gebhart/patrepeval huggingface dataset:
Proteomics in the genome engineering era (2015)

Genome engineering experiments used to be lengthy, inefficient, and often expensive, preventing a widespread adoption of such experiments for the full assessment of endogenous protein functions. With the revolutionary clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 technology, genome engineering became accessible to the broad life sciences community and is now implemented in several research areas. One particular field that can benefit significantly from this evolution is proteomics where a substantial impact on experimental design and general proteome biology can be expected. In this review, we describe the main applications of genome engineering in proteomics, including the use of engineered disease models and endogenous epitope tagging. In addition, we provide an overview on current literature and highlight important considerations when launching genome engineering technologies in proteomics workflows.
Enhanced coupling to microsphere resonances with optical fibers (1997)

Morphology-dependent resonances (MDR's) of polystyrene microspheres were excited by an optical fiber coupler. For optical elimination of the air–cladding interface at the optical fiber coupler surface, the microsphere was immersed in an index-matching oil. MDR's were observed, even though the relative refractive index between the microsphere and the oil was only 1.09. The observed MDR spectra are in good agreement with the generalized Lorenz–Mie theory and the localization principle. The scattering efficiency into each MDR is estimated as a function of the impact parameter by means of generalized Lorenz–Mie theory.
Geometric Deep Learned Descriptors for 3D Shape Recognition (2018)

The availability of large 3D shape benchmarks has sparked a flurry of research activity in the development of efficient techniques for 3D shape recognition, which is a fundamental problem in a variety of domains such as pattern recognition, computer vision, and geometry processing. A key element in virtually any shape recognition method is to represent a 3D shape by a concise and compact shape descriptor aimed at facilitating the recognition tasks.&#13;\n&#13;\nThe recent trend in shape recognition is geared toward using deep neural networks to learn features at various levels of abstraction, and has been driven, in large part, by a combination of affordable computing hardware, open source software, and the availability of large-scale datasets. In this thesis, we propose deep learning approaches to 3D shape classification and retrieval. Our approaches inherit many useful properties from the geodesic distance, most notably the capture of the intrinsic geometric structure of 3D shapes and the invariance to isometric deformations. More specifically, we present an integrated framework for 3D shape classification that extracts discriminative geometric shape descriptors with geodesic moments. Further, we introduce a geometric framework for unsupervised 3D shape retrieval using geodesic moments and stacked sparse autoencoders. The key idea is to learn deep shape representations in an unsupervised manner. Such discriminative shape descriptors can then be used to compute pairwise dissimilarities between shapes in a dataset, and to find the retrieved set of the most relevant shapes to a given shape query. Experimental evaluation on three standard 3D shape benchmarks demonstrate the competitive performance of our approach in comparison with existing techniques.&#13;\n&#13;\nWe also introduce a deep similarity network fusion framework for 3D shape classification using a graph convolutional neural network, which is an efficient and scalable deep learning model for graph-structured data. The proposed approach coalesces the geometrical discriminative power of geodesic moments and similarity network fusion in an effort to design a simple, yet discriminative shape descriptor. This geometric shape descriptor is then fed into the graph convolutional neural network to learn a deep feature representation of a 3D shape. We validate our method on ModelNet shape benchmarks, demonstrating that the proposed framework yields significant performance gains compared to state-of-the-art approaches.
Addition to “A Wideband 2.4-GHz Delta-Sigma Fractional-$N$PLL With 1-Mb/s In-Loop Modulation” (2005)

[1] I. Bietti, E. Ternporitil, G. Albasini, and R. Castello, “An UMTS sigma delta fractional synthesizer with 200 kHz bandwidth and 128 dBc/Hz at 1 MHz using spurs compensation and linearization techniques,” in Proc. IEEE Custom Integrated Circuits Conf., Sep. 2003, pp. 463–466. [2] S. Pamarti, L. Jansson, and I. Galton, “A wideband 2.4-GHz delta-sigma fractional-N PLL with 1-Mb/s in-loop modulation,” IEEE J. Solid-State Circuits, vol. 39, no. 1, pp. 49–62, Jan. 2004.
ChemInform Abstract: Rhodium‐Catalyzed Reaction of N‐(2‐Pyridinyl)piperazines with CO and Ethylene. A Novel Carbonylation at a C—H Bond in the Piperazine Ring. (1997)

