformylation of propene with zeolite-supported rhodium phosphine complexes (1985)

Rhodium phosphine complexes synthesized in situ on zeolite NaY are active for propene hydroformylation at 150 °C and 1 atm; the catalysts are not stable yet show an enhancement in linear vs. branched products with an increased production of alcohols compared to rhodium zeolites without phosphines.
Bit Error Rate Analysis of Rectangular QAM/FSO Systems Using an APD Receiver Over Atmospheric Turbulence Channels (2013)

We theoretically analyze the performance of free-space optical (FSO) systems using rectangular quadrature-amplitude modulation (QAM) and an avalanche photodiode (APD) receiver over atmospheric turbulence channels. Both log-normal and gamma&#x2013;gamma channel models are used in the analysis for the cases of weak/moderate and strong atmospheric turbulence. The system bit error rate, when Gray code mapping is employed, is theoretically derived taking into account various link conditions and system parameters, including the APD shot noise, thermal noise, channel attenuation and geometrical loss, atmospheric turbulence strengths, and link distances. The numerical results show that using APD with a proper selection of the average gain could greatly benefit the performance of the system; as a matter of fact, in the case of optimal gain, the system using an APD receiver could provide 7&#xA0;dB gain in comparison with the one with a positive-instrinsic-negative receiver. We also quantitatively discuss the impact of link conditions and system parameters on the selection of optimal APD gain.
Photosynthesis and Phosphorylation (1943)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotosynthesis and PhosphorylationS. RubenCite this: J. Am. Chem. Soc. 1943, 65, 2, 279–282Publication Date (Print):February 1, 1943Publication History Published online1 May 2002Published inissue 1 February 1943https://pubs.acs.org/doi/10.1021/ja01242a041https://doi.org/10.1021/ja01242a041research-articleACS PublicationsRequest reuse permissionsArticle Views124Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Compressed sensing in imaging mass spectrometry (2013)

Imaging mass spectrometry (IMS) is a technique of analytical chemistry for spatially resolved, label-free and multipurpose analysis of biological samples that is able to detect the spatial distribution of hundreds of molecules in one experiment. The hyperspectral IMS data is typically generated by a mass spectrometer analyzing the surface of the sample. In this paper, we propose a compressed sensing approach to IMS which potentially allows for faster data?acquisition by collecting only a part of the pixels in the hyperspectral image and reconstructing the full image from this data. We present an integrative approach to perform both peak-picking spectra and denoising m/z-images simultaneously, whereas the state of the art data analysis methods solve these problems separately. We provide a proof of the robustness of the recovery of both the spectra and individual channels of the hyperspectral image and propose an algorithm to solve our optimization problem which is based on proximal mappings. The paper concludes with the numerical reconstruction results for an IMS dataset of a rat brain coronal section.
Correction: Distinct Roles of IL-23 and IL-17 in the Development of Psoriasis-Like Lesions in a Mouse Model (2011)

Nakajima, K., T. Kanda, M. Takaishi, T. Shiga, K. Miyoshi, H. Nakajima, R. Kamijima, M. Tarutani, J. M. Benson, M. M. Elloso, L. L. Gutshall, M. F. Naso, Y. Iwakura, J. DiGiovanni, and S. Sano. 2011. Distinct roles of IL-23 and IL-17 in the development of psoriasis-like lesions in a mouse model. J.
Influence of Battery Parametric Uncertainties on the State-of-Charge Estimation of Lithium Titanate Oxide-Based Batteries (2018)

State of charge (SOC) is one of the most important parameters in battery management systems, as it indicates the available battery capacity at every moment. There are numerous battery model-based methods used for SOC estimation, the accuracy of which depends on the accuracy of the model considered to describe the battery dynamics. The SOC estimation method proposed in this paper is based on an Extended Kalman Filter (EKF) and nonlinear battery model which was parameterized using extended laboratory tests performed on several 13 Ah lithium titanate oxide (LTO)-based lithium-ion batteries. The developed SOC estimation algorithm was successfully verified for a step discharge profile at five different temperatures and considering various initial SOC initialization values, showing a maximum SOC estimation error of 1.16% and a maximum voltage estimation error of 44 mV. Furthermore, by carrying out a sensitivity analysis it was showed that the SOC and voltage estimation error are only slightly dependent on the variation of the battery model parameters with the SOC.
Wireless mobile networking with ANSI-41 (2001)

