gebhart/patrepeval huggingface dataset:
Folate Antagonists (2022)

Overview Folic acid antagonists (antifols) are cytotoxic drugs used as antineoplastic, antimicrobial, anti‐inflammatory, and immune‐suppressive agents. While several folate antagonists have been developed, methotrexate (4‐amino‐4‐deoxy‐10‐ N ‐methyl‐pteroylglutamic acid, MTX) is the antifol with the most extensive history and widest spectrum of use. MTX remains an essential drug in curative chemotherapy regimens used to treat patients with acute lymphoblastic leukemia, osteosarcoma, and choriocarcinoma, and is an important agent in the therapy of patients with lymphoma, breast cancer, bladder cancer, and head and neck cancer. In addition, it is used for patients with nonmalignant diseases such as rheumatoid arthritis, psoriasis, autoimmune diseases, and graft‐versus‐host disease. This article will review the clinical use of and metabolism of MTX and discuss structurally related folate antagonists that have been developed to overcome resistance or have alternate intracellular targets.
Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity (2018)

Small non-coding RNAs (sncRNA) are regulators of cell functions and circulating sncRNAs from the majority of RNA classes are potential non-invasive biomarkers. Understanding how common traits influence ncRNA expression is essential for assessing their biomarker potential. In this study, we identify associations between sncRNA expression and common traits (sex, age, self-reported smoking, body mass, self-reported physical activity). We used RNAseq data from 526 serum samples from the Janus Serum Bank and traits from health examination surveys. Ageing showed the strongest association with sncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. piRNAs were abundant in the serum samples and they were associated to sex. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some sncRNAs smoking-related expression levels persisted. Pathway analysis suggests that smoking-related sncRNAs target the cholinergic synapses and may therefore potentially play a role in smoking addiction. Our results show that common traits influence circulating sncRNA expression. It is clear that sncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific sncRNAs, analyses should also be adjusted for body mass, smoking, physical activity and technical factors.
ChemInform Abstract: Ruthenium Catalyzed Homocoupling of Terminal Alkynes. (1998)

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.
Characterization and Control of Reduced Sulfur Odors from Lime Stabilized and Digested Biosolids (2002)

Characterization and Control of Reduced Sulfur Odors from Lime Stabilized and Digested BiosolidsThe reduced sulfur odors derived from lime stabilized and digested biosolids were evaluated in this study. It was determined that the reduced sulfur odor compounds emitted from lime stabilized biosolids are typically dimethyl disulfide and dimethyl sulfide. The source conditions for these biosolids odors was found to be due to a combination of upstream conditions during thickening that led to low...Author(s)Sudhir N. MurthyChris PeotJason NorthJohn NovakDietmar GlindemannMatthew HigginsSourceProceedings of the Water Environment FederationSubjectSession 18: Odor Control for BiosolidsDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2002ISSN1938-6478SICI1938-6478(20020101)2002:3L.1105;1-DOI10.2175/193864702785302195Volume / Issue2002 / 3Content sourceResiduals and Biosolids ConferenceFirst / last page(s)1105 - 1124Copyright2002Word count199
VGAE-MCTS: a New Molecular Generative Model combining Variational Graph Auto-Encoder and Monte Carlo Tree Search (2023)

Molecular generation is crucial for advancing drug discovery, material design, and chemical exploration. It expedites the search for new drug candidates, facilitates tailored material creation, and enhances our understanding of molecular diversity. By employing artificial intelligence techniques, such as molecular generative models based on molecular graphs, researchers have tackled the challenge of efficiently molecules with desired properties. We proposed a new molecular generative model combining deep learning and reinforcement learning evaluated the validity, novelty, and optimized physicochemical properties of the generated molecules. Importantly, the model explored uncharted regions of chemical space, allowing for the efficient discovery and design of new molecules. This innovative approach has significant potential to revolutionize drug discovery, material science, and chemical research for accelerating scientific innovation. By leveraging advanced techniques and exploring previously unexplored chemical spaces, this study offers promising prospects for the efficient discovery and design of new molecules in the field of drug development.
Protection against SARS-CoV-2 infection by a mucosal vaccine in rhesus macaques (2021)

Effective SARS-CoV-2 vaccines are urgently needed. Although most vaccine strategies have focused on systemic immunization, here we compared the protective efficacy of 2 adjuvanted subunit vaccines with spike protein S1: an intramuscularly primed/boosted vaccine and an intramuscularly primed/intranasally boosted mucosal vaccine in rhesus macaques. The intramuscular-alum-only vaccine induced robust binding and neutralizing antibody and persistent cellular immunity systemically and mucosally, whereas intranasal boosting with nanoparticles, including IL-15 and TLR agonists, elicited weaker T cell and Ab responses but higher dimeric IgA and IFN-α. Nevertheless, following SARS-CoV-2 challenge, neither group showed detectable subgenomic RNA in upper or lower respiratory tracts versus naive controls, indicating full protection against viral replication. Although mucosal and systemic protective mechanisms may differ, results demonstrate both vaccines can protect against respiratory SARS-CoV-2 exposure. In summary, we have demonstrated that the mucosal vaccine was safe after multiple doses and cleared the input virus more efficiently in the nasal cavity and thus may act as a potent complementary reinforcing boost for conventional systemic vaccines to provide overall better protection.
Intracellular Magnetic Labeling of Lymphocytes for In Vivo Trafficking Studies (1998)

Lymphocyte adhesion and trafficking is difficult to observe in vivo over time. We used magnetic resonance imaging (MRI) to identify magnetically labeled lymphocytes in phantom experiments and in tissue. A method of lymphocyte labeling was developed that is based on fluid-phase endocytosis of nanometer-sized biocompatible superparamagnetic particles. The maximum cell uptake in culture was 0.11 ng Fe/cell corresponding to 5 x 10(6) particles/lymphocyte. Cells stably retained the label and were fully viable for at least 3 days. Labeled lymphocytes showed adhesion to human endothelial cells similar to unlabeled cells, indicating no effect of labeling on cell surface expression of adhesion proteins. No particle-mediated cytotoxicity could be observed. The detection threshold of MRI for detecting labeled lymphocytes in the current study was 2.5 x 10(6) cells/30 microL sampling volume. Following intravenous injection of labeled lymphocytes into rats, cells accumulated in spleen, lymph nodes and liver with a similar bio-distribution as unlabeled cells. Lymphocyte accumulation in the spleen resulted in MRI signal intensity changes readily detectable by MRI. These findings suggest that intracellular lymphocyte labeling with superparamagnetic particles is feasible, does not alter the viability or tissue distribution of labeled cells and allows the detection of labeled lymphocytes by MRI.
Organic Materials for Solar Photovoltaics (2009)

A promising new technology for photovoltaic energy conversion involves the use of organic materials in lamellar photovoltaic cells. We are exploring the use of new organic materials as donors, acceptors and buffer layers in organic photovoltaic cells (OPVs). We have found that metalloporphyrins and subphthalocyanines make excellent donor materials in OPVs, with some giving higher than expected open circuit voltages. The properties of these devices and model for understanding the origin of the open circuit voltage for OPVs will be presented.
Monte Carlo validation of spike-timing-dependent plasticity identification from spiking activity (2016)

As increasingly complex non-stationary models become possible to be identified from neural data, rigorous validation approaches must be developed to rule out overfitting and the potential to identify features by chance. Specifically, identification of spike-timing-dependent plasticity (STDP) from recorded spontaneous in vivo spike timing is a potentially powerful tool to quantify activity-dependent plasticity. In previous work, we presented a methodology to perform this STDP identification from spike timing alone and successfully identified a generative model. Validation was straightforward with the generative model because the underlying model was known, but becomes challenging when applied to experimental data. Here, we introduce a set of null hypothesis tests that can be performed with Monte Carlo (MC) simulations of null models to rule out cases of overfitting with experimental data. We demonstrate the identification of these null models and null hypothesis testing on a generative model in two test cases, one with and one without overfitting. Importantly, we show that it is possible to distinguish an identified STDP rule from a null case where there are similar weight fluctuations which are activity-independent. With the development of the null hypothesis tests described here, STDP identification can be effectively applied to experimental data recordings.
Healing of Retinal Photocoagulation Lesions (2008)

The decreasing width of the retinal damage zone suggests that photoreceptors migrating from unaffected areas fill in the gap in the photoreceptor layer. Laser photocoagulation parameters can be specified to avoid not only the inner retinal damage, but also permanent disorganization and scarring in the photoreceptor layer. These data may facilitate studies to determine those aspects of laser treatment necessary for beneficial clinical response and those that result in extraneous retinal damage.
Ion Implantation in Silicon for Trimming the Operating Wavelength of Ring Resonators (2018)

