gebhart/patrepeval huggingface dataset:
Synthesis of Polyhalogenated 4,4′-Bipyridines via a Simple Dimerization Procedure (2010)

Polyhalogenated 4,4'-bipyridines were conveniently synthesized in a single step starting from dihalopyridines. A mechanism was proposed on the basis of experiments performed with 2-chloro-5-bromopyridine 1a. 2-Chloro-4-lithio-5-bromopyridine A1 was produced via ortholithiation of 1a by using either LDA or t-BuLi bases. When LDA was used, dimer 3a containing two chlorines and two bromine atoms was formed predominantly accompanied by several byproducts whose structure and mechanism of formation are discussed. In the case of t-BuLi, although the major product was 2-chloropyridine 7, a new pyridone product 8 was formed that is probably the result of the dihydropyridine intermediate hydrolysis. The dimerization procedure involving LDA was employed to prepare a large number of halogenated 4,4'-bipyridines in moderate to good yields. In some specific cases, halogenated 3,4' and 2,4'-bipyridines were obtained in lower yields and their structures were unambiguously assigned by X-ray diffraction analysis.
Catalytic Conversion of Ethanol to n-Butanol Using Ruthenium P–N Ligand Complexes (2015)

We report several ruthenium catalysts incorporating mixed donor phosphine-amine ligands for the upgrade of ethanol to the advanced biofuel n-butanol, which show high selectivity (≥90%) at good (up to 31%) conversion. In situ formation of catalysts from mixtures of [RuCl2(η6-p-cymene)]2 and 2-(diphenylphosphino)ethylamine (1) shows enhanced activity at initial water concentrations higher than those of our previously reported diphosphine systems. Preliminary mechanistic studies (electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy) suggest the possibility of ligand-assisted proton transfer in some derivatives.
Using ConSurf to Detect Functionally Important Regions in RNA (2021)

The ConSurf web server (https://consurf.tau.ac.il/) for using evolutionary data to detect functional regions is useful for analyzing proteins. The analysis is based on the premise that functional regions, which may for example facilitate ligand binding and catalysis, often evolve slowly. The analysis requires finding enough effective, i.e., non-redundant, sufficiently remote homologs. Indeed, the ConSurf pipeline, which is based on state-of-the-art protein sequence databases and analysis tools, is highly valuable for protein analysis. ConSurf also allows evolutionary analysis of RNA, but the analysis often fails due to insufficient data, particularly the inability of the current pipeline to detect enough effective RNA homologs. This is because the RNA search tools and databases offered are not as good as those used for protein analysis. Fortunately, ConSurf also allows importing external collections of homologs in the form of a multiple sequence alignment (MSA). Leveraging this, here we describe various protocols for constructing MSAs for successful ConSurf analysis of RNA queries. We report the level of success of these protocols on an exemplary set comprising a dozen RNA molecules of diverse structure and function. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Standard ConSurf evolutionary conservation analysis of an RNA query. Basic Protocol 2: ConSurf evolutionary conservation analysis of an RNA query with external MSA. Support Protocol 1: Construction of an MSA for an RNA query using other online servers. Support Protocol 2: Construction of an MSA for an RNA query using nHMMER locally.
Computational modeling of deep tissue heating by an automatic thermal massage bed: predicting the effects on circulation (2022)

Automatic thermal and mechanical massage beds support selfmanaged treatment, including reduction of pain and stress, enhanced circulation, and improved mobility. As the devices become more sophisticated (increasing the degrees of freedom), it is essential to identify the settings that best target the desired tissue. To that end, we developed an MRI-derived model of the lower back and simulated the physiological effects of a commercial thermal-mechanical massage bed. Here we specifically estimated the tissue temperature and increased circulation under steady-state conditions for typical thermal actuator settings (i.e., 45-65°C). Energy transfer across nine tissues was simulated with finite element modeling (FEM) and the resulting heating was coupled to blood flow with an empirically-guided model of temperature-dependent circulation. Our findings indicate that thermal massage increases tissue temperature by 3-8°C and 1-3°C at depths of 2 and 3 cm, respectively. Importantly, due to the rapid (non-linear) increase of circulation with local temperature, this is expected to increase blood flow four-fold (4x) at depths occupied by deep tissue and muscle. These predictions are consistent with prior clinical observations of therapeutic benefits derived from spinal thermal massage.
The Reconstruction and Analysis of a Peruvian Middle Horizon Tapestry Fragment (1983)

A large fragment of unknown provenience in the Syracuse University Art Collections contains iconographic elements whose antecedents suggest the continuance of an ancient Andean religious tradition. Analysis of design elements has made possible a conceptual reconstruction of the original, much larger, textile.
Knee joint kinematics with dynamic augmentation of primary anterior cruciate ligament repair ‐ a biomechanical study (2016)

Increase in anteroposterior translation of knees treated with this dynamic augmentation procedure is low. The procedure maintains translation close to the immediate post-operative level over a simulated rehabilitation period of 50'000 gait cycles and therefore supports anterior cruciate ligament repair during biological healing.
Reducing health care costs using claims adjudication software. (1993)

An important area for reduction in health care costs is incorrect coding of physician services. Current software systems provide high-volume, consistent claims review with substantial savings for payers. The third generation of such systems offers comprehensive coverage across clinical disciplines, across individual claims, and across an entire history of claims. It is likely that these systems will be useful to both nontraditional payers, such as physician groups and hospital-based networks, and traditional payers seeking to reduce costs and enhance competitiveness.
Fog Computing Architecture, Evaluation, and Future Research Directions (2018)

IoT has been gaining a lot of attention in recent years. In fact, the number of connected devices has already surpassed the total population on Earth. Current developments in various technologies have paved the way for many IoT services that are now being deployed in different sectors. IoT can extend its scope and service provisioning capabilities with the integration of the cloud computing paradigm. Similarly, cloud cannot only access underlying IoT nodes and provide them with cloud services, but can also create further enhanced services based on the data collected from IoT nodes. However, IoT and sensor networks on the ground are often far from the cloud, which is normally accessible via the Internet. Some services require fast response and a great deal of pre-processing and filtering, and may also have security and privacy requirements. For all such cases, middleware, also known as fog, is required between the cloud and IoT devices. We present cloud-IoT integration issues followed by a comparison between fog and cloud computing. We evaluate the performance of fog computing using performance metrics such as processing delay, processing costs, and processing power, and derive the performance gains obtained in comparison to a cloud computing only approach. Finally, we identify some future research directions for fog computing.
BOOK REVIEW (1937)

Book reviewed in this article: The Mogollon Culture of Southwestern New Mexico. E. W. H aury . Some Southwestern Pottery Types, Series IV. E. W. H aury .
3D VIRTUAL AND PHYSICAL SIMULATION OF AUTOMATED CONTAINER TERMINAL AND ANALYSIS OF IMPACT ON IN LAND TRANSPORTATION (2000)

This study reports the efficacy of the combined application of chitosan (CH) and Locust Bean Gum (LBG) in combination with different citrus essential oils (EOs) to inhibit Aspergillus flavus in vitro and on artificially infected dates for a storage period of 12 days. The effect of these treatments on the fruits' sensory characteristics was evaluated to verify the complete absence of off-odours and off-flavours. Bergamot EO was the most effective in reducing mycelial growth, followed by bitter orange EO. Both bergamot and bitter orange oils significantly reduced conidial germination and a complete inhibition was obtained at concentrations higher than 2%. The mixtures based on CH-2% (v/v) bergamot EO or CH-2% (v/v) bitter orange EO proved to be the most effective coatings to reduce conidial germination resulting in an 87-90% inhibition compared with the control. In fruit decay assays coatings based on CH incorporating citrus oils were able to reduce fungal decay in the range of 52-62% at day 12. The study results and the complete absence of off-flavours and off-odours demonstrate the potential of CH coatings carrying citrus EOs at sub-inhibitory concentrations to control postharvest growth of A. flavus in dates.
Improvement of DNA Vector Delivery of DOTAP Lipoplexes by Short-Chain Aminolipids (2020)

