gebhart/patrepeval huggingface dataset:
Effect of Sulforaphane and 5-Aza-2’-Deoxycytidine on Melanoma Cell Growth (2019)

<b>Background:</b> UV exposure-induced oxidative stress is implicated as a driving mechanism for melanoma. Increased oxidative stress results in DNA damage and epigenetic dysregulation. Accordingly, we explored whether a low dose of the antioxidant sulforaphane (SFN) in combination with the epigenetic drug 5-aza-2'-deoxycytidine (DAC) could slow melanoma cell growth. SFN is a natural bioactivated product of the cruciferous family, while DAC is a DNA methyltransferase inhibitor. <b>Methods:</b> Melanoma cell growth characteristics, gene transcription profiles, and histone epigenetic modifications were measured after single and combination treatments with SFN and DAC. <b>Results:</b> We detected melanoma cell growth inhibition and specific changes in gene expression profiles upon combinational treatments with SFN and DAC, while no significant alterations in histone epigenetic modifications were observed. Dysregulated gene transcription of a key immunoregulator cytokine-C-C motif ligand 5 (CCL-5)-was validated. <b>Conclusions:</b> These results indicate a potential combinatorial effect of a dietary antioxidant and an FDA-approved epigenetic drug in controlling melanoma cell growth.
State Constraint Control for Uncertain Nonlinear Systems With Disturbance Compensation (2019)

In this paper, a state constraint controller with disturbance compensation is proposed for uncertain nonlinear systems to improve the control performance without violating the full state constraints. A series of extended state observers are designed to estimate disturbances that include the unmodeled dynamics and the modeling errors. To guarantee non-violation of state constraints while compensating the disturbances, based on the backstepping technique, the state constraint controller with extended state observer is proposed by using the barrier Lyapunov function. Then, the stability of the closed-loop system is proved theoretically. Moreover, exponentially asymptotic tracking is achieved when the disturbances are not time-variant. Finally, the effectiveness of the proposed approach is verified by two examples.
BING, a novel antimicrobial peptide isolated from Japanese medaka plasma, targets bacterial envelope stress response by suppressing cpxR expression (2021)

Antimicrobial peptides (AMPs) have emerged as a promising alternative to small molecule antibiotics. Although AMPs have previously been isolated in many organisms, efforts on the systematic identification of AMPs in fish have been lagging. Here, we collected peptides from the plasma of medaka (Oryzias latipes) fish. By using mass spectrometry, 6399 unique sequences were identified from the isolated peptides, among which 430 peptides were bioinformatically predicted to be potential AMPs. One of them, a thermostable 13-residue peptide named BING, shows a broad-spectrum toxicity against pathogenic bacteria including drug-resistant strains, at concentrations that presented relatively low toxicity to mammalian cell lines and medaka. Proteomic analysis indicated that BING treatment induced a deregulation of periplasmic peptidyl-prolyl isomerases in gram-negative bacteria. We observed that BING reduced the RNA level of cpxR, an upstream regulator of envelope stress responses. cpxR is known to play a crucial role in the development of antimicrobial resistance, including the regulation of genes involved in drug efflux. BING downregulated the expression of efflux pump components mexB, mexY and oprM in P. aeruginosa and significantly synergised the toxicity of antibiotics towards these bacteria. In addition, exposure to sublethal doses of BING delayed the development of antibiotic resistance. To our knowledge, BING is the first AMP shown to suppress cpxR expression in Gram-negative bacteria. This discovery highlights the cpxR pathway as a potential antimicrobial target.
Supplementary Figure S1 from miR-629 Targets TRIM33 to Promote TGFβ/Smad Signaling and Metastatic Phenotypes in ccRCC (2023)