Part 1: Introduction to Wireless Telecommunications, Network Architecture, and Functions. Chapter 1: What Are Wireless Telecommunications? Chapter 2: Wireless Telecommunications Standards. Chapter 3: Wireless Telecommunications Network Signaling. Chapter 4: Wireless Telecommunications Network Reference Models. Chapter 5: Introduction to Wireless Functionality. Part 2: ANSI-41 Explained. Chapter 6: The Road to ANSI-41. Chapter 7: Structure of the ANSI-41 Standard. Chapter 8: The ANSI-41 Protocol Architecture. Chapter 9: Basic Intersystem Handoff Functions. Chapter 10: Basic Automatic Roaming Functions. Chapter 11: Authentication Functions. Chapter 12: Call Processing Functions. Chapter 13: Short-Message Service Functions. Chapter 14: Operations, Administration, and Maintenance Functions. Chapter 15: Over-the-Air Service Provisioning. Chapter 16: Looking Ahead. Part 3: ANSI-41 Network Implementations. Chapter 17: ANSI-41 Interoperation with Other Networks. Chapter 18: ANSI-41 Implementations. Chapter 19: Other Technologies Related to ANSI-41.
Pulse Timing and Amplitude Stability of a Monolithic Passively Mode-Locked Quantum Dot Laser at 1310 nm Directly Grown on Silicon (2019)

Passively mode-locked (PML) InAs/InGaAs quantum dot (QD) lasers directly grown on silicon and emitting at 1310nm are promising sources for high-speed, high-capacity communication applications. To overcome the low light generation efficiency of silicon, QD are directly grown on Si. Their ultrafast carrier dynamics, broadband gain spectra and easily saturated gain and absorption allow for the generation of ultra-short optical pulses as demonstrated very recently. The QD laser epitaxial growth was completed on an on-axis (001) Si substrate with a 45 nm GaP buffer layer by solid-source molecular beam epitaxy.
Photocurable dielectrics for electronic packaging and encapsulant applications (2016)

This article consists of a collection of slides from the author's conference presentation.
Shear-induced isotropic-to-lamellar transition (1993)

Reciprocating shear is found to increase the isotropic-to-lamellar transition temperature in a symmetric diblock copolymer melt. The temperature at which the isotropic state becomes unstable rapidly approaches the ordering transition as the shear rate increases. Shear-induced ordering results in lamellae orientation with wave vectors directed normal to the shear and velocity gradient directions. These results are anticipated by a recent theory that accounts for the suppression of fluctuations by a symmetry breaking field in this class of weakly first-order phase transitions.
Revealing the metabolic sites of atazanavir in human by parallel administrations of D‐atazanavir analogs (2013)

Atazanavir (Reyataz(®)) is an important member of the HIV protease inhibitor class. Because of the complexity of its chemical structure, metabolite identification and structural elucidation face serious challenges. So far, only seven non-conjugated metabolites in human plasma have been reported, and their structural elucidation is not complete, especially for the major metabolites produced by oxidations. To probe the exact sites of metabolism and to elucidate the relationship among in vivo metabolites of atazanavir, we designed and performed two sets of experiments. The first set of experiments was to determine atazanavir metabolites in human plasma by LC-MS, from which more than a dozen metabolites were discovered, including seven new ones that have not been reported. The second set involved deuterium labeling on potential metabolic sites to generate D-atazanavir analogs. D-atazanavir analogs were dosed to human in parallel with atazanavir. Metabolites of D-atazanavir were identified by the same LC-MS method, and the results were compared with those of atazanavir. A metabolite structure can be readily elucidated by comparing the results of the analogs and the pathway by which the metabolite is formed can be proposed with confidence. Experimental results demonstrated that oxidation is the most common metabolic pathway of atazanavir, resulting in the formation of six metabolites of monooxidation (M1, M2, M7, M8, M13, and M14) and four of dioxidation (M15, M16, M17, and M18). The second metabolic pathway is hydrolysis, and the third is N-dealkylation. Metabolites produced by hydrolysis include M3, M4, and M19. Metabolites formed by N-dealkylation are M5, M6a, and M6b.
Impedance images of the chest (1992)