Cellular delivery of DNA vectors for the expression of therapeutic proteins is a promising approach to treat monogenic disorders or cancer. Significant efforts in a preclinical and clinical setting have been made to develop potent nonviral gene delivery systems based on lipoplexes composed of permanently cationic lipids. However, transfection efficiency and tolerability of such systems are in most cases not satisfactory. Here, we present a one-pot combinatorial method based on double-reductive amination for the synthesis of short-chain aminolipids. These lipids can be used to maximize the DNA vector delivery when combined with the cationic lipid 1,2-dioleoyl-3-trimethylammonium propane (DOTAP). We incorporated various aminolipids into such lipoplexes to complex minicircle DNA and screened these systems in a human liver-derived cell line (HuH7) for gene expression and cytotoxicity. The lead aminolipid AL-A12 showed twofold enhanced gene delivery and reduced toxicity compared to the native DOTAP:cholesterol lipoplexes. Moreover, AL-A12-containing lipoplexes enabled enhanced transgene expression <i>in vivo</i> in the zebrafish embryo model.
Comparative Analysis of Four Oxidized Guanine Lesions from Reactions of DNA with Peroxynitrite, Singlet Oxygen, and γ-Radiation (2012)

Oxidative damage to DNA has many origins, including irradiation, inflammation, and oxidative stress, but the chemistries are not the same. The most oxidizable base in DNA is 2-deoxyguanosine (dG), and the primary oxidation products are 8-oxodG and 2-amino-imidazolone. The latter rapidly converts to 2,2-diamino-oxazolone (Ox), and 8-oxodG is further oxidized to spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). In this study, we have examined the dose–response relationship for the formation of the above four products arising in calf thymus DNA exposed to gamma irradiation, photoactivated rose bengal, and two sources of peroxynitrite. In order to carry out these experiments, we developed a chromatographic system and synthesized isotopomeric internal standards to enable accurate and precise analysis based upon selected reaction monitoring mass spectrometry. 8-OxodG was the most abundant products in all cases, but its accumulation was highly dependent on the nature of the oxidizing agent and the subsequent conversion to Sp and Gh. Among the other oxidation products, Ox was the most abundant, and Sp was formed in significantly greater yield than Gh.
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA (2007)

This report presents a valuable new bioinformatics package for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service, which is not available elsewhere, enables a user to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. Our tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of new tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database available publicly at http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms.
Passively athermalized broadband optical design using doublet combinations (2014)

In this paper we propose a method for broadband achromatic and passive athermal optical system design using a combination of three doublets. In the implementation of this method, the first-order color dispersion is corrected by distributing proper power to the elements inside the doublets; the thermal and secondary color dispersion are corrected by distributing proper power to the doublet group units. The theoretical deviation is given and we summarize the power distribution equations. A design of an example system using this method, which covers the 350-1200 nm wavelength band, is given and the image quality evaluation is presented. It is shown that the example system maintains high imaging qualities over the required wavelength and temperature range, which proves the effectiveness of the method.
Abstract 2881: Proper priming of T cells is crucial for the anti-tumor effect of mPTX-35, an anti-TNFRSF25 agonist antibody (2022)