&lt;p&gt;Supplementary Figure S1. A, ACHN cells were transfected with miR-629 mimic or negative control mimic for 72 h. TRIM33 mRNA levels were examined by quantitative real-time PCR. Data are the relative expression normalized to GAPDH mRNA. Values are means {plus minus} S.D. of 3 independent experiments. **p &lt; 0.01 vs. control mimic. B, The expression of miR-629 and TRIM33 mRNAs expression (fold-change: tumor vs. normal) were examined in 41 matched-pair samples of ccRCC by quantitative real-time PCR, and the relationship was evaluated.&lt;/p&gt;
An interferometric theory of source-receiver scattering and imaging (2010)

Abstract It is known that there is a link between the theory of seismic interferometry and theories of seismic imaging and inversion. However, although this has been discussed in several studies, there are few where any explicit links have been derived. We use reciprocity theorems for scattering media to derive a new form of seismic interferometry that describes the scattered wavefield between a source and a receiver in an acoustic medium, using both sources and receivers on two enclosing boundaries. This form of seismic interferometry is equivalent to a generalized imaging condition (IC) that combines the full wavefield inside any finite-sized subregion of the medium of interest. By using the Born (single-scattering) approximation, this generalized IC reduces to the method of imaging by double-focusing originally derived by Michael Oristaglio in 1989. Thus an explicit link is made between seismic interferometry, new generalized full-wavefield ICs, and existing single-scattering imaging methods.
Diels-Alder reactions of cycloalkenones. 13. Reactions of 2-cyclohexenones with (E)-1-methoxy-1,3-butadiene (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiels-Alder reactions of cycloalkenones. 13. Reactions of 2-cyclohexenones with (E)-1-methoxy-1,3-butadieneFrancesco Fringuelli, Lucio Minuti, Lajos Radics, Aldo Taticchi, and Ernest WenkertCite this: J. Org. Chem. 1988, 53, 19, 4607–4610Publication Date (Print):September 1, 1988Publication History Published online1 May 2002Published inissue 1 September 1988https://pubs.acs.org/doi/10.1021/jo00254a045https://doi.org/10.1021/jo00254a045research-articleACS PublicationsRequest reuse permissionsArticle Views348Altmetric-Citations10LEARN 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
Support Vector Machines as Probabilistic Models (2011)

We show how the SVM can be viewed as a maximum likelihood estimate of a class of probabilistic models. This model class can be viewed as a reparametrization of the SVM in a similar vein to the v-SVM reparametrizing the classical (C-)SVM. It is not discriminative, but has a non-uniform marginal. We illustrate the benefits of this new view by rederiving and re-investigating two established SVM-related algorithms.
Displacement of polarons by vibrational modes in doped conjugated polymers (2017)

Organic pi-conjugated polymers are deemed to be soft materials with strong electron-phonon coupling, which results in the formation of polarons, i.e., charge carriers dressed by self-localized distortion of the nuclei. Universal signatures for polarons are optical resonances below the band gap and intense vibrational modes (IVMs), both found in the infrared (IR) spectral region. Here, we study $p$-doped conjugated homo- and copolymers by combining first-principles modelling and optical spectroscopy from the far-IR to the visible. Polaronic IVMs are found to feature absorption intensities comparable to purely electronic transitions and, most remarkably, show only loose resemblance to the Raman or IR-active modes of the neutral polymer. The IVM frequency is dramatically scaled down (up to 50%) compared to the backbone carbon-stretching modes in the pristine polymers. The very large intensity of IVMs is associated with displacement of the excess positive charge along the backbone driven by specific vibrational modes. We propose a quantitative picture for the identification of these polaron shifting modes that solely based on structural information, directly correlates with their IR intensity. This finding finally discloses the elusive microscopic mechanism behind the huge IR intensity of IVMs in doped polymeric semiconductors.
Telemedicine in the Wake of the COVID-19 Pandemic: Increasing Access to Surgical Care (2020)

This study indicates a reduction in disparity and an increase in access following the dramatically increased use of telemedicine in the wake of the COVID-19 pandemic. Although drawbacks to telemedicine exist and remain to be addressed, the vast majority of literature points to an overwhelming benefit-both for patient experience and outcomes-of utilizing telemedicine. Future studies should focus on improving access, reducing technological barriers, and policy reform to improve the spread of telemedicine.
Carrier generation in highly oriented WO3 films by proton or helium implantation (2002)