This paper reports the results of electrical impedance imaging of the thorax of normal human subjects. The data collection and reconstruction algorithms used permit an assessment of the absolute value of the resistivities reported as well as changes in those resistivities.
Probabilistic Modeling of Deep Features for Out-of-Distribution and Adversarial Detection (2019)

We present a principled approach for detecting out-of-distribution (OOD) and adversarial samples in deep neural networks. Our approach consists in modeling the outputs of the various layers (deep features) with parametric probability distributions once training is completed. At inference, the likelihoods of the deep features w.r.t the previously learnt distributions are calculated and used to derive uncertainty estimates that can discriminate in-distribution samples from OOD samples. We explore the use of two classes of multivariate distributions for modeling the deep features - Gaussian and Gaussian mixture - and study the trade-off between accuracy and computational complexity. We demonstrate benefits of our approach on image features by detecting OOD images and adversarially-generated images, using popular DNN architectures on MNIST and CIFAR10 datasets. We show that more precise modeling of the feature distributions result in significantly improved detection of OOD and adversarial samples; up to 12 percentage points in AUPR and AUROC metrics. We further show that our approach remains extremely effective when applied to video data and associated spatio-temporal features by detecting adversarial samples on activity classification tasks using UCF101 dataset, and the C3D network. To our knowledge, our methodology is the first one reported for reliably detecting white-box adversarial framing, a state-of-the-art adversarial attack for video classifiers.
Thin glass substrates development and integration for through glass vias (TGV) with copper (Cu) interconnects (2012)

Silicon interposers have attracted a lot of interest for Three-Dimensional Stacked Integrated Circuit (3DS-IC) integration. Development of an advanced Si interposer derives from three essential technologies: front-side multi-level-metallization, through-substrate-vias and backside metallization. The approaches used for these technologies are greatly dependent on the application requirements, especially for the through silicon via (TSV) technology. Process development, optimization, and cost remain challenges to the industry. While silicon traditionally has been used in this application, glass has properties that make it a very intriguing material for through-substrate via applications. We note that “glass” describes a broad material set, with a wide range of properties driven by composition. Compositional changes allow tailoring of various properties, such as mechanical, thermal, electrical, optical characteristics, and even chemical durability. Compared to Si, one notable advantage of glass is the ability to alter the coefficient of thermal expansion (CTE), making glass a promising material for different applications in the 3DS-IC, because stack warpage due to CTE mismatch is a significant reliability concern. Another key advantage of glass interposer over Si interposer is that glass is an inherent insulator. This is useful for Cu interconnects, because no dielectric layer is required before the Cu plating/filling process to achieve low level leakage current. The elimination of this process step provides the benefits of reduced cost and complexity. Conventionally, a Si interposer has to be ground and polished in order to form the TSV. This step is cost prohibitive and time-consuming. On the other hand, due to the fusion-draw glass forming process used at Corning, ultra-thin glass can be provided in high volume as-formed (no polishing), with a pristine surface and tight tolerances (300 mm OD, thickness <; 0.10 mm (see Fig. 1), 30 μm warp and 1 μm total thickness variation (TTV)). Such a supply of as-formed ultra-thin glass wafers can compete very favorably in cost relative to polished or thinned glass or silicon wafers. Various technologies can be used to form through holes in glass. However, via size and pitch, wafer strength, and feasibility of mass production, are always challenges. At Corning we have made substantial progress in TGV processes, demonstrating high-quality through and blind holes in glass, with dimensions as small as 20 μm in diameter, and with glass as thin as 100 μm. Outstanding strength properties of TGV substrates have also been demonstrated. In brief, we have implemented through-substrate vias on glass with integrated Cu interconnects for 2.5D-IC and 3DS-IC application. Fusion-formed glass accompanied with new via formation processes provides advantages in cost and flexibility, along with excellent material attributes (CTE, electrical, strength, etc.). The significant advantages provided make a glass interposer a promising component for 3DS-IC technology.
A catheter system for the safe and efficient delivery of tissue glues (bucrylate) for visceral embolization (1981)

