gebhart/patrepeval huggingface dataset:
Data from IGKV3 Proteins as Candidate “Off-the-Shelf” Vaccines for Kappa-Light Chain–Restricted B-Cell Non-Hodgkin Lymphomas (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; An increasing set of B-cell non-Hodgkin lymphomas (B-NHL) show a biased usage of &lt;i&gt;IGKV&lt;/i&gt;3-20 and &lt;i&gt;IGKV&lt;/i&gt;3-15 immunoglobulin genes, a feature that could be exploited for the development of ready-to-use, broadly applicable cancer vaccines.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The immunogenic properties of clonal IGKV3-20 and IGKV3-15 proteins were analyzed with particular focus on their ability to elicit cross-reactive responses against molecularly related IGKV proteins expressed by different B-cell lymphoproliferative disorders.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; IGK+ lymphoma patients show humoral and T-cell responses to IGKV3-20 and IGKV3-15 proteins and IGKV3-specific cytotoxic T lymphocytes (CTL) can be easily induced &lt;i&gt;ex vivo&lt;/i&gt;. IGKV3-20–specific CTLs cross-react against different IGKV3 proteins, an effect mediated by the presence of 21 shared, sometimes promiscuous, T-cell epitopes, presented by common HLA class I allele products, thus assuring a broad HLA coverage of IGKV3-based vaccines. Many natural epitope variants are carried by IGK light chains expressed by a broad spectrum of B-NHLs and we show that IGKV3-20–specific CTLs cross-react also against several of these variant epitopes. Both humoral and CTL-specific responses were induced by KLH-conjugated IGKV3-20 protein in HLA-A2-transgenic mice and coinjection of IGKV3-20–specific CTLs with IGKV3-20+ or IGKV3-15+ lymphoma cells into SCID mice totally prevented tumor growth, thus confirming the ability of these effectors to mediate efficient and cross-reactive cytotoxic responses also &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These results provide the rationale to exploit IGKV3 proteins as “off-the-shelf” vaccines for a large fraction of lymphoma patients. &lt;i&gt;Clin Cancer Res; 18(15); 4080–91. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Molecular Magnetic Resonance and Ultra Sound Imaging of Tumor Angiogenesis (2017)

Seeking out and identifying imaging biomarkers for early cancer diagnosis and the evaluation of patient response to therapy requires an improvement in the specificity of imaging techniques. This study explores in vivo neo-angiogenesis assessment using molecular mechanisms through target molecular Magnetic Resonance (MR) and Ultrasound (US).
Transcriptional Down-Regulation of N-myc Expression during B-Cell Development (1992)

We have used nuclear run-on and DNase I sensitivity analyses to study the activity of the N-myc genes in cell lines that represent different stages of B-cell development. Both transformed pre-B-cell lines and a nontransformed pre-B-cell clone transcribe the N- and c-myc genes at substantial levels; in the nontransformed clone, transcription of these genes is regulated by the pre-B-cell growth factor interleukin-7. In contrast, transformed cell lines that represent the more mature stages of the B-cell pathway and mitogen-stimulated normal splenic B lymphocytes express the c-myc gene but do not express the N-myc gene at detectable levels. Down-regulation of N-myc expression in these cells occurs at the level of transcriptional initiation. Correspondingly, a set of DNase I-hypersensitive sites present in the 5' region of the N-myc promoter of pre-B-cell lines are absent in B-cell lines. To further elucidate this process, we have constructed fusion cell lines between an N-myc-expressing pre-B-cell line and a nonexpressing myeloma line; the hybrid cell lines transcriptionally down-regulate the pre-B copies of the N-myc gene. Lack of N-myc expression in a number of nonlymphoid cell lines also resulted from lack of N-myc transcription. Together, our findings demonstrate that the down-regulation of N-myc expression in the later stages of B-cell development is mediated primarily at the level of transcriptional initiation. They further show that dominant, trans-acting factors present in more mature B-lineage cell lines act to down-regulate the transcription of N-myc.
Inhibition of Phospholipase D by a Protein Factor from Bovine Brain Cytosol (1996)