Implantation of H+ or He+ ions into highly oriented WO3 films, which were deposited on sapphire R-plane substrates by the pulsed laser deposition method, was carried out to generate carrier electrons. X-ray diffraction measurements revealed that the films consisted of only the two types of grains that were epitaxially grown with their c axes perpendicular to the surface of the substrate. After implantation to a dose of 1×1017 cm−2, a remarkable increase in conductivity at 300 K was observed to 200 Scm−1 for H+ implantation or to 3 Scm−1 for He+ implantation. The efficiency of carrier generation was ∼60% for H+ implantation or ∼10−3% for He+ implantation. This striking difference demonstrates that the chemical effect of bronze formation is much more effective for carrier generation in WO3 than is the physical effect of oxygen vacancy formation by nuclear collision processes. The resulting conductivity of the oriented films was higher by 1–3 orders of magnitude than that of the corresponding polycrystalline film prepared by the rf sputtering method. Hall mobility in the oriented films (∼1 cm2 V−1 s−1) was as high as that (1–2 cm2 V−1 s−1) in single-crystal Na0.40WO3 or WO2.99 and was higher by several orders of magnitude than that in polycrystalline films. The results of Hall voltage and x-ray diffraction measurements led to the conclusion that the higher conductivity in the highly oriented films mainly originates from an increase in carrier mobility, which results from decreases in grain boundary effects as scattering centers.
Structure and Mechanism of Pseudomonas aeruginosa PhzD, an Isochorismatase from the Phenazine Biosynthetic Pathway,, (2003)

PhzD from Pseudomonas aeruginosa is an isochorismatase involved in phenazine biosynthesis. Phenazines are antimicrobial compounds that provide Pseudomonas with a competitive advantage in certain environments and may be partly responsible for the persistence of Pseudomonas infections. In vivo, PhzD catalyzes the hydrolysis of the vinyl ether functional group of 2-amino-2-deoxyisochorismate, yielding pyruvate and trans-2,3-dihydro-3-hydroxyanthranilic acid, which is then utilized in the phenazine biosynthetic pathway. PhzD also catalyzes hydrolysis of the related vinyl ethers isochorismate, chorismate, and 4-amino-4-deoxychorismate. Here we report the 1.5 A crystal structure of native PhzD, and the 1.6 A structure of the inactive D38A variant in complex with isochorismate. The structures reveal that isochorismate binds to the PhzD active site in a trans-diaxial conformation, and superposition of the structures indicates that the methylene pyruvyl carbon of isochorismate is adjacent to the side chain carboxylate of aspartate 38. The proximity of aspartate 38 to isochorismate and the complete loss of activity resulting from the conversion of aspartate 38 to alanine suggest a mechanism in which the carboxylate acts as a general acid to protonate the substrate, yielding a carbocation/oxocarbonium ion that is then rapidly hydrated to form a hemiketal intermediate, which then decomposes spontaneously to products. The structure of PhzD is remarkably similar to other structures from a subfamily of alpha/beta-hydrolase enzymes that includes pyrazinamidase and N-carbamoylsarcosine amidohydrolase. However, PhzD catalyzes unrelated chemistry and lacks a nucleophilic cysteine found in its close structural relatives. The vinyl ether hydrolysis catalyzed by PhzD represents yet another example of the catalytic diversity seen in the alpha/beta-hydrolase family, whose members are also known to hydrolyze amides, phosphates, phosphonates, epoxides, and C-X bonds.
Development and Application of a New Theoretical Model for Additive Impacts on Mineral Crystallization (2017)

Additives play an important role in crystallization controls in both natural and industrial processes. Due to the lack of theoretical understanding of how additives work, the use and design of additives in various disciplines are mostly conducted empirically. This study has developed a new theoretical model to predict the additive impacts on crystallization based on the classical nucleation theory and regular solution theory. The new model assumes that additives can impact the nucleus partial molar volume and the apparent saturation status of the crystallization minerals. These two impacts were parametrized to be proportional to additive concentrations and vary with inhibitors. As a practical example, this new model has been used to predict barite induction times without inhibitors from 4 to 250 °C and in the presence of eight different scale inhibitors from 4 to 90 °C. The predicted induction times showed close agreement with the experimental data published previously or produced in this study. Such agreement indicates that this new theoretical model can be widely adopted in various disciplines to evaluate mineral formation kinetics, elucidate mechanisms of additive impacts, predict minimum effective dosage (MED) of additives, and guide the design of new additives, to mention a few.
Laryngeal mask airway and transient hypercapnic hyperpnea for video‐endoscopic assessment of unilateral laryngeal paralysis in dogs (2018)

Laryngeal endoscopy through an LMA coupled with administration of CO<sub>2</sub> in anesthetized dogs facilitates the observation of arytenoid function and may improve the diagnosis of naturally occurring mild laryngeal paralysis.
Temporary Solitaire Stent Scaffolding during Cerebral Aneurysm Coil Embolization (2014)

Background: Endovascular therapy gains acceptance as an alternative to open surgical clipping for an ever increasing subset of ruptured and unruptured brain aneurysms. Despite ongoing improvements of hardware and technique, coil embolization of distally located wide neck aneurysms remains associated with a comparatively higher rate of coil basket instability, coil mass compaction, and hence the risk of aneurysm reperfusion and recurrence over time. Balloon remodeling harbors the hazard of ischemia secondary to the transient flow arrest within the parent artery or trapped branches. Vessel rupture may also become a concern particularly during multiple balloon inflations and deflations in small diameter arteries. Stent-remodeling and flow-diversion strategies generally require instituting prolonged antiplatelet coverage; which is largely felt to complicate patient management particularly in the context of recent aneurysm rupture.
STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA (2015)

The heterogeneity among tumor cells within human glioma underlie their ability resist chemotherapy and radiation, ultimately leading to disease progression. While current chemotherapy and radiation treatment focuses on the effect on bulk tumor, mounting evidence indicates that rarer subpopulations of tumor cells are endowed with stem-like properties, which are capable of resisting these treatments, proliferating, and causing more aggressive recurrent tumors. However, unbiased evidence for cancer stem-like cells (CSCs) in solid human malignancies remains elusive. To better understand intratumoral heterogeneity, we sequenced the transcriptome of 3,348 single cells from human oligodendrogliomas using RNA-seq and reconstructed the cellular architecture within freshly resected tumor specimens from consented patients. We found that most tumor cells are differentiated along two specialized glial programs, while a third, rarer subpopulation of tumor cells express a neural stem/progenitor-like program. Surprisingly, cellular proliferation was restricted to this rare stem/progenitor-like subpopulation, consistent with the existence of a stem/progenitor-like compartment that is solely responsible for fueling growth of oligodendrogliomas in humans. By studying chromosomal copy number variation, we detect distinct genetic clones in which these three tumor subpopulations are preserved, indicating that the cellular hierarchy and genetic influences together determine tumor architecture. These results provide unprecedented insight into the cellular composition of brain tumors at single-cell resolution and have the potential to harmonize the cancer stem cell and genetic models of cancer, with critical implications for disease management.
Animal Models for Treating Spinal Cord Injury Using Biomaterials-Based Tissue Engineering Strategies (2020)

The aim of the study is to provide an up-to-date review of studies that used preclinical animal models for the evaluation of tissue engineering treatments for spinal cord injury (SCI), which involved the use of biomaterials with or without the addition of cells or biomolecules. Electronic search of the PubMed, Web of Science, and Embase databases was performed for relevant studies published between January 2009 and December 2019. In total, 1579 articles were retrieved, of which 58 studies were included for analysis. Among the included studies, rats were the most common species used for animal models of SCI, while complete transection was the most commonly used injury pattern. Immediate intervention after injury was conducted in the majority of studies, and 8 weeks was the most common final time point of outcome assessment. A wide range of natural and synthetic biomaterials with different morphologies were used as a part of tissue engineering treatments for SCI, including scaffolds, hydrogels, and particles. Experimental parameters in studies using SCI animal models to evaluate tissue engineering treatments should be carefully considered to match the purpose of the study. Biomaterials that have functional modifications or are applied in combination with cells and biomolecules can be effective in creating a permissive environment for SCI repair in preclinical animal models. Impact statement This review provides an up-to-date summary of the preclinical landscape where tissue engineering treatments involving biomaterials were tested in animal models of spinal cord injury (SCI). Using studies published within the last 10 years, novel perspectives were presented on the animal species used, injury pattern, timing of intervention and outcome measurement, and biomaterials selection, as well as a summary of the individual findings of each study. This review provides unique insight into biomaterials-based tissue engineering strategies that have progressed to testing in animal models of SCI, which will help shape future research in the field and propel the clinical translation of discoveries.
Comparison of 7 and 11–12 French Access for REBOA: Results from the AAST Aortic Occlusion for Resuscitation in Trauma and Acute Care Surgery (AORTA) Registry (2019)

Background: The introduction of low-profile devices designed for resuscitative endovascular balloon occlusion of the aorta (REBOA) after trauma has the potential to change practice, outcomes, and complication profiles.Methods: The AAST Aortic Occlusion for Resuscitation in Trauma and Acute Care Surgery (AORTA) registry was used to identify REBOA patients from 16 centers. Presentation, intervention, and outcome variables were compared via traditional 11–12 French access platforms and trauma-specific devices requiring only 7 French access.Results: From November 2013 to December 2017, 242 patients with complete data were identified, constituting 124 7 French and 118 11–12 French uses. Demographics of presentation were not diff erent between the two groups, except that patients using the 7 French had a higher mean Injury Severity Score (39.2 vs. 34.1, p = 0.028). The 7 French was associated with a lower cut-down requirement for access (22.6% vs. 37.3%, p = 0.049) and increased ultrasound guidance utilization (29.0% vs. 23.7%, p = 0.049). The 7 French afforded earlier aortic occlusion in the course of resuscitation (median 25.0 mins vs. 30 mins, p = 0.010) and a lower median requirement of packed red blood cells (10.0 vs. 15.5 units, p = 0.006) and fresh frozen plasma (7.5 vs. 14.0 units, p = 0.005). The 7 French patients were more likely to survive 24 h (58.1% vs. 42.4%, p = 0.015) and less likely to suff er in-hospital mortality (57.3% vs. 75.4%, p = 0.003). Finally, the 7 French device was associated with a four times lower rate of distal extremity embolism (20.0% vs. 5.6%, p = 0.014; OR 95% CI 4.25 [1.25–14.45]) compared to the 11–12 French. Conclusions: The introduction of trauma-specific 7 French REBOA devices appears to have infl uenced REBOA practices, with earlier use in severely injured hypotensive patients via less invasive means that are associated with lower transfusion requirements, fewer thrombotic complications, and improved survival. Additional study is required to determine optimal REBOA use.
Tetrahydrofuran amino acids—versatile building blocks for unnatural biopolymers: lack of secondary structure in oligomeric carbopeptoids derived from a D-galacto-5-(aminomethyl) tetrahydrofuran-2-carboxylic acid (2000)

The efficient synthesis of a D-galacto-configured tetrahydrofuran amino acid from a seven-carbon lactone as a monomer for the generation of sequence-defined structured biopolymer mimics is described. Investigations into the characteristics of homooligomeric derivatives of this monomer indicate that they do not adopt well defined secondary structures. The unanticipated formation of a heterooligomeric derivative and investigations into its solution structure are also described.