Abstract TNFRSF25, also known as Death Receptor 3 (DR3), is a cell surface receptor of the tumor necrosis factor receptor superfamily (TNFRSF) which is expressed on T cells, innate lymphoid cells, and B cells. Upon binding with TL1A ligand, this co-stimulatory molecule induces T cell activation, leading either to inflammation or cell death. Mouse PTX-35 (mPTX-35) is a TNFRSF25 functional agonist derived from a CDR that was humanized and affinity matured, then fused to a mouse IgG1-Fc backbone. Since costimulatory agonist antibodies have shown limited efficacy in clinical trials, our aims were to (i) determine the anti-tumor efficacy of mPTX-35, (ii) elucidate any mechanisms of resistance, and (iii) identify immune conditions that provide effective anti-tumor immune responses to mPTX-35 treatment. We studied the anti-tumor immune effects of mPTX-35 in both cold and hot tumor models. In a TC-1 cold tumor, we found that treatment with an anti-TNFRSF25 agonist antibody does not affect tumor growth or survival. In contrast, vaccination with an E7 antigen-specific vaccine leads to an environment that reverses primary resistance to the agonist antibody, inhibiting the tumor growth, and enhancing overall survival. Interestingly, we found that similar to other co-stimulatory agonist molecules, the immune effects of the anti-TNFRSF25 agonist are dose-dependent with lower (0.2 mg/kg) and higher (5 mg/kg) doses of mPTX-35 showing a reduced anti-tumor response than a dose of 1 mg/kg, resulting in a bell-shaped response in all tumor models. Similar immune-mediated anti-tumor effects of mPTX-35 were found in a CT26 (hot) tumor model. In conclusion, these results show that anti-TNFRSF25 agonist antibody demonstrates high anti-tumor efficacy in tumors that are infiltrated with T cells while the absence of properly antigen activated CD8 T cells (such as in cold tumors) incurs primary resistance to TNFRSF25 agonist that is reversed by proper priming of CD8 T cells. These results highlight the importance of optimal priming to limit primary resistance mechanisms and drive an efficacious immune response via the TNSFR25 axis. Citation Format: Dareen Sarhan, Lara Rabah, Vikas Tahiliani, Anh M. Trinh, Rahul R. Jasuja, Eric P. Dixon, Matthew Seavey, Vivek Verma, Seema Gupta, Samir N. Khleif. Proper priming of T cells is crucial for the anti-tumor effect of mPTX-35, an anti-TNFRSF25 agonist antibody [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2881.
PD-L1 expression is strongly associated with TIGIT, FOXP3 and LAG3 across advanced cancers, but not OX40, TIM3 and IDO (2018)

Background: Multiple trials are ongoing to evaluate combinations of immune checkpoint inhibitors (ICIs) across a variety of tumor types. Most of these studies utilize programmed death-1(PD-1) or programmed death-ligand 1 (PD-L1) inhibitors as a backbone. We interrogate the relationship of PD-L1 with other immune checkpoints to inform rational combination strategies. Methods: We performed whole transcriptomic sequencing (RNA-Seq; ∼200x106 reads/tumor) across 1,467 unselected clinical cases (NantHealth; Culver City, CA). Cases reflected 38 distinct histologies; the most common histologies were breast (17.8%), colon (9.5%) and lung (7.9%). High and low PD-L1 was delineated as the top and bottom 15th percentile of expression values. Co-expression of checkpoint markers (TIGIT, FOXP3, LAG3, OX40, TIM3 and IDO) was analyzed within PD-L1-defined categories, along with putative markers of ICI resistance (e.g, VEGF-A/B/C). Tumor mutational burden (TMB; defined as exonic nonsynonymous mutations) was characterized across checkpoints. Results: High PD-L1 expression was strongly associated with high expression of TIGIT, FOXP3 and LAG3 (P < 0.001 for each). In contrast, there was no significant difference in expression of OX40, TIM3 and IDO in groups subdivided by high and low PD-L1 expression. High expression of PD-L1 was associated with elevated levels of VEGF-C, but there was no relationship with VEGF-A or VEGF-B expression. Very limited concordance was seen between elevated TMB (> 200 nonsynonymous mutations) and checkpoint expression. Conclusions: Recent results of combination trials assessing IDO and PD-1 inhibitors may be attributable to a lack of concomitant expression of these markers, thereby limiting synergy. Combinations of PD-1/-L1-directed therapies with TIGIT and LAG3 inhibitors may therefore be of greater interest. Enrichment strategies using TMB for these combinations may be challenging, given the lack of association with checkpoint expression. Legal entity responsible for the study: Sumanta Pal. Funding: Has not received any funding. Disclosure: S.K. Pal: Consultant: Pfizer, Inc., Novartis, Aveo Pharmaceuticals, Inc., Myriad Genetics, Genentech, Inc., Exelixis, Bristol-Myers Squibb Company, Astellas Pharma, Inc.; Research/grant support: Medivation, Inc,; Honorarium: Novartis, Medivation, Inc., and Astellas Pharma, Inc. C. Szeto, S. Reddy: Employee and stockholder: NantOmics LLC. O. Hamid: Consultant: Amgen, Novartis, Roche, BMS, Merck; Speaker: BMS, Genentech, Novartis, Amgen; Contracted research (for institution): AstraZeneca, BMS, Celldex, Genentech, Immunocore, Incyte, Merck, Merck-Serono, MedImmune, Novartis, Pfizer, Rinat, Roche. All other authors have declared no conflicts of interest.
Increases in cytosolic Ca2+ accompany basophil activation by eosinophil granule major basic protein (1997)