A specific protein inhibitor of partially purified bovine brain phospholipase D (PLD) was identified from bovine brain cytosol. The PLD inhibitor has been enriched through several chromatographic steps and characterized with respect to size and mechanism of inhibition. The inhibitor showed an apparent molecular mass of 30 kDa by Superose 12 gel exclusion chromatography and inhibited PLD activity with an IC50 of 7 nM. The inhibitor had neither proteolytic activity nor phospholipid-hydrolyzing activity. Because phosphatidylinositol 4,5-bisphosphate (PIP2), which is included in substrate vesicles, is an essential cofactor for PLD, we examined whether the inhibition might be mediated by sequestration of PIP2. PIP2 hydrolysis by phospholipase C (PLC)-beta1 was not affected by the inhibitor and the inhibitor did not bind to substrate vesicles containing PIP2. In contrast, a PH domain derived from PLC-delta1, which could bind to PIP2, showed a nearly identical inhibition of both PLC-beta1 and PLD activities. Thus, the PLD inhibition by the inhibitor is due to the specific interaction with not PIP2 but PLD. The suppression of PLD activity by the inhibitor was largely eliminated by the addition of ADP-ribosylation factor (ARF) and GTPgammaS. We propose that the inhibitor plays a negative role in regulation of PLD activity by PIP2 and ARF.
Determining the influence of biocompatible oxygenators during cardiopulmonary bypass by 99mTc-DTPA aerosol assessment of pulmonary permeability (2002)

Changes in pulmonary permeability provide a partial measure of the clinical impact of biocompatible oxygenator use during cardiopulmonary bypass surgery. Previous research has shown that the clearance rate of 99mTc-labelled diethylene triamine penta-acetic acid (99mTc-DTPA) aerosol from the lungs is increased following cardiopulmonary bypass, resulting from an increase in pulmonary permeability. The aerosol clearance rate has been shown to return to normal after a period of 7 days. A blind trial was set up to assess the clinical impact of a biocompatible, Trillium-coated oxygenator compared with a standard oxygenator. In a group of 25 patients 99mTc-DTPA aerosol studies were carried out prior to cardiopulmonary bypass surgery for mitral valve surgery. Repeat studies were undertaken 3-4 h and 24-28 h after surgery. Analysis of the rates of pulmonary clearance reproduced the trends seen in earlier research. There was however no statistically significant difference in the variation of serial clearance times between the groups of patients undergoing surgery using the Trillium-coated oxygenators and those using the standard oxygenators.
ChemInform Abstract: Methyltrioxorhenium(VII) in Oxidation Catalysis (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Combining properties of different classes of PI3Kα inhibitors to understand the molecular features that confer selectivity (2017)

Phosphoinositide 3-kinases (PI3Ks) are major regulators of many cellular functions, and hyperactivation of PI3K cell signalling pathways is a major target for anticancer drug discovery. PI3Kα is the isoform most implicated in cancer, and our aim is to selectively inhibit this isoform, which may be more beneficial than concurrent inhibition of all Class I PI3Ks. We have used structure-guided design to merge high-selectivity and high-affinity characteristics found in existing compounds. Molecular docking, including the prediction of water-mediated interactions, was used to model interactions between the ligands and the PI3Kα affinity pocket. Inhibition was tested using lipid kinase assays, and active compounds were tested for effects on PI3K cell signalling. The first-generation compounds synthesized had IC50 (half maximal inhibitory concentration) values &amp;gt;4 μM for PI3Kα yet were selective for PI3Kα over the other Class I isoforms (β, δ and γ). The second-generation compounds explored were predicted to better engage the affinity pocket through direct and water-mediated interactions with the enzyme, and the IC50 values decreased by ∼30-fold. Cell signalling analysis showed that some of the new PI3Kα inhibitors were more active in the H1047R mutant bearing cell lines SK-OV-3 and T47D, compared with the E545K mutant harbouring MCF-7 cell line. In conclusion, we have used a structure-based design approach to combine features from two different compound classes to create new PI3Kα-selective inhibitors. This provides new insights into the contribution of different chemical units and interactions with different parts of the active site to the selectivity and potency of PI3Kα inhibitors.
Controlled Formation of Emissive Gold Nanoclusters with a Synthetic Self-Assembled Protein Toroid (2022)

Self-assembled proteins are privileged building blocks for the bottom-up organization of matter at the nanoscale. However, since most proteins are very large, they have to be produced by recombinant expression, which is less versatile and flexible than chemical synthesis. Here, we show that we can bridge the potential of proteins for nanofabrication with the simplicity and versatility of solid-phase peptide synthesis by relying on the self-assembly of the viral protein gp23.1, a small 50-residue protein that oligomerizes in solution to form a stable toroidal hexamer. We report the chemical synthesis and basic biophysical characterization of a gp23.1 mutant and show that its self-assembled hexamer templates the formation of highly monodisperse luminescent gold nanoclusters of about 1.3 nm inside its central cavity. This work demonstrates the versatility of this small self-assembled ring protein for a variety of nanotechnological applications.
Abstract 15979: Endothