gebhart/patrepeval huggingface dataset:
B Cell-Derived IL-15 Enhances CD8 T Cell Cytotoxicity and Is Increased in Multiple Sclerosis Patients (2011)

Multiple lines of evidence suggest that CD8 T cells contribute to the pathogenesis of multiple sclerosis (MS). However, the sources and involvement of cytokines such as IL-15 in activating these cells is still unresolved. To investigate the role of IL-15 in enhancing the activation of CD8 T cells in the context of MS, we determined cell types expressing the bioactive surface IL-15 in the peripheral blood of patients and evaluated the impact of this cytokine on CD8 T cell cytotoxicity and migration. Flow cytometric analysis showed a significantly greater proportion of B cells and monocytes from MS patients expressing IL-15 relative to controls. We established that CD40L activation of B cells from healthy donors increased their IL-15 levels, reaching those of MS patients. We also demonstrated an enhanced cytotoxic profile in CD8 T cells from MS patients upon stimulation with IL-15. Furthermore, we showed that IL-15 expressed by B cells and monocytes is sufficient and functional, enhancing granzyme B production by CD8 T cells upon coculture. Exposure of CD8 T cells to this cytokine enhanced their ability to kill glial cells as well as to migrate across an in vitro inflamed human blood-brain barrier. The elevated levels of IL-15 in patients relative to controls, the greater susceptibility of CD8 T cells from patients to IL-15, in addition to the enhanced cytotoxic responses by IL-15-exposed CD8 T cells, stresses the potential of therapeutic strategies to reduce peripheral sources of IL-15 in MS.
Structure of the mini-RNA-guided endonuclease CRISPR-Cas12j3 (2021)

CRISPR-Cas12j is a recently identified family of miniaturized RNA-guided endonucleases from phages. These ribonucleoproteins provide a compact scaffold gathering all key activities of a genome editing tool. We provide the first structural insight into the Cas12j family by determining the cryoEM structure of Cas12j3/R-loop complex after DNA cleavage. The structure reveals the machinery for PAM recognition, hybrid assembly and DNA cleavage. The crRNA-DNA hybrid is directed to the stop domain that splits the hybrid, guiding the T-strand towards the catalytic site. The conserved RuvC insertion is anchored in the stop domain and interacts along the phosphate backbone of the crRNA in the hybrid. The assembly of a hybrid longer than 12-nt activates catalysis through key functional residues in the RuvC insertion. Our findings suggest why Cas12j unleashes unspecific ssDNA degradation after activation. A site-directed mutagenesis analysis supports the DNA cutting mechanism, providing new avenues to redesign CRISPR-Cas12j nucleases for genome editing.
Reduced ultraviolet-induced DNA damage and apoptosis in human skin with topical application of a photolyase-containing DNA repair enzyme cream: Clues to skin cancer prevention (2011)

The exposure of human skin to ultraviolet radiation (UVR) results in the formation of DNA photolesions that give rise to photoaging, mutations, cell death and the onset of carcinogenic events. Photolyase (EC 4.1.99.3) is a DNA repair enzyme that reverses damage caused by exposure to UVR. We sought to investigate whether addition of photolyase enhances the protection provided by a traditional sunscreen (SS), by reducing the in vivo formation of cyclobutane-type pyrimidine dimers (CPDs) and UVR-induced apoptosis in human skin. Ten volunteers (Fitzpatrick skin type II) were exposed to solar-simulated (ss) UVR at a three times minimal erythema dose for 4 consecutive days. Thirty minutes prior to each exposure, the test materials [vehicle, SS (sun protection factor 50) alone, and SS plus photolyase from Anacystis nidulans] were applied topically to three different sites. One additional site was left untreated and one received ssUVR only. Biopsy specimens were taken 72 h after the last irradiation. The amount of CPDs and the extent of apoptosis were measured by ELISA. Photolyase plus SS was superior to SS alone in reducing both the formation of CPDs and apoptotic cell death (both P<0.001). In conclusion, the addition of photolyase to a traditional SS contributes significantly to the prevention of UVR-induced DNA damage and apoptosis when applied topically to human skin.
A multistage-approach to the dynamics and control of elastic robots (2003)