The response of basophil cytosolic free Ca2+ concentrations ([Ca2+]i) to stimulation by eosinophil granule major basic protein (MBP) was assessed using digital video microscopy. MBP stimulated an elevation in basophil [Ca2+]i that, in general, developed slowly and increased monotonically. In some experiments, however, the average rise in [Ca2+]i was biphasic, with an initial transient increase followed by a larger and more sustained elevation. At the single cell level MBP stimulation caused frequent, asynchronous oscillations in [Ca2+]i that ranged up to 300 nM in amplitude. Chelation of extracellular Ca2+ selectively blocked the second, sustained rise in [Ca2+]i as well as MBP-induced histamine release. Within individual experiments, the increase in [Ca2+]i paralleled the level of histamine release. These results demonstrate that, unlike the activation of neutrophils or eosinophils, basophil activation by MBP correlates with an elevation in [Ca2+]i. Further, the MBP induced [Ca2+]i response exhibits several features in common with the IgE-mediated [Ca2+]i response.
The Choice of HLA‐Associated Peptide Enrichment and Purification Strategy Affects Peptide Yields and Creates a Bias in Detected Sequence Repertoire (2020)

Understanding the most appropriate workflow for biochemical human leukocyte antigen (HLA)-associated peptide enrichment prior to ligand sequencing is essential to achieve optimal sensitivity in immunopeptidomics experiments. The use of different detergents for HLA solubilization as well as complementary workflows to separate HLA-bound peptides from HLA protein complex components after their immunoprecipitation including HPLC, C18 cartridge, and 5 kDa filter are described. It is observed that all solubilization approaches tested led to similar peptide ligand identification rates; however, a higher number of peptides are identified in samples lysed with CHAPS compared with other methods. The HPLC method is superior in terms of HLA-I peptide recovery compared with 5 kDa filter and C18 cartridge peptide purification methods. Most importantly, it is observed that both the choice of detergent and peptide purification strategy creates a significant bias for the identified peptide sequences, and that allele-specific peptide repertoires are affected depending on the workflow of choice. The results highlight the importance of employing a suitable strategy for HLA peptide enrichment and that the obtained peptide repertoires do not necessarily reflect the true distributions of peptide sequences in the sample.
Influence of Air Supply Velocity on Temperature Field in the Self Heating Process of Coal (2017)

The air supply velocity is an important factor affecting the spontaneous combustion of coal. The appropriate air velocity can not only provide the oxygen required for the oxidation reaction, but maintains the good heat storage environment. Therefore, it is necessary to study the influence of the actual air velocity in the pore space on the self-heating process of coal particles. This paper focuses on studying the real space piled up by spherical particles. CFD simulation software is used to establish the numerical model from pore scale. Good fitness of the simulation results with the existing results verifies the feasibility of the calculation method. Later, the calculation conditions are changed to calculate and analyze the velocity field and the temperature field for self-heating of some particles (the surface of the particles is at a certain temperature) and expound the effect of different air supply velocities on gathering and dissipating the heat.
Capacity enhancement and interference management for interactive satellite networks (2019)

We investigate the effect of aggressive frequency reuse in multibeam satellite systems using novel techniques. The techniques include our previously proposed non-spreading non-orthogonal multiple access (NOMA) scheme as well as spread spectrum code division multiplexing (CDM) NOMA. The 4-color frequency reuse is used as benchmarks, while the 2-color 70-beam and 1-color 20-beam, exhibiting significant co-channel interference (CCI), were considered as interference-limited scenarios for comparative capacity performance evaluations. The operation accuracy of the successive interference cancellation (SIC) at the core of our interference mitigation (IM) techniques was also investigated. In terms of overall achievable capacity, the results show promising achievements in the 1-color 20-beam scenario while there are no capacity gains indicated in 70-beam scenario with 2-color frequency mapping. However, a significant fairness enhancement has been shown in both scenarios.