gebhart/patrepeval huggingface dataset:
An antibody-catalyzed dehydration reaction (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn antibody-catalyzed dehydration reactionTetsuo Uno and Peter G. SchultzCite this: J. Am. Chem. Soc. 1992, 114, 16, 6573–6574Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/ja00042a055https://doi.org/10.1021/ja00042a055research-articleACS PublicationsRequest reuse permissionsArticle Views184Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
mTORC1 activates PASK-Wdr5 signaling to epigenetically connect the nutrient status with myogenesis (2017)

Summary In the tissue microenvironment, stem cell functions are modulated by extrinsic signaling cues such as peptide hormones and dietary nutrients. These signaling cues maintain the balance between self-renewal and differentiation of its resident stem cells. The mechanistic Target of Rapamycin Complex 1 (mTORC1) is implicated to play an important role in regulating this balance, although its downstream effectors in stem cells have been elusive. We have recently shown that the PASK protein kinase phosphorylates Wdr5 to stimulate muscle stem cell differentiation by epigenetically activating the Myogenin promoter. Here, we show that the PASK-Wdr5 signaling pathway is a nutrient-sensitive downstream target of mTORC1 in muscle stem cells. We show that phosphorylation of PASK, and in turn of Wdr5, by mTORC1 is required for the activation of Myogenin transcription, exit from the self-renewal and induction of the myogenesis program. Thus, mTOR connects the diverse extrinsic signaling cues to a central epigenetic process to regulate the muscle stem cell fate between self-renewal and differentiation.
Fig. S3 from Small-Molecule–Mediated Stabilization of PP2A Modulates the Homologous Recombination Pathway and Potentiates DNA Damage-Induced Cell Death (2023)

&lt;p&gt;Fig. S3&lt;/p&gt;
Force Pulling of Single Cellulose Chains at the Crystalline Cellulose−Liquid Interface: A Molecular Dynamics Study (2009)

Pulling single cellulose molecules from a crystalline cellulose surface has been modeled by molecular dynamics (MD) simulations of the experimental procedure used in atomic force microscopy (AFM). Specifically, the aim of the study was to investigate cellulose interactions at desorption. Simulations were performed in both water and the organic solvent cyclohexane. Moreover, the effects of initial octamer conformation and orientation with respect to the surface chains were studied. A strong effect from the solvent was observed. In cyclohexane, normal forces of 200-500 pN and energies of 43.5+/-6.0 kJ/mol glucose unit were required to pull off the octamer. The normal forces in water were substantially lower, around 58 pN, and the energies were 18.2+/-3.6 kJ/mol glucose unit. In addition, the lateral components of the pull-off force were shown to provide information on initial conformation and orientation. Hydrogen bonds between the octamer and surface were analyzed and found to be an important factor in the pull-off behavior. Altogether, it was shown that MD provides detailed information on the desorption processes that may be useful for the interpretation of AFM experiments.
Measuring Total and Germinable Spore Populations (2011)

It has been shown that bacterial endospores can be enumerated using a microscopy based assay that images the luminescent halos from terbium ions bound to dipicolinic acid, a spore specific chemical marker released upon spore germination. Further development of the instrument has simplified it towards automation while at the same time improving image quality. Enumeration of total spore populations has also been developed allowing measurement of the percentage of viable spores in any population by comparing the germinable/culturable spores to the total. Percentage viability will allow a more quantitative comparison of the ability of spores to survive across a wide range of extreme environments.
Wafer Level Packaging to Address Future Direct Chip Attach Needs (2012)

This paper covers results from early pathfinding investigations of a wafer level package (WLP) technology that addresses future direct chip attach (DCA) needs. An overview of the WLP technology and pathfinding results covering key process flow evaluations and future challenges to apply the concept to DCA are presented. Proof-of-concept (POC) of 300mm wafer-level mold integrating with Cu bumps was demonstrated by investigating the mold thickness uniformity, wafer warpage, and solder joint reliability on the board. We conclude with a discussion of the key risk areas remaining challenges that includes the mold grinding thickness variance control, optimization of the material properties, and alternative low cost bumping technologies scalable less than 0.3mm pitch, and outline the next steps to continue data collection on the wafer warpage behavior, the die breakage strength, and the board level assembly process using a standard surface mount infrastructure in our pathfinding work.
Designing the Next Generation of Vaccines for Global Public Health (2011)

Vaccine research and development are experiencing a renaissance of interest from the global scientific community. There are four major reasons for this: (1) the lack of efficacious treatment for many devastating infections; (2) the emergence of multidrug resistant bacteria; (3) the need for improving the safety of the more traditional licensed vaccines; and finally, (4) the great promise for innovative vaccine design and research with convergence of omics sciences, such as genomics, proteomics, immunomics, and vaccinology. Our first project based on omics was initiated in 2000 and was termed reverse vaccinology. At that time, antigen identification was mainly based on bioinformatic analysis of a singular genome. Since then, omics-guided approaches have been applied to its full potential in several proof-of-concept studies in the industry, with the first reverse vaccinology-derived vaccine now in late stage clinical trials and several vaccines developed by omics in preclinical studies. In the meantime, vaccine discovery and development has been further improved with the support of proteomics, functional genomics, comparative genomics, structural biology, and most recently vaccinomics. We illustrate in this review how omics biotechnologies and integrative biology are expected to accelerate the identification of vaccine candidates against difficult pathogens for which traditional vaccine development has thus far been failing, and how research will provide safer vaccines and improved formulations for immunocompromised patients in the near future. Finally, we present a discussion to situate omics-guided rational vaccine design in the broader context of global public health and how it can benefit citizens in both developed and developing countries.
Agents and Emergence Agents and Emergence (1998)

GENTS CAN WORK AS noninteractive individuals or as a collective. When agents work as individuals with little or no interaction, what you get is just that: agents simply doing what they are asked to do. As a collective, however, something new and different can result—something that is more than the sum of the individual participants. The stock market, immune systems, and ant colonies are all examples of agents acting individually, yet from the interactions of these agents a new phenomenon arises. With the stock market, thousands of agents act independently to buy and sell shares of particular stocks and bonds. Yet from this independent behavior, an organismlike product called the stock market emerges. In other words, the rise and fall of the market is not controlled by a central process: it results from agents interacting. The stock market crash of ‘29 was a result of individual human agents—not a central controller. The crash of October ‘87 partly resulted from individual software agents that buy and sell securities according to programmed rules. The stock market, its crashes, temporary bubbles, dead-cat bounces, and all are more than the sum of the parts; it is an entity in its own right. Such entities are called emergent structures. Ant colonies are emergent structures that arise from individual ants acting interactively. The immune system emerges from the collective behavior of agents such as antigens, T cells, B cells, NK cells, immunoglobulins, lymph nodes, and the spleen. Other examples of emergent structures include families, organizations, societies, markets, flocks of birds, and traffic jams.
Raman Radial Mode Revealed from Curved Graphene (2017)

One of the unsolved fundamental issues of graphene is establishing an appropriate way to discern layers of graphene structures. We report a simple methodology to analyze graphene structures using Raman signals in the range of ∼100 to ∼500 cm<sup>-1</sup> comprising clear 118 or 175 cm<sup>-1</sup> peaks. We demonstrate that the low-energy signals on Raman spectra of plasma-seeded grown graphene sheets originated from nanocurvature (c) of mono- (175 and 325-500 cm<sup>-1</sup> signals) (c ≈ 1 nm) and bilayer (118 cm<sup>-1</sup> peak) (c ≈ 2 nm) graphene with Raman simulations, based on Raman radial mode (RM) Eigen vectors. Our RM model provides a standard way of identifying and evaluating graphene structures.
Pterostilbene Increases LDL Metabolism in HL-1 Cardiomyocytes by Modulating the PCSK9/HNF1α/SREBP2/LDLR Signaling Cascade, Upregulating Epigenetic hsa-miR-335 and hsa-miR-6825, and LDL Receptor Expression (2021)

Proprotein convertase subtilisin/kexin type 9 (PCSK9) can promote the degradation of low-density lipoprotein (LDL) receptor (LDLR), leading to hypercholesterolemia and myocardial dysfunction. The intracellular regulatory mechanism by which the natural polyphenol pterostilbene modulates the PCSK9/LDLR signaling pathway in cardiomyocytes has not been evaluated. We conducted Western blotting, flow cytometry, immunofluorescence staining, and mean fluorescence intensity analyses of pterostilbene-treated mouse HL-1 cardiomyocytes. Pterostilbene did not alter cardiomyocyte viability. Compared to the control group, treatment with both 2.5 and 5 μM pterostilbene significantly increased the LDLR protein expression accompanied by increased uptake of LDL. The expression of the mature PCSK9 was significantly suppressed at the protein and mRNA level by the treatment with both 2.5 and 5 μM pterostilbene, respectively, compared to the control. Furthermore, 2.5 and 5 μM pterostilbene treatment resulted in a significant reduction in the protein hepatic nuclear factor 1α (HNF1α)/histone deacetylase 2 (HDAC2) ratio and sterol regulatory element-binding protein-2 (SREBP2)/HDAC2 ratio. The expression of both hypoxia-inducible factor-1 α (HIF1α) and nuclear factor erythroid 2-related factor 2 (Nrf2) at the protein level was also suppressed. Pterostilbene as compared to short hairpin RNA against SREBP2 induced a higher protein expression of LDLR and lower nuclear accumulation of HNF1α and SREBP2. In addition, pterostilbene reduced PCSK9/SREBP2 interaction and mRNA expression by increasing the expression of hsa-miR-335 and hsa-miR-6825, which, in turn, increased LDLR mRNA expression. In cardiomyocytes, pterostilbene dose-dependently decreases and increases the protein and mRNA expression of PCSK9 and LDLR, respectively, by suppressing four transcription factors, HNF1α, SREBP2, HIF1α, and Nrf2, and enhancing the expression of hsa-miR-335 and hsa-miR-6825, which suppress PCSK9/SREBP2 interaction.
HLA-DR beta genes vary in number between different DR specificities, whereas the number of DQ beta genes is constant. (1985)

Probes isolated from DR and DQ beta cDNA and genomic clones were used in hybridizations to restriction enzyme-digested DNA from human homozygous typing cells (HTC) as well as other DR homozygous cells in order to estimate the number of beta genes in the DR/DQ class II region. Varying numbers of DR beta genes were found in HTC of different DR specificities, from possibly one in DR 8 cells to three in cells of DR 2 to 7. The DR beta genes of different specificities seem to be related to one another in a distinct fashion. In contrast, all HTC contain two DQ beta genes per chromosome. The restriction site polymorphism of DQ beta genes is considerably more extensive than that of DQ serology, although one of the genes seems to be nonpolymorphic. In addition to the two DP beta genes identified previously, a minimum of three to five DQ and DR beta genes exist in the human haploid genome.
Nutraceutical Apigenin regulates DC function in a RelB-dependent manner during neuroinflammation. (2022)

Abstract Apigenin, a natural flavonoid, found in several plants is known to have anti-oxidant and anti-inflammatory properties indicated by its use for centuries as a medicinal approach to treat inflammatory disorders. However, there are significant gaps in knowledge regarding its effect on dendritic cell (DC) function in maintaining an immune balance in immunospecialized locations like the central nervous system (CNS). In order to establish the potential utility of Apigenin as a therapeutic agent against neuroinflammatory diseases, we tested and found that Apigenin treatment ameliorated severity of disease progression and relapse after onset of experimental autoimmune encephalomyelitis (EAE) in C57BL/6 and SJL mouse models of multiple sclerosis. An increased retention of DCs and other myeloid cells in the periphery correlated with decreased immune cell infiltration and reduced demyelination in the CNS in treated mice. Mechanistically, Apigenin treatment reduced RelB expression in presence of LPS in human peripheral blood DCs, which is central to DC maturation, its antigen presentation capabilities and DC-mediated T cell activation. IL-12A and IL-23, downstream pro-inflammatory targets of RelB were reduced upon Apigenin treatment in these cells. Further, RelB causes a metabolic switch in immune cells upon inflammation, which was seen as a decrease in glucose uptake and lactate production (glycolysis), and an increase in mitochondrial activity when LPS-induced DCs were treated with Apigenin. These results indicate a protective role of Apigenin against DC-regulated neurodegenerative effects through a probable RelB mediated pathway thus implicating a potential therapy for neuroinflammatory disease. Supported by grants from NIH: 1R01NS0971-47
Signature of elastic turbulence of viscoelastic fluid flow in a single pore throat (2020)

When a viscoelastic fluid, such as an aqueous polymer solution, flows through a porous medium, the fluid undergoes a repetitive expansion and contraction as it passes from one pore to the next. Above a critical flow rate, the interaction between the viscoelastic nature of the polymer and the pore configuration results in spatial and temporal flow instabilities reminiscent of turbulentlike behavior, even though the Reynolds number Re≪1. To investigate whether this is caused by many repeated pore body-pore throat sequences, or simply a consequence of the converging (diverging) nature present in a single pore throat, we performed experiments using anionic hydrolyzed polyacrylamide (HPAM) in a microfluidic flow geometry representing a single pore throat. This allows the viscoelastic fluid to be characterized at increasing flow rates using microparticle image velocimetry in combination with pressure drop measurements. The key finding is that the effect, popularly known as "elastic turbulence," occurs already in a single pore throat geometry. The critical Deborah number at which the transition in rheological flow behavior from pseudoplastic (shear thinning) to dilatant (shear thickening) strongly depends on the ionic strength, the type of cation in the anionic HPAM solution, and the nature of pore configuration. The transition towards the elastic turbulence regime was found to directly correlate with an increase in normal stresses. The topology parameter, Q_{f}, computed from the velocity distribution, suggests that the "shear thickening" regime, where much of the elastic turbulence occurs in a single pore throat, is a consequence of viscoelastic normal stresses that cause a complex flow field. This flow field consists of extensional, shear, and rotational features around the constriction, as well as upstream and downstream of the constriction. Furthermore, this elastic turbulence regime, has high-pressure fluctuations, with a power-law decay exponent of up to |-2.1| which is higher than the Kolmogorov value for turbulence of |-5/3|.
Immunizing Patients with Adverse Events Following Immunization in the Canadian Special Immunization Clinic Network (2015–2017) (2017)

The experience of an adverse event following immunization (AEFI) can increase vaccine hesitancy among patients and health professionals who may be concerned about the risk of a recurrent or more severe event following revaccination. Infectious disease physicians and allergists in the Canadian Special Immunization Clinic (SIC) Network developed standard protocols for evaluation and revaccination of patients with prior AEFIs. We analyzed the outcomes of patients evaluated for AEFIs from 2015 to 2017. Patients are referred to one of 11 SICs in Canada by a physician or Public Health. Inclusion criteria are: patients of any age with injection-site reaction (ISR) ≥10 cm, allergic-like events (ALE) <24h post-immunization, neurological symptoms, and other AEFIs of concern. SIC physicians evaluate eligible patients and make immunization recommendations according to standard protocols. Patients are followed up after revaccination to capture AEFI recurrence. Recommendations and outcomes of revaccination(s) are transmitted to referring providers and Public Health. Following individual consent, data are transferred to a central database for analysis. For patients with more than one AEFI, the most severe event was included in the analysis. From June 2015 to May 2017, 230 patients were referred to the network for prior AEFI and 124 patients were enrolled. Most participants (86%) were <18 years of age and 49% were female. The most common types of AEFI were ALEs (37%; 46/124), followed by ISRs (23%; 29/124), neurologic events (15%; 19/124), and other systemic events (e.g., high fever) (24%; 30/124). Revaccination was recommended for 89 (72%) patients. AEFI recurrences occurred in 9/63 (14%) patients who were revaccinated and followed up: 2/22 (9%) ALEs (both less severe than first AEFI) and 7/14 (50%) ISRs (5 less severe, 2 equally severe as first AEFI). Patients with AEFIs benefit from clinical assessment by physicians with expertise in vaccines. The results suggest that most AEFIs do not contraindicate future immunizations. The risk of AEFI recurrence is low, except for ISRs, which are generally less severe that the initial AEFI. Specialized immunization services can support health professionals in managing patients with prior AEFIs. K. A. Top, Pfizer: Investigator, Research support; GSK: Investigator, Research grant; M. Sadarangani, Pfizer: Grant Investigator, Research grant; S. A. McNeil, GSK/Merck: Grant Investigator, Investigator and Scientific Advisor, Consulting fee, Grant recipient, Research grant, Research support and Speaker honorarium; G. De Serres, GlaxoSmithKline: Investigator and Scientific Advisor, Grant recipient and travel reimbursement; Ontario Nurses Association: Consultant, compensation for expert testimony
Peridiscal Vascular Anatomy of the Lower Lumbar Spine (1999)

The results of this study suggest that a laparoscopic approach to the L3-L4 intervertebral disc will seldom be accomplished without significant retraction of the aorta. Access to the L4-L5 space will be accomplished readily in approximately one third of the patients. In the others, it will require significant vascular dissection. The L5-S1 space, conversely, will be readily accessible by the authors' definitions without significant vessel dissection in the majority of patients.
Feline degenerative joint disease: a genomic and proteomic approach (2013)

The underlying disease mechanisms for feline degenerative joint disease (DJD) are mostly unidentified. Today, most of what is published on mammalian arthritis is based on human clinical findings or on mammalian models of human arthritis. However, DJD is a common occurrence in the millions of domestic felines worldwide. To get a better understanding of the changes in biological pathways that are associated with feline DJD, this study employed a custom-designed feline GeneChip, and the institution's unique access to large sample populations to investigate genes and proteins from whole blood and serum that may be up- or down-regulated in DJD cats. The GeneChip results centered around three main pathways that were affected in DJD cats: immune function, apoptosis and oxidative phosphorylation. By identifying these key disease-associated pathways it will then be possible to better understand disease pathogenesis and diagnose it more easily, and to better target it with pharmaceutical and nutritional intervention.
Space Transformation for Vortex Beam Generation (2018)

An all-dielectric oblate cylindrical shaped reflecting lens is proposed. The plane wave emitted from a wave port can be transformed into a vortex wave after being transmitted through the proposed lens and reflected by a planar metallic surface. The space transformation concept is applied for theoretical design of the lens, which results in a graded permittivity distribution profile. The far-field patterns are numerically simulated and reported in order to validate the proposed microwave lens over a wide frequency range spanning from 8 GHz to 12 GHz. Such an all-dielectric microwave lens can be potentially fabricated by low-cost materials through three-dimensional (3D) printing technology.
Outcomes of Endoscopic Therapy for Luminal Strictures in Crohn’s Disease (2018)

In a large cohort, endoscopic stricture dilation in CD was safe and effective. About 33% of patients required a second dilation at 1 year after the initial dilation; younger age and smaller inner diameter of the index stricture predicted need for a second dilation. 10.1093/ibd/izy049_video1izy049.video15794820307001.