A number of different materials are used for transcatheter embolization because no single substance is suitable for all situations (Berenstein and Krischeff, 1979). In general, it should be possible to control the depth of vessel penetration and to avoid remote embolization or reflux. The material should have low histo-toxicity and be easy to deliver. In addition, liquid emboli need to have low viscosity to pass easily through fine catheters; to be radio-opaque, produce permanent occlusion, have a short setting time and not adhere to the delivery catheters. Bucrylate (isobutylcyanoacrylate) fulfils, or can be made to fulfil, these conditions. As it is difficult to handle, preliminary laboratory and animal studies are essential. Complications are caused by reflux of emboli or excessive penetration of the capillary bed (White et al., 1977; Greenfield et al., 1978; Lancet editorial, 1978). Our animal study shows that circulatory flow control is highly desirable when using liquid emboli (Fig. 1). We used a circulatory model to show that a 1:1 v/v suspension of bucrylate and Pantopaque (iophendlate) is suitable for trans-catheter embolization. This suspension is homogeneous and stable and sufficiently opaque to be visualized on fluoroscopy, and its viscosity is low enough for delivery through fine catheters. Pantopaque facilitates the delivery of bucrylate by retarding its polymerization (Cromwell and Kerber, 1979).
Implications of the human microbiome in inflammatory bowel diseases (2013)

The study of the human microbiome or community of microorganisms and collection of genomes found in the human body is one of the fastest growing research areas because many diseases are reported to be associated with microbiome imbalance or dysbiosis. With the improvement in novel sequencing techniques, researchers are now generating millions of sequences of different sites from the human body and evaluating specific differences in microbial communities. The importance of microbiome constituency is so relevant that several consortia like the Human Microbiome project (HMP) and Metagenomics of the Human Intestinal Tract (MetaHIT) project are focusing mainly on the human microbiome. The aim of this review is to highlight points of research in this field, mainly focusing on particular factors that modulate the microbiome and important insights into its potential impact on our health and well-being.
Influence of molecular structure on the antimicrobial function of phenylenevinylene conjugated oligoelectrolytes (2016)

Conjugated oligoelectrolytes (COEs) with phenylenevinylene (PV) repeat units are known to spontaneously intercalate into cell membranes. Twelve COEs, including seven structures reported here for the first time, were investigated for the relationship between their membrane disrupting properties and structural modifications, including the length of the PV backbone and the presence of either a tetraalkylammonium or a pyridinium ionic pendant group. Optical characteristics and interactions with cell membranes were determined using UV-Vis absorption and photoluminescence spectroscopies, and confocal microscopy. Toxicity tests on representative Gram-positive (<i>Enterococcus faecalis</i>) and Gram-negative (<i>Escherichia coli</i>) bacteria reveal generally greater toxicity to <i>E. faecalis</i> than to <i>E. coli</i> and indicate that shorter molecules have superior antimicrobial activity. Increased antimicrobial potency was observed in three-ring COEs appended with pyridinium ionic groups but not with COEs with four or five PV repeat units. Studies with mutants having cell envelope modifications indicate a possible charge based interaction with pyridinium-appended compounds. Fluorine substitutions on COE backbones result in structures that are less toxic to <i>E. coli</i>, while the addition of benzothiadiazole to COE backbones has no effect on increasing antimicrobial function. A weakly membrane-intercalating COE with only two PV repeat units allowed us to determine the synthetic limitations as a result of competition between solubility in aqueous media and association with cell membranes. We describe, for the first time, the most membrane disrupting structure achievable within two homologous series of COEs and that around a critical three-ring backbone length, structural modifications have the most effect on antimicrobial activity.