In recent years, we have presented results on the development of erasable gratings in silicon to facilitate wafer scale testing of photonics circuits via ion implantation of germanium. Similar technology can be employed to control the operating wavelength of ring resonators, which is very sensitive to fabrication imperfections. Ion implantation into silicon causes radiation damage resulting in a refractive index increase, and can therefore form the basis of multiple optical devices. In this paper we discuss design, modelling and fabrication of ring resonators and their subsequent trimming using ion implantation of germanium into silicon, followed by either rapid thermal annealing or localized laser annealing. The results confirm the ability permanently tune the position of the resonant wavelength to any point inside the free spectral range of the ring resonator, thus greatly reducing the amount of power required for active tuning of these devices.
ENDOSCOPIC SUBMUCOSAL DISSECTION FOR BARRETT'S ESOPHAGUS LARGE OR FIBROTIC VISIBLE LESIONS: A BICENTRIC WESTERN COUNTRY PROSPECTIVELY COLLECTED EXPERIENCE (2019)

Some suspected submucosal or fibrotic Barrett esophagus (BE) lesions, have been proposed by the ESGE to be treated by endoscopic submucosal dissection (ESD). The aim of this study is to review two tertiary centers experience in the endoscopic treatment of early BE cancer by ESD.
ChemInform Abstract: Tetramic and Tetronic Acids: An Update on New Derivatives and Biological Aspects (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Risk-Aware Planning: Methods and Case Study on Safe Driving Route (2017)

&#x0D; &#x0D; &#x0D; Vehicle crashes account for over one million fatalities and many more millions of injuries annually worldwide. Some roads are safer than others, so driving routes optimized for safety may re- duce the number of crashes. We have developed a method to estimate the probability of a crash on any road as a function of the traffic volume, road characteristics, and environmental condi- tions. We trained a regression model to estimate traffic volume and a binary classifier to estimate crash probability on road seg- ments. Modeling a route’s crash probability as a series of Ber- noulli trials, we employ the Dijkstra routing algorithm to compute the safest route between two locations. We find that, compared to the fastest route, the safest route is approximately 1.7 times as long in duration and about half as dangerous. We also show how to smoothly trade off safety for travel time, and demonstrate how drivers could be offered several route options, each with different crash probabilities and durations.&#x0D; &#x0D; &#x0D;
ChemInform Abstract: Selective Conversion of α‐Tetralones to Dihydronaphthalenes. (1996)

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.
Plastoglobules Are Lipoprotein Subcompartments of the Chloroplast That Are Permanently Coupled to Thylakoid Membranes and Contain Biosynthetic Enzymes (2006)

Plastoglobules are lipoprotein particles inside chloroplasts. Their numbers have been shown to increase during the upregulation of plastid lipid metabolism in response to oxidative stress and during senescence. In this study, we used state-of-the-art high-pressure freezing/freeze-substitution methods combined with electron tomography as well as freeze-etch electron microscopy to characterize the structure and spatial relationship of plastoglobules to thylakoid membranes in developing, mature, and senescing chloroplasts. We demonstrate that plastoglobules are attached to thylakoids through a half-lipid bilayer that surrounds the globule contents and is continuous with the stroma-side leaflet of the thylakoid membrane. During oxidative stress and senescence, plastoglobules form linkage groups that are attached to each other and remain continuous with the thylakoid membrane by extensions of the half-lipid bilayer. Using three-dimensional tomography combined with immunolabeling techniques, we show that the plastoglobules contain the enzyme tocopherol cyclase (VTE1) and that this enzyme extends across the surface monolayer into the interior of the plastoglobules. These findings demonstrate that plastoglobules function as both lipid biosynthesis and storage subcompartments of thylakoid membranes. The permanent structural coupling between plastoglobules and thylakoid membranes suggests that the lipid molecules contained in the plastoglobule cores (carotenoids, plastoquinone, and tocopherol [vitamin E]) are in a dynamic equilibrium with those located in the thylakoid membranes.
A catalytic method for the reduction of esters to alcohols (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA catalytic method for the reduction of esters to alcoholsScott C. Berk, Kristina A. Kreutzer, and Stephen L. BuchwaldCite this: J. Am. Chem. Soc. 1991, 113, 13, 5093–5095Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/ja00013a074https://doi.org/10.1021/ja00013a074research-articleACS PublicationsRequest reuse permissionsArticle Views2092Altmetric-Citations136LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
TLA in pictures (1995)

Predicate-action diagrams, which are similar to standard state-transition diagrams, are precisely defined as formulas of TLA (the Temporal Logic of Actions). We explain how these diagrams can be used to describe aspects of a specification-and those descriptions then proved correct-even when the complete specification cannot be written as a diagram. We also use the diagrams to illustrate proofs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization and organization of DNA sequences adjacent to the human telomere associated repeat (TTAGGG)n (1990)

