gebhart/patrepeval huggingface dataset:
Catalytic Cross-Metathesis Reactions That Afford E- and Z-Trisubstituted Alkenyl Bromides: Scope, Applications, and Mechanistic Insights (2023)

Stereochemically defined trisubstituted alkenes with a bromide and a methyl group at a terminus can be readily and stereoretentively derivatized through catalytic cross-coupling, affording unsaturated fragments found in many bioactive natural products. A direct method for generating such entities would be by stereocontrolled catalytic cross-metathesis (CM). Such methods are scarce however. Here, we present a stereoretentive strategy for CM between tri-, <i>Z</i>- or <i>E</i>-di, or monosubstituted olefins and <i>Z</i>- or <i>E</i>-2-bromo-2-butene, affording an assortment of <i>E</i>- or <i>Z</i>-trisubstituted alkenyl bromides. The majority of the transformations were catalyzed by two Mo monoaryloxide pyrrolide (MAP) complexes, one purchasable and the other accessible by well-established protocols. Substrates, such as feedstock trisubstituted olefins, can be purchased; the alkenyl bromide reagents are commercially available or can be prepared in two steps in a multigram scale. The catalytic process can be used to generate products that contain polar moieties, such as an amine or an alcohol, or sterically hindered alkenes that are α- or β-branched. The utility of the approach is highlighted by a brief and stereocontrolled synthesis of an unsaturated fragment of phomactin A and a concise total synthesis of ambrein. An unexpected outcome of these investigations was the discovery of a new role for the presence of a small-molecule alkene in an olefin metathesis reaction. DFT studies indicate that this additive swiftly reacts with a short-lived Mo alkylidene and probably helps circumvent the formation of catalytically inactive square pyramidal metallacyclobutanes, enhancing the efficiency of a transformation.
Familial hypercholesterolemia: A review (2014)

Familial hypercholesterolemia (FH) is a genetic disorder of lipoprotein metabolism resulting in elevated serum low-density lipoprotein (LDL) cholesterol levels leading to increased risk for premature cardiovascular diseases (CVDs). The diagnosis of this condition is based on clinical features, family history, and elevated LDL-cholesterol levels aided more recently by genetic testing. As the atherosclerotic burden is dependent on the degree and duration of exposure to raised LDL-cholesterol levels, early diagnosis and initiation of treatment is paramount. Statins are presently the mainstay in the management of these patients, although newer drugs, LDL apheresis, and other investigational therapies may play a role in certain subsets of FH, which are challenging to treat. Together these novel treatments have notably improved the prognosis of FH, especially that of the heterozygous patients. Despite these achievements, a majority of children fail to attain targeted lipid goals owing to persistent shortcomings in diagnosis, monitoring, and treatment. This review aims to highlight the screening, diagnosis, goals of therapy, and management options in patients with FH.
Application of PCA-LSTM model in human behavior recognition (2020)

Abstract For the problem that the recognition rate of human upper extremity movements is not high and existing models are prone to “dimensional disaster”, a pattern recognition algorithm based on PCA-LSTM neural network is studied. Collect and process the surface electromyography signal (sEMG) of the human upper limbs, and put it into the PCA model for data dimensionality reduction, put the dimensionality-reduced data into the LSTM neural network model to classify the human behavior, count the classification efficiency and recognition rate. Comparing PCA-LSTM with the traditional classification algorithm SVM and random forest, the calculation efficiency is improved by 31% and 53%, the recognition rate is increased by 3.9% and 4.6% and the classification effect is significant.
Two Dimensional Adaptive Equalizer For Voiceband Data Transmission (2005)

A fully integrated single chip monolithic 2400 bits/s voiceband modem that meets CCITT V.22 bis recommendation is under development. A critical subcircuit within this integrated circuit (IC) which will be described is the Adaptive Equalizer. Both analog switched capacitor and digital circuit techniques are employed to achieve the required performance and the efficient utilization of chip area. Such circuit will be integrated using an established 3um silicon gate, double-poly CMOS technology.
Noninvasive measurement of total hemoglobin and hemoglobin derivatives using multiwavelength pulse spectrophotometry -In vitro study with a mock circulatory system (2006)