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.
Observation of Micro-Water droplets on Several Materials Surfaces and Evaluation of Wettability by Means of AFM (2003)

The wetting characteristics of micro-droplets of distilled water on natural mica and pretreated (wet polishing, air oxidation and water immersion) metals surfaces were observed with an atomic force microscope (AFM) in AC non-contact mode. The micro-droplets were more stable than the macro-droplets in ambient air. The micro-wettabilities were higher than the macro-ones for all specimens and the scatter of values was large. A thin liquid layer of adsorbed water and organic contaminants was found on the chromium surface in ambient air. Micro-droplets deposited by post-wetting always occupied positions with little or none organic contaminant, which might explain the observed higher wettability for micro-droplets than macro-droplets.
An integrated Mg battery-powered iontophoresis patch for efficient and controllable transdermal drug delivery (2023)

Abstract Wearable transdermal iontophoresis eliminating the need for external power sources offers advantages for patient-comfort when deploying epidermal diseases treatments. However, current self-powered iontophoresis based on energy harvesters is limited to support efficient therapeutic administration over the long-term operation, owing to the low and inconsistent energy supply. Here we propose a simplified wearable iontophoresis patch with a built-in Mg battery for efficient and controllable transdermal delivery. This system decreases the system complexity and form factors by using viologen-based hydrogels as an integrated drug reservoir and cathode material, eliminating the conventional interface impedance between the electrode and drug reservoir. The redox-active polyelectrolyte hydrogel offers a high energy density of 3.57 mWh cm −2 , and an optimal bioelectronic interface with ultra-soft nature and low tissue-interface impedance. The delivery dosage can be readily manipulated by tuning the viologen hydrogel and the iontophoresis stimulation mode. This iontophoresis patch demonstrates an effective treatment of an imiquimod-induced psoriasis mouse. Considering the advantages of being a reliable and efficient energy supply, simplified configuration, and optimal electrical skin-device interface, this battery-powered iontophoresis may provide a new non-invasive treatment for chronic epidermal diseases.
Syntheses, Structural Characterization, and First Electroluminescent Properties of Mono-cyclometalated Platinum(II) Complexes with Greater than Classical π−π Stacking and Pt−Pt Distances (2005)

A series of mono-cyclometalated Pt(II) complexes (9, 10, 13, 15, and 17) bearing 2-(3,5-bis(trifluoromethyl)phenyl)-4-methylpyridine (1) as the same chromophoric N∧C cyclometalated ligand and the second nonchromophoric bidenate ligands with increasing bulkiness were synthesized by the following steps. The palladium-catalyzed cross-coupling reaction between 2-chloro-4-methylpyridine (2) and 3,5-bis(trifluoromethyl)phenylboronic acid (3) was used to prepare 2-(3,5-bis(trifluoromethyl)phenyl)-4-methylpyridine (1). Di-tert-butyl(trimethylsilyl)anylmethylphosphine, tert-Bu2P-CH2-SiMe3 (5), was used as a ligand for the Suzuki coupling. The cyclometalation of 1 by K2PtCl4 (7) was carried out in (MeO)3PO (8) with the formation of a chloro-bridged dimer N∧CPt(μ-Cl)2PtC∧N (9). The reactions of 9 with 2,2,6,6-tetramethylheptane-3,5-dionate (11), 1,1,1,3,3,3-hexafluoro-2-pyrazol-1-ylmethylpropan-2-ol (12), 2-[(diphenylphosphanyl)methyl]-1,1,1,3,3,3-hexafluoropropan-2-ol (14), and 2-[(di-tert-butylphosphanyl)methyl]-1,1,1,3,3,3-hexafluoropropan-2-ol (16) afforded square-planar Pt(II) complexes 10, 13, 15, and 17, correspondingly. According to X-ray analyses, the plane-to-plane distances of the π−π stacked complexes (10, 13, 15, and 17) increase from 3.478 Å for 10 to 4.203 Å for 15. The value of 4.203 Å for aromatic−aromatic π−π interaction is greater than the usual range of 3.3−3.8 Å for these phenomena. Pt−Pt distances increase from 5.076 Å for 13 to 8.123 Å for 17. The geometry of complex 17 deviates greatly from square planar and is best described as “bowl-shaped”. The effect of an increased π−π stacking distance on the electroluminescent properties of these Pt compounds is studied. The typical yellow luminescence band associated with the excimers of Pt compounds is absent for complex 15; however, it shows a green 540 nm electroluminesce band instead. An efficient LED constructed using compound 15 shows green electroluminescence with a peak efficiency of 6 cd/A.
Low-Renin (Volume Dependent) Mild-Hypertensive Patients Have Impaired Flow-Mediated and Glyceryl-Trinitrate Stimulated Vascular Reactivity (2005)

This study showed impaired FMD and reduced GTN response in mildly hypertensive patients with low-renin plasma levels.
Hegemonic Masculinities, the Multinational Corporation, and the Developmental State (2007)

This article analyzes how the mainstream study of multinational corporations (MNCs) reflects a set of gendered assumptions that construct the firm as a hegemonically masculine political actor. It is suggested that the same masculinist assumptions that are found in these writings on MNCs take shape within firms in the form of a masculinist managerialism that constructs women workers in terms of their “productive femininity.” There is an extensive literature on women's employment in MNCs and their subsidiaries; the author suggests that this focus on women workers is only a starting point for developing a gendered understanding of global production. Importantly, a focus on “feminine” work and the role that masculinist managerial practices play in underpinning this construction provides insight into the gendered structures and institutions that support the workings of the global political economy.
In Situ XRD and Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy Unravel the Deactivation Mechanism of CaO-Based, Ca3Al2O6-Stabilized CO2 Sorbents (2018)

CaO is an effective high temperature CO2 sorbent that, however, suffers from a loss of its CO2 absorption capacity upon cycling due to sintering. The cyclic CO2 uptake of CaO-based sorbents is improved by Ca3Al2O6 as a structural stabilizer. Nonetheless, the initially rather stable CO2 uptake of Ca3Al2O6-stabilized CaO yet starts to decay after around 10 cycles of CO2 capture and sorbent regeneration, albeit at a significantly reduced rate compared to the unmodified reference material. Here, we show by a combined use of in situ XRD together with textural and morphological characterization techniques (SEM, STEM, and N2 physisorption) and solid-state 27Al NMR (in particular dynamic nuclear polarization surface enhanced NMR spectroscopy, DNP SENS) how microscopic changes trigger the sudden onset of deactivation of Ca3Al2O6-stabilized CaO. After a certain number of CO2 capture and regeneration cycles (approximately 10), Ca3Al2O6 transformed into Ca12Al14O33, followed by Al2O3 segregation and enrichment at the surface in the form of small nanoparticles. Al2O3 in such a form is not able to stabilize effectively the initially highly porous structure against thermal sintering, leading in turn to a reduced CO2 uptake.
Single photon superradiance and cooperative Lamb shift in an optoelectronic device (2016)

Single photon superradiance is a strong enhancement of spontaneous emission appearing when a single excitation is shared between a large number of two-level systems. This enhanced rate can be accompanied by a shift of the emission frequency, the cooperative Lamb shift, issued from the exchange of virtual photons between the emitters. In this work we present a semiconductor optoelectronic device allowing the observation of these two phenomena at room temperature. We demonstrate experimentally and theoretically that plasma oscillations in spatially separated quantum wells interact through real and virtual photon exchange. This gives rise to a superradiant mode displaying a large cooperative Lamb shift.
Mortality of One-Week-Old Chickens During Naturally Occurring Marek’s Disease Virus Infection (2011)