We present a strategy for the cloning of DNA sequences adjacent to the tandemly repeated DNA sequence (TTAGGG)n. Sequence analysis of 14 independently isolated clones revealed the presence of non-repetitive sequences immediately adjacent to or flanked by blocks of the simple repeat (TTAGGG)n. In addition, we provide sequence information on two previously undescribed tandemly repeated sequences, including a 9 bp repeat and a modification of the (TTAGGG)n repeat. Using different mapping approaches six sub-clones, free of the TTAGGG repeat, were assigned to a single human chromosome. Moreover, in situ hybridization mapped one of these subclones, G2 - 1H, definitively to the telomeric band on chromosome 4q. However, Bal 31 insensitivity suggests a location in a more subterminal region. All the (TTAGGG)n-adjacent unique sequences tested are highly conserved among primates but are not present in other mammalian species. Identification and mapping of TTAGGG-adjacent sequences will provide a refined insight into the genomic organization of the (TTAGGG)n repeat. The isolation of chromosome specific TTAGGG-adjacent sequences from subtelomeric regions of all human chromosomes will serve as important end points for the genetic maps and will be useful for the molecular characterization of chromosomal rearrangements involving telomeres.
Finite-difference Time-domain (FDTD) Optical Simulations: A Primer for the Life Sciences and Bio-Inspired Engineering (2021)

Light influences most ecosystems on earth, from sun-dappled forests to bioluminescent creatures in the ocean deep. Biologists have long studied nano- and micro-scale organismal adaptations to manipulate light using ever-more sophisticated microscopy, spectroscopy, and other analytical equipment. In combination with experimental tools, simulations of light interacting with objects can help researchers determine the impact of observed structures and explore how variations affect optical function. In particular, the finite-difference time-domain (FDTD) method is widely used throughout the nanophotonics community to efficiently simulate light interacting with a variety of materials and optical devices. More recently, FDTD has been used to characterize optical adaptations in nature, such as camouflage in fish and other organisms, colors in sexually-selected birds and spiders, and photosynthetic efficiency in plants. FDTD is also common in bioengineering, as the design of biologically-inspired engineered structures can be guided and optimized through FDTD simulations. Parameter sweeps are a particularly useful application of FDTD, which allows researchers to explore a range of variables and modifications in natural and synthetic systems (e.g., to investigate the optical effects of changing the sizes, shape, or refractive indices of a structure). Here, we review the use of FDTD simulations in biology and present a brief methods primer tailored for life scientists, with a focus on the commercially available software Lumerical FDTD. We give special attention to whether FDTD is the right tool to use, how experimental techniques are used to acquire and import the structures of interest, and how their optical properties such as refractive index and absorption are obtained. This primer is intended to help researchers understand FDTD, implement the method to model optical effects, and learn about the benefits and limitations of this tool. Altogether, FDTD is well-suited to (i) characterize optical adaptations and (ii) provide mechanistic explanations; by doing so, it helps (iii) make conclusions about evolutionary theory and (iv) inspire new technologies based on natural structures.
Adapting an Unadaptable ASR System (2023)

As speech recognition model sizes and training data requirements grow, it is increasingly common for systems to only be available via APIs from online service providers rather than having direct access to models themselves.In this scenario it is challenging to adapt systems to a specific target domain.To address this problem we consider the recently released OpenAI Whisper ASR as an example of a large-scale ASR system to assess adaptation methods.An error correction based approach is adopted, as this does not require access to the model, but can be trained from either 1-best or N-best outputs that are normally available via the ASR API.LibriSpeech is used as the primary target domain for adaptation.The generalization ability of the system in two distinct dimensions are then evaluated.First, whether the form of correction model is portable to other speech recognition domains, and secondly whether it can be used for ASR models having a different architecture.
Genetically engineered dual-band fractal antennas (2002)

Fractal antenna engineering concepts have been successfully combined with genetic algorithms to develop a powerful design optimization tool. The genetic optimization approach developed can simultaneously optimize the geometry of a fractal antenna, locations of loads, component values of loads, and the projected length of the fractal antenna. The results suggest that a 30-55% size reduction can be achieved by optimizing the fractalization and loading of a given antenna. The knowledge gained as a result of this study is directly applicable to the design of miniature fractal antennas.
RETINAL TOXICITY OF COMMERCIALLY AVAILABLE INTRAVITREAL KETOROLAC IN ALBINO RABBITS (2009)

Commercially available ketorolac tromethamine was found to be toxic to the retinas of albino rabbits following multiple intravitreal injections at a dose of 3 mg while no electrophysiologic toxicity was found. Therefore, the use of commercially available ketorolac containing alcohol, for intravitreal injection is not recommended.