Total hemoglobin (tHb), carboxyhemoglobin (COHb), and methemoglobin (MetHb) are usually measured with a CO-oximeter. Noninvasive and continuous measurement of these blood components is expected to decrease the pain of a patient. Therefore, we developed an instrument to measure oxygen saturation (SpO(2), tHb, COHb, and MetHb non invasively. Multiwavelength LED (600, 625, 660, 760, 800, 940, and 1300 nm) and a combined detector (Si, InGaAs) were built into the instrument (Seven wavelengths transparent pulse spectrophotometer). We used the Waseda mock circulatory system, which can simulate blood circulation in tissues and generate a pulse wave mechanically, to estimate the instrument's performance. Furthermore we proposed new calculation formula including DC components of optical density (this method). Under conditions without any change of other components, the mean error +/- standard deviation between this method and the CO-oximetry were SaO(2)=0.0 +/- 1.4%, tHb=0.0 +/- 0.0 g/dl, COHb=0.0 +/- 2.0%, and MetHb=0.0 +/- 0.3%. When the concentration of other components was changed, this method showed mean errors and standard deviations of SaO(2)=0.2 +/- 1.6%, tHb=0.0 +/- 0.4 g/dl, COHb=0.5 +/- 4.1%, and MetHb=0.0 +/- 0.3%
Heteromultimeric CLC chloride channels with novel properties (1996)

The skeletal muscle chloride channel CLC-1 and the ubiquitous volume-activated chloride channel CLC-2 belong to a large gene family whose members often show overlapping expression patterns. CLC-1 and CLC-2 are coexpressed in skeletal and smooth muscle and in the heart. By coexpressing CLC-1 and CLC-2 in Xenopus oocytes, we now show the formation of novel CLC-1/CLC-2 heterooligomers that yield time-independent linear chloride currents with a chloride-->bromide-->iodide selectivity sequence. Formation of heterooligomeric CLC channels increases the number and possible functions of chloride channels.
Matrix‐Embedded Cells: Matrix‐Embedded Endothelial Cells Attain a Progenitor‐Like Phenotype (Adv. Biosys. 9/2017) (2017)

Natalie Artzi and co-workers describe how matrix-embedded endothelial cells (MEEC) attain a progenitor-like phenotype as defined by comparisons of secretome, phenotype, and genetic fingerprint of MEECs with that of endothelial progenitor cells, in article number 1700057. The cover shows MEECs (green) wrapping around the denatured collagen structure (red) of the matrix, recapitulating in vivo endothelial structure much more closely than endothelial cells grown on 2D surfaces.
Tissue Regeneration through Cyber‐Physical Systems and Microbots (2021)

Abstract Tissue engineering is a systematic approach of assembling cells onto a 3D scaffold to form a functional tissue in the presence of critical growth factors. The scaffolding system guides stem cells through topological, physiochemical, and mechanical cues to differentiate and integrate to form a functional tissue. However, cellular communication during tissue formation taking place in a reactor needs to be understood properly to enable appropriate positioning of the cells in a 3D environment. Hence, sensors and actuators integrated with cyber‐physical system (CPS) may be able to sense the tissue microenvironment and direct cells/cellular aggregates to an appropriate position, respectively. This can facilitate better cell‐to‐cell communication and cell–extracellular matrix communication for proper tissue morphogenesis. Advancements are made in the field of smart scaffolds that can morph cells/cellular aggregates after sensing the cellular microenvironment in a desired 3D architecture by providing appropriate cues. Recent scientific developments in the additive manufacturing technology have enabled the fabrication of smart scaffolds to create structural and functional tissue constructs. Sensors/actuators, cyber‐systems, smart materials, and additive manufacturing put together is expected to lead to improved tissue‐engineered medical products. The present review aims to highlight the possibilities of advancement of BioCPS for tissue engineering and regenerative medicine.
Fixed-grid method for the modelling of unsteady partial oxidation of a spherical coal particle (2012)

This article refers to:Fixed-grid method for the modelling of unsteady partial oxidation of a spherical coal particle
Selective-Area Growth of Thick Diamond Films Using Chemically Stable Masks of Ru/Au and Mo/Au (2012)

Selective-area growth of diamond films in microwave-plasma chemical vapor deposition was performed using newly developed masks. By forming chemically stable masks made of Ru/Au or Mo/Au, which have high melting points, good adhesion to diamond, and difficulty in forming carbide compounds, patterned diamond films with a large thickness of 50 µm, a large area of 5 mm 2 , and a high orientation in the [001] direction were successfully grown on (001) diamond substrates without degradation of the crystal quality of masked areas.
Substrate-Independent Control of Polymorphs in Tetraphenylporphyrin Thin Films by Varying the Solvent Evaporation Time Using a Simple Spin-Coating Technique (2021)

Porphyrin derivatives are promising materials for various thin-film-based devices such as solar cells, field-effect transistors, and gas sensors. Since the molecular aggregation structure in a thin film significantly influences the device performance, controlling the aggregation structure is of crucial importance. In this study, we show that three different crystalline polymorphs of free-base tetraphenylporphyrin (H2TPP) can be made to form in spin-coated thin films depending on the evaporation time of the solvent. The results show that the aggregation structure in the as-spun films is controlled by the solvent evaporation time, and the initial film structure determines the polymorphs obtained after thermal annealing.
Protein kinase cascades activated by stress and inflammatory cytokines (1996)

Signal transduction pathways constructed around a core module of three consecutive protein kinases, the most distal being a member of the extracellular signal-regulated kinase (ERK) family, are ubiquitous among eukaryotes. Recent work has defined two cascades activated preferentially by the inflammatory cytokines TNF-alpha and IL-1-beta, as well as by a wide variety of cellular stresses such as UV and ionizing radiation, hyperosmolarity, heat stress, oxidative stress, etc. One pathway converges on the ERK subfamily known as the "stress activated' protein kinases (SAPKs, also termed Jun N-terminal kinases, JNKs), whereas the second pathway recruits the p38 kinases. Upstream inputs are diverse, and include small GTPases (primarily Rac and Cdc42; secondarily Ras) acting through mammalian homologs of the yeast Ste20 kinase, other kinase subfamilies (e.g. GC kinase) and ceramide, a putative second messenger for certain TNF-alpha actions. These two cascades signal cell cycle delay, cellular repair or apoptosis in most cells, as well as activation of immune and reticuloendothelial cells.
Stable Cuprous Hydroxide Nanostructures by Organic Ligand Functionalization (2022)

Copper compounds have been extensively investigated for diverse applications. However, studies of cuprous hydroxide (CuOH) have been scarce due to structural metastability. Herein, a facile, wet-chemistry procedure is reported for the preparation of stable CuOH nanostructures via deliberate functionalization with select organic ligands, such as acetylene and mercapto derivatives. The resulting nanostructures are found to exhibit a nanoribbon morphology consisting of small nanocrystals embedded within a largely amorphous nanosheet-like scaffold. The acetylene derivatives are found to anchor onto the CuOH forming CuC linkages, whereas CuS interfacial bonds are formed with the mercapto ligands. Effective electronic coupling occurs at the ligand-core interface in the former, in contrast to mostly non-conjugated interfacial bonds in the latter, as manifested in spectroscopic measurements and confirmed in theoretical studies based on first principles calculations. Notably, the acetylene-capped CuOH nanostructures exhibit markedly enhanced photodynamic activity in the inhibition of bacteria growth, as compared to the mercapto-capped counterparts due to a reduced material bandgap and effective photocatalytic generation of reactive oxygen species. Results from this study demonstrate that deliberate structural engineering with select organic ligands is an effective strategy in the stabilization and functionalization of CuOH nanostructures, a critical first step in exploring their diverse applications.
Increased Compression Efficiency of AVC and HEVC CABAC by Precise Statistics Estimation (2018)

The paper presents Improved Adaptive Arithmetic Coding algorithm for application in future video compression technology. The proposed solution is based on the Context-based Adaptive Binary Arithmetic Coding (CABAC) technique and uses the authors mechanism of symbols probability estimation that exploits Context-Tree Weighting (CTW) technique. This paper proposes the version of the algorithm, that allows an arbitrary selection of depth D of context trees, when activating the algorithm in the framework of the AVC or HEVC video encoders. The algorithm has been tested in terms of coding efficiency of data and its computational complexity. Results showed, that depending on depth of context trees from 0.1% to 0.86% reduction of bitrate is achieved, when using the algorithm in the HEVC video encoder and 0.4% to 2.3% compression gain in the case of the AVC. The new solution increases complexity of entropy encoder itself, however, this does not cause an increase of the complexity of the whole video encoder.
SemTag and seeker (2003)

This paper describes Seeker, a platform for large-scale text analytics, and SemTag, an application written on the platform to perform automated semantic tagging of large corpora. We apply SemTag to a collection of approximately 264 million web pages, and generate approximately 434 million automatically disambiguated semantic tags, published to the web as a label bureau providing metadata regarding the 434 million annotations. To our knowledge, this is the largest scale semantic tagging effort to date.We describe the Seeker platform, discuss the architecture of the SemTag application, describe a new disambiguation algorithm specialized to support ontological disambiguation of large-scale data, evaluate the algorithm, and present our final results with information about acquiring and making use of the semantic tags. We argue that automated large scale semantic tagging of ambiguous content can bootstrap and accelerate the creation of the semantic web.
Figure S5 from Macrophage-Derived Cholesterol Contributes to Therapeutic Resistance in Prostate Cancer (2023)

&lt;p&gt;Effect of LXR agonist and antagonist on prostate cancer gene expression and LDL uptake&lt;/p&gt;
Observation of Defocus Images of a Single Metal Nanorod (2012)

We examined an emission of light from a single metallic nanoparticle based on surface plasmon (SP) resonance for determination of three-dimensional orientation of nanoparticles as well as their optical properties. The defocused image of individual Au nanorods (Au NRs) is recorded by changing the focus distance under total internal reflection microscopy (TIRM) observations. Numerical and statistical analysis revealed that the observed light distribution patterns of Au NRs defocused images were classified into two groups. One is explained by considering that a single dipole dominates its light emission property. The other is explained by assuming the presence of multidipoles. This result leads us to a consideration that the emission of light coupled with the transverse and the longitudinal SP modes was observed reflecting the optical characteristics of NRs. Additionally, unique multiple ring patterns were also observed by placing Au NRs at the vicinity of nanoscopic structure, reflecting the distance between NRs and the wall of the structure in the scale less than a few tens of nanometers. The inclusive SP measurement for both the transverse and longitudinal axes of these anisotropic metal NRs using a defocused imaging system brings us reliable optical and conformational information.
Tigecycline resistance tet(X3) gene is going wild (2020)

The emergence of mobile Tigecycline-resistant tet(X3) and tet(X4) is believed to be a global threat to public health. Here, we investigated the prevalence of tet(X3) and tet(X4) in our metagenomic data of migratory birds. While tet(X4) was not identified in our samples, tet(X3) was found in two gut microbiomes of bird fecal samples, with 100% amino acid identity of sites 150–387. These results suggest that tet(X3) has been spreading into the environment for a long period of time and that there is an urgent need to control its further transmission.
Ultrathin side-viewing needle probe for optical coherence tomography (2011)

We present the smallest reported side-viewing needle probe for optical coherence tomography (OCT). Design, fabrication, optical characterization, and initial application of a 30-gauge (outer diameter 0.31 mm) needle probe are demonstrated. Extreme miniaturization is achieved by using a simple all-fiber probe design incorporating an angle-polished and reflection-coated fiber-tip beam deflector. When inserted into biological tissue, aqueous interstitial fluids reduce the probe's inherent astigmatism ratio to 1.8, resulting in a working distance of 300 μm and a depth-of-field of 550 μm with beam diameters below 30 μm. The needle probe was interfaced with an 840 nm spectral-domain OCT system and the measured sensitivity was shown to be only 7 dB lower than that of a comparable galvo-scanning sample arm configuration. 3D OCT images of lamb lungs were acquired over a depth range of ~600 μm, showing individual alveoli and bronchioles.
Self-Knowledge Distillation for Surgical Phase Recognition (2023)

Purpose: Advances in surgical phase recognition are generally led by training deeper networks. Rather than going further with a more complex solution, we believe that current models can be exploited better. We propose a self-knowledge distillation framework that can be integrated into current state-of-the-art (SOTA) models without requiring any extra complexity to the models or annotations. Methods: Knowledge distillation is a framework for network regularization where knowledge is distilled from a teacher network to a student network. In self-knowledge distillation, the student model becomes the teacher such that the network learns from itself. Most phase recognition models follow an encoder-decoder framework. Our framework utilizes self-knowledge distillation in both stages. The teacher model guides the training process of the student model to extract enhanced feature representations from the encoder and build a more robust temporal decoder to tackle the over-segmentation problem. Results: We validate our proposed framework on the public dataset Cholec80. Our framework is embedded on top of four popular SOTA approaches and consistently improves their performance. Specifically, our best GRU model boosts performance by +3.33% accuracy and +3.95% F1-score over the same baseline model. Conclusion: We embed a self-knowledge distillation framework for the first time in the surgical phase recognition training pipeline. Experimental results demonstrate that our simple yet powerful framework can improve performance of existing phase recognition models. Moreover, our extensive experiments show that even with 75% of the training set we still achieve performance on par with the same baseline model trained on the full set.
Frequency Self-tuning Scheme for Broadband Vibration Energy Harvesting (2010)

The recent proliferation of microscale devices has raised the issue of energy harvesting for replacing batteries that present maintenance and recycling problems. Particularly, piezoelectric seismic microgenerators offer the advantages of easy maintenance and high power output, but are very sensitive to frequency drifts that can dramatically decrease their performance. The purpose of the present article is to expose a technique to ensure that the harvester resonance frequency matches the base motion frequency, without any external intervention. The principles of the proposed method rely on ultralow-cost frequency sensing combined with an energy-efficient stiffness tuning, through the use of an additional actuator. Experimental results carried out to validate the model show that such an approach permits increasing the effective bandwidth of the structure by a factor of 4 in terms of mechanical vibrations and having a 100% frequency band gain in terms of total power output of the device (i.e., taking into account the energy spent by the actuation). The total energy produced by the harvesting device, taking into account the actuation cost, is discussed as well.
Placental Malaria-Associated Suppression of Parasite-Specific Immune Response in Neonates Has No Major Impact on Systemic CD4 T Cell Homeostasis (2011)

In areas where Plasmodium falciparum is endemic, pregnancy is associated with accumulation of infected red blood cells (RBCs) in the placenta, a condition referred to as placental malaria (PM). Infants born to PM-positive mothers are at an increased risk of malaria, which is putatively related to the transplacental passage of parasite-derived antigens, with consequent tolerization of the fetal immune system. Here we addressed the impact of PM on the regulation of neonatal T cell responses. We found that the frequency of regulatory CD25(+) CD127(-/low) Foxp3(+) CD4(+) T cells was significantly decreased in neonates born to mothers with high levels of P. falciparum-induced placental inflammation, consisting mainly of primigravid mothers. However, at the individual level, the ratio between regulatory and effector (CD25(+) CD127(+) Foxp3(-)) CD4(+) T cells was unaffected by PM. In addition, parasite-induced CD4(+) T cell activation and production of interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), and IL-10 were strongly reduced in neonates born to PM-positive mothers. Thus, our results show that active PM at delivery is associated with a marked suppression of P. falciparum-specific cellular neonatal immune responses, affecting secretion of both pro- and anti-inflammatory cytokines. Additionally, our results suggest that, as in adults, effector and regulatory CD4(+) T cell populations are tightly coregulated in all neonates, irrespective of the maternal infection status.