Marek's disease (MD) is a disease of chickens that occurs worldwide and has serious economic consequences. MD can present as one of several forms, with the most commonly occurring forms being the lymphoproliferative diseases. Under experimental conditions, an early mortality syndrome has been recognized following infection by some but not all strains of MD virus (MDV). This is the first report of a confirmed case of mortality due to naturally occurring MDV infection in 1-week-old, nonvaccinated, chickens. Necrotizing lesions were observed in the bursa of Fabricius, lung, duodenum, jejunum, and proventriculus, and large intranuclear inclusion bodies were a striking feature in tissues with lesions in all birds. Immunohistochemical staining for the pp38 protein of MDV revealed abundant pp38 antigen in the affected tissues, confirming the presence of MDV within the lesions. PCR yielded an amplicon with 97% homology to the meq gene of MDV. No evidence of co-infection by either of the immunosuppressive agents chicken anemia virus and infectious bursal disease virus was detected.
Os produtos naturais e a química medicinal moderna (2006)

Natural products have been utilized by humans since ancient times and the relief and cure of their diseases was the first purpose for using natural products in medicine. The history of the oriental and occidental civilizations is very rich in examples of the utilization of natural products in medicine and health care. Chinese traditional medicine is one of the most important examples of how natural products can be efficient in the treatment of diseases, and it points to the importance of scientific research on natural products, concerning the discovery of new active chemical entities. The complexity, chemical diversity and biological properties of natural products always fascinated people, and during the last 200 years, this led to the discovery of important new drugs. In the last 30 years, the development of new bioassay techniques, biotechnology methods, bio-guided phytochemical studies, automated high throughput screening and high performance analytical methods, have introduced new concepts and possibilities of rational drug design and drug discovery. In this context, natural products have played an important and decisive role in the development of modern medicinal chemistry.
Resonant electron transfer and luminescent enhancement in a toluene suspension of Si nanocrystals (2006)

Efficient resonant electron transfer from the surface bonding structure to the conduction band of quantum confined Si nanocrystals is observed by Si nanocrystals in a toluene suspension. Based on the electron transfer mechanism, the enhancement of photoluminescence originates from the band-to-band recombination in the p-type Si nanocrystals suspended in a toluene solution. The energy levels of the electrons in the Si nanocrystals chemisorbed with toluene molecules are calculated using the method of linear combination of atomic orbitals, and the characteristics of the obtained density of states is in good agreement with the observed photoluminescence properties.
Asymmetric Synthesis of 3,3‐Diarylpropanals with Chiral Diene—Rhodium Catalysts. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
The Non-Healing Wound: Mechanisms and Dressings (2001)

Chronic dermal ulcers are a major cause of disability and have a significant socioeconomic impact. Annual health care expenditures for the treatment of chronic dermal ulcers exceeds $3 billion in the United States alone. The development of improved treatment strategies should proceed from a better understanding of the pathophysiology of these problem wounds. A consistent feature of chronic leg and pressure ulcers is the presence of large numbers of activated neutrophils and perhaps other inflammatory cells. These cells, especially neutrophils, generate large amounts of degradative enzymes and oxygen metabolites that may overwhelm endogenous controls leading to tissue damage. This article summarizes studies that have focused on characterizing the proteolytic environment of chronic dermal ulcers and the implications that this may have for current and future treatment strategies of chronic nonhealing wounds.
Quantification and clustering of phenotypic screening data using time-series analysis for chemotherapy of schistosomiasis (2012)

The methods and results presented in this paper enable automatic and quantitative scoring of high-throughput phenotypic screens focused on helmintic diseases. Furthermore, these methods allow us to analyze and stratify parasites based on their phenotypic response to drugs. Together, these advancements represent a significant breakthrough for the process of drug discovery against schistosomiasis in particular and can be extended to other helmintic diseases which together afflict a large part of humankind.
Simplified Placement of Multiple Artificial Mitral Valve Chords (2005)

Chordal replacement for both anterior and posterior leaflet prolapse is an effective treatment for MR when combined with standard mitral valve repair techniques. The authors' technique of determining proper chordal height and placing multiple chordae is also discussed.
MEMS Inertial Sensors (2015)

Inertial sensors are devices that respond to physical motion, such as linear displacement or angular rotation, and transform this response into electrical signals that can be amplified and processed by electronic circuits. Accelerometers and gyroscopes are among the most common types of micro-electromechanical systems (MEMS) inertial sensors. Accelerometers detect axial acceleration along particular coordinates of interest; whereas gyroscopes, measure the rate of rotation or angular velocity around the x, or z axis (i.e., roll, pitch, and yaw rotation, respectively). This chapter describes the operation principles of accelerometers and gyroscopes including the benefits and challenges of implementing them as resonant MEMS sensors. High-frequency bulk-acoustic wave (BAW) devices are used as a case study to serve as a contrast to traditional MEMS architectures. The efforts on the development, miniaturization, and performance enhancement of integrated inertial measurement units (IMUs) are also highlighted.
Demons Kernel Computation with Single-pass Stream Processing on FPGA (2012)

Non-rigid registration is crucial in imaging, in particular, to adjust deformities produced during image acquisition and improve the accuracy of datasets. However, conventional imaging systems lack the desired speed and computational bandwidth for additional non-rigid registration of the deformed images. Therefore, such functionality is usually unavailable in time-critical settings. Expensive computations and memory intensive characteristics of non-rigid image registration algorithms such as the Demons algorithm further limits the realization of such systems. In response, we propose an alternative and efficient custom hardware-based Demons registration algorithm which utilizes pipelined streaming models to minimize memory fetches for computation. Designed for highly customizable hardware, our design only requires single-pass of images to compute the Demons kernel. Implementation results on the Xilinx ML605 FPGA system is presented and quantitatively evaluated in clock cycle counts in contrast with a software-based implementation.
An early role for theDrosophila melanogastermale seminal protein Acp36DE in female sperm storage (2003)

Female sperm storage is an essential component of reproduction in many animals. In insects, female sperm storage affects fecundity, sperm competition/preference and receptivity to re-mating. Female sperm storage consists of several stages, including sperm entry into the sperm storage organs (SSOs), maintenance within the SSOs and exit from the SSOs. The Drosophila melanogaster male seminal protein Acp36DE is essential for female sperm storage. Acp36DE associates with sperm and localizes to specific regions of the female reproductive tract, including the SSOs. We determined the stage of sperm storage at which Acp36DE acts by comparing the timing of initial sperm entry into storage as well as the rates of sperm accumulation and release from the SSOs in the presence or absence of Acp36DE. Acp36DE accelerates sperm accumulation into storage but does not mediate the entry of the first sperm into storage. This finding also demonstrates that the initial stage of sperm storage consists of multiple steps. Acp36DE enters the SSOs before sperm, and its residence within the SSOs does not require sperm. We propose that once sperm storage has initiated, Acp36DE acts as a guidance factor helping subsequent sperm move into storage, a corral concentrating sperm around the SSO entrances and/or a trigger for responses within the female that accelerate storage of sperm.
Fuzzy Integral Sliding Mode Control Based on Microbial Fuel Cell (2021)

Microbial fuel cell (MFC) is a renewable clean energy. Microorganisms are used as catalysts to convert the chemical energy of organic matter in the sewage into electrical energy to realize sewage treatment and recover energy at the same time. It has good development prospects. However, the output power of MFC is affected by many factors, and it is difficult to achieve a stable voltage output. For the control‐oriented single‐chamber MFC, a fuzzy integral sliding mode control is designed. The continuous adjustment of the sliding surface ensures that the system only moves on the sliding surface, which eliminates the arrival stage and improves robustness. For chattering existing in the system, the control scheme is further optimized to obtain fuzzy integral sliding mode control, and the fuzzy module adaptively adjusts the control parameters according to the system state, which effectively reduces the system chattering. Experiments prove that the control scheme reduces chattering while ensuring the stable output of the system.
Control of HIV Infection Dynamics (2008)

This article describes a drug scheduling method based on a reduced-order model, which does not require estimates of all of the parameters and states of the full-order model. To this end, we divide the full-order model into two subsystems, one of which is modified to approximate the full-order model. We show that the suggested method drives the HIV patient state into the LTNP region of attraction. This article is organized as follows. First, the problem under consideration is formulated, and a description of the HIV infection model is provided. Then, measurement methods for the states of the HIV model are surveyed. Subsequently the HIV infection model is modified to yield a reduced-order model. Finally, two control strategies based on this modified model are presented along with simulation results. The article concludes with a discussion and ideas for future work.