The control of an elastic robot along a reference trajectory is performed in several steps. An optimal reference path for a rigid robot is generated, taking into account any restrictions and arbitrary robot/trajectory configurations. Tracking of that path is improved by regarding the elastic influences of all links and joints. For the purpose the robot is modeled as an elastic multibody system. A control scheme is added which feeds back strain-gauge measurements at the elastic arms to damp remaining oscillations. These three stages together allow high performance control of an elastic robot, which is proven by measurements at a three-degree-of-freedom laboratory robot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phase III Study Comparing a Reduced Dose of Cabazitaxel (20 mg/m2) and the Currently Approved Dose (25 mg/m2) in Postdocetaxel Patients With Metastatic Castration-Resistant Prostate Cancer—PROSELICA (2017)

Purpose Cabazitaxel 25 mg/m<sup>2</sup> (C25) significantly improved overall survival (OS) versus mitoxantrone ( P < .001) in postdocetaxel patients with metastatic castration-resistant prostate cancer (mCRPC) in the phase III TROPIC study. The phase III PROSELICA study ( ClinicalTrials.gov identifier: NCT01308580) assessed the noninferiority of cabazitaxel 20 mg/m<sup>2</sup> (C20) versus C25 in postdocetaxel patients with mCRPC. Methods Patients were stratified by Eastern Cooperative Oncology Group performance status, measurability of disease per Response Evaluation Criteria in Solid Tumors (RECIST), and region, and randomly assigned to receive C20 or C25. To claim noninferiority of C20 (maintenance of ≥ 50% of the OS benefit of C25 v mitoxantrone in TROPIC) with 95% confidence level, the upper boundary of the CI of the hazard ratio (HR) for C20 versus C25 could not exceed 1.214 under a one-sided 98.89% CI after interim analyses. Secondary end points included progression-free survival, prostate-specific antigen (PSA), tumor and pain responses and progression, health-related quality of life, and safety. Results Overall, 1,200 patients were randomly assigned (C20, n = 598; C25, n = 602). Baseline characteristics were similar in both arms. Median OS was 13.4 months for C20 and 14.5 months for C25 (HR, 1.024). The upper boundary of the HR CI was 1.184 (less than the 1.214 noninferiority margin). Significant differences were observed in favor of C25 for PSA response (C20, 29.5%; C25, 42.9%; nominal P < .001) and time to PSA progression (median: C20, 5.7 months; C25, 6.8 months; HR for C20 v C25, 1.195; 95% CI, 1.025 to 1.393). Health-related quality of life did not differ between cohorts. Rates of grade 3 or 4 treatment-emergent adverse events were 39.7% for C20 and 54.5% for C25. Conclusion The efficacy of cabazitaxel in postdocetaxel patients with mCRPC was confirmed. The noninferiority end point was met; C20 maintained ≥ 50% of the OS benefit of C25 versus mitoxantrone in TROPIC. Secondary efficacy end points favored C25. Fewer adverse events were observed with C20.
A cluster of bacterial genes for anaerobic benzene ring biodegradation (1997)

A reductive benzoate pathway is the central conduit for the anaerobic biodegradation of aromatic pollutants and lignin monomers. Benzene ring reduction requires a large input of energy and this metabolic capability has, so far, been reported only in bacteria. To determine the molecular basis for this environmentally important process, we cloned and analyzed genes required for the anaerobic degradation of benzoate and related compounds from the phototrophic bacterium, Rhodopseudomonas palustris. A cluster of 24 genes was identified that includes twelve genes likely to be involved in anaerobic benzoate degradation and additional genes that convert the related compounds 4-hydroxybenzoate and cyclohexanecarboxylate to benzoyl-CoA. Genes encoding benzoyl-CoA reductase, a novel enzyme able to overcome the resonance stability of the aromatic ring, were identified by directed mutagenesis. The gene encoding the ring-cleavage enzyme, 2-ketocyclohexanecarboxyl-CoA hydrolase, was identified by assaying the enzymatic activity of the protein expressed in Escherichia coli. Physiological data and DNA sequence analyses indicate that the benzoate pathway consists of unusual enzymes for ring reduction and cleavage interposed among enzymes homologous to those catalyzing fatty acid degradation. The cloned genes should be useful as probes to identify benzoate degradation genes from other metabolically distinct groups of anaerobic bacteria, such as denitrifying bacteria and sulfate-reducing bacteria.
Isoxazolylpyridinium salts. A new class of hypoglycemic agents (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsoxazolylpyridinium salts. A new class of hypoglycemic agentsVictor J. Bauer, William J. Fanshawe, Harry P. Dalalian, and S. R. SafirCite this: J. Med. Chem. 1968, 11, 5, 984–986Publication Date (Print):September 1, 1968Publication History Published online1 May 2002Published inissue 1 September 1968https://pubs.acs.org/doi/10.1021/jm00311a016https://doi.org/10.1021/jm00311a016research-articleACS PublicationsRequest reuse permissionsArticle Views61Altmetric-Citations8LEARN 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
ASRP: the Arabidopsis Small RNA Project Database (2004)

Eukaryotes produce functionally diverse classes of small RNAs (20-25 nt). These include microRNAs (miRNAs), which act as regulatory factors during growth and development, and short-interfering RNAs (siRNAs), which function in several epigenetic and post-transcriptional silencing systems. The Arabidopsis Small RNA Project (ASRP) seeks to characterize and functionally analyze the major classes of endogenous small RNAs in plants. The ASRP database provides a repository for sequences of small RNAs cloned from various Arabidopsis genotypes and tissues. Version 3.0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu.
Frequency and Risk Factors Associated With Osteonecrosis of the Jaw in Cancer Patients Treated With Intravenous Bisphosphonates (2008)

ONJ is an uncommon but long-lasting disorder that occurs mainly in breast cancer and multiple myeloma patients treated with intravenous bisphosphonates. High cumulative doses of bisphosphonates, poor oral health, and dental extractions may be significant risk factors for ONJ development. ONJ resolved in 23% of patients with conservative therapy.
Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis (2013)

Defective gut colonisation by F. prausnitzii occurred in UC patients during remission and in their unaffected relatives. The recovery of the F. prausnitzii population after relapse is associated with maintenance of clinical remission.
Evolution of Robust Developmental Neural Networks (2004)

We present the first evolved solutions to a computational task within the Neuronal Organism Evolution model (Norgev) of artificial neural network development. These networks display a remarkable robustness to external noise sources, and can regrow to functionality when severely damaged. In this framework, we evolved a doubling of network functionality (double-NAND circuit). The network structure of these evolved solutions does not follow the logic of human coding, and instead more resembles the decentralized dendritic connection pattern of more biological networks such as the C. ele gans brain.
Nephrotoxicity in Mice After Repeated Imaging Using 111In-Labeled Peptides (2010)

Micro-SPECT enables longitudinal studies in 1 animal. However, long-term nephrotoxic effects may be induced after high renal radiation doses, even with (111)In-labeled radiotracers.
Tofacitinib Citrate for the Treatment of Vitiligo (2015)

The results suggest that tofacitinib and other Janus kinase inhibitors may be effective in the treatment of vitiligo. Additional studies will be needed to confirm their efficacy and to explore their safety.
Hybrid trellis-coded 8/4-PSK systems (2003)

It is shown how trellis-coded 8-PSK (phase-shift-keying) signals can be modified to become more robust against carrier phase variations, thus allowing more stable carrier recovery. A more robust performance can be achieved by using rate 2/3 trellis-coded 8-PSK and 4-PSK signals in a time-varying manner. In its simplest form, trellis-coded 8-PSK and 4-PSK signals alternate in time. The distance spectra and bit error probability are evaluated with and without phase offset. Simulation results of bit error rate (BER) and performance of the recovery loop (S-curve) are also presented. At 7.5 degrees RMS phase jitter, the cycle slip rate of the conventional trellis-coded 8-PSK system is about 25%. For the new schemes it is reduced to less than 0.1%. This is achieved with almost no penalty in BER in blocks received without cycle slips.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rate-accelerating metal ion effects on decarboxylation of α-keto acids by a thiazolium ton bearing a metal binding site (1991)

Decarboxylation of α-keto acids by a thiazolium ion bearing a bipyridine moiety was found to be markedly enhanced by divalent metal ions such as Zn2+, Mn2+ and Mg2+ in EtOH.
Targeted gene walking polymerase chain reaction (1991)

We describe a modification of a polymerase chain reaction method called 'targeted gene walking' that can be used for the amplification of unknown DNA sequences adjacent to a short stretch of known sequence by using the combination of a single, targeted sequence specific PCR primer with a second, nonspecific 'walking' primer. This technique can replace conventional cloning and screening methods with a single step PCR protocol to greatly expedite the isolation of sequences either upstream or downstream from a known sequence. A number of potential applications are discussed, including its utility as an alternative to cloning and screening for new genes or cDNAs, as a method for searching for polymorphic sites, restriction endonuclease or regulatory regions, and its adaptation to rapidly sequence DNA of lengthy unknown regions that are contiguous to known genes.
Direct simulation of material permittivities by using an eigen-susceptibility formulation of the vector variational approach (2009)

This paper presents a new method for the extraction of material parameters, in this case the permittivity, by formulating the Maxwell equations as an eigen-susceptibility problem of the considered sample. This offers a direct solution of the desired material parameters by utilizing adequate and well proven numerical techniques. Hence, it is very useful if analytical approaches do not provide the aimed accuracy or even fail completely. The procedure will be demonstrated by applying the variational approach to a triple mode cavity perturbation method for the characterization of the complex permittivity tensor of general biaxial anisotropic media.
Mucoadhesive Ophthalmic Vehicles: Evaluation of Polymeric Low-Viscosity Formulations (1994)

A series of polyanionic natural or semi-synthetic polymers (polygalacturonic acid, hyaluronic acid, carboxymethylamylose, carboxymethylchitin, chondroitin sulfate, heparan sulfate and mesoglycan) were evaluated as potential mucoadhesive carriers for ophthalmic drugs. Solutions containing cyclopentolate (CY) or pilocarpine (PI) as salts (or polyanionic complexes) with the acidic polymers, all showing a low viscosity, were tested for miotic (resp. mydriatic) activity in albino rabbits. In the case of some polymeric complexes, small but significant increases of the areas under the activity vs. time curves (AUC) over reference cyclopentolate hydrochloride (CYHC1) or pilocarpine nitrate (PINO3) vehicles, and significant AUC decreases after removal of precorneal mucin by treatment with N-acetylcysteine were observed. A correlation was found between these data, considered indicative of the occurrence of a mucoadhesive interaction "in vivo", and "in vitro" viscometric data expressing the polymers-mucin force of interaction. The advantages and limitations of the mucoadhesive non-viscous approach in the formulation of ophthalmic vehicles are presented and discussed.
Transcranial ultrasound focus reconstruction with phase and amplitude correction (2005)

Therapeutic and diagnostic ultrasound procedures performed noninvasively through the skull require a reliable method for maintaining acoustic focus integrity after transmission through layered bone structures. This study used a multiple-element, phased-array transducer to reconstruct ultrasound foci through the human skull by amplitude and phase correction. It was previously demonstrated that adaptive phase correction using a multiple-element, focused transducer array yields a significant correction to an acoustic field that has been distorted by the heterogeneities of the skull bone. The introduction of amplitude correction, in a regime in which acoustic pressures from individual transducer array elements are adjusted to be normalized at the focus, has demonstrated a 6% (-0.27 dB) average decrease in acoustic sidelobe acoustic intensity relative to the focal intensity and a 2% (-0.09 dB) average decrease in the full-width-at-half-maximum (FWHM) of the acoustic intensity profile at the focus. These improvements come at the expense of significant ultrasound intensity loss--as much as 30% lower (-1.55 dB)--at the focus because the amplitude correction method requires that, at constant power, a larger proportion of energy is absorbed or reflected by regions of the skull that transmit less energy. In contrast, a second correction method that distributes pressure amplitudes such that the sections of the skull which transmit more ultrasound energy are exposed with higher ultrasound intensities has demonstrated an average sidelobe intensity decrease of 3% (-0.13 dB) with no change in the FWHM at the focus. On average, there was a 2% (0.09 dB) increase in the acoustic intensity at the focus for this inverse amplitude correction method. These results indicate that amplitude correction according to the transmission properties of various segments of the skull have a clear effect on ultrasound energy throughput into a target site within the brain parenchyma.
Graph Regularized Sparse Coding for Image Representation (2010)

Sparse coding has received an increasing amount of interest in recent years. It is an unsupervised learning algorithm, which finds a basis set capturing high-level semantics in the data and learns sparse coordinates in terms of the basis set. Originally applied to modeling the human visual cortex, sparse coding has been shown useful for many applications. However, most of the existing approaches to sparse coding fail to consider the geometrical structure of the data space. In many real applications, the data is more likely to reside on a low-dimensional submanifold embedded in the high-dimensional ambient space. It has been shown that the geometrical information of the data is important for discrimination. In this paper, we propose a graph based algorithm, called graph regularized sparse coding, to learn the sparse representations that explicitly take into account the local manifold structure of the data. By using graph Laplacian as a smooth operator, the obtained sparse representations vary smoothly along the geodesics of the data manifold. The extensive experimental results on image classification and clustering have demonstrated the effectiveness of our proposed algorithm.
Low intensity ultrasound-induced apoptosis in human gastric carcinoma cells (2008)

Low intensity US could induce apoptosis in human gastric carcinoma cells. US-induced apoptosis is related to US intensity/culture time. US-induced apoptosis may be caspases-dependent and endoplasmic reticulum (ER) stress-triggered apoptosis may also contribute to it. Proteomic experimental system is useful in finding the protein alteration in carcinoma cells after US irradiation, helping to develop a new cancer therapy.
Metallic nanoparticle on micro ring resonator for bio optical detection and sensing (2010)

We have numerically investigated the unique effects of metallic nanoparticle on the ring resonator, especially multiple Au nanoparticles on the micro ring resonator with the 4-port configuration on chip. For the Au nanoparticle, because it has smaller real refractive index than air and large absorption refractive index, we found that there is a blue shift for the ring resonance wavelength, instead of red shift normally observed for dielectric nanoparticles. The drop port intensity is strongly dependent on both number and size of nanoparticles, while relatively independent on position of nanoparticles. The correlation between the penetration depth of Au and the resonance mode evanescent tail is also discussed to reveal the unique properties of Au nanoparticle to be used for detection, sensing and nano medicine.
Influence of asparagine-linked oligosaccharides on antigenicity, processing, and cell surface expression of herpes simplex virus type 1 glycoprotein D (1989)

Glycoprotein D (gD) is an envelope component of herpes simplex virus types 1 and 2. gD-1 contains three sites for the addition of N-linked carbohydrate (N-CHO), all of which are used. Three mutants were constructed by site-directed mutagenesis, each of which altered one N-CHO addition site from Asn-X-Thr/Ser to Asn-X-Ala. A fourth mutant was altered at all three sites. The mutant genes were inserted into an expression vector, and the expressed protein was analyzed in transiently transfected COS-1 cells. The mutant protein lacking N-CHO at site 1 (Asn-94) had a reduced affinity for monoclonal antibodies (MAbs) to discontinuous epitopes, suggesting that the conformation of the protein had been altered. However, the protein was processed and transported to the cell surface. The absence of N-CHO at site 2 (Asn-121) had no apparent effect on processing or transport of gD-1 but resulted in reduced binding of two MAbs previously shown to be in group VI. Binding of other MAbs to discontinuous epitopes (including other group VI MAbs) was not affected. The absence of N-CHO at site 3 (Asn-262) had no effect on processing, transport, or conformation of the gD-1 protein. The absence of N-CHO from site 1 or from all three sites resulted in the formation of high-molecular-weight aggregates or complexes and a reduction in MAb binding. However, these proteins were modified by the addition of O-glycans and transported to the cell surface. We conclude that the absence of the first or all N-linked carbohydrates alters the native conformation of gD-1 but does not prevent its transport to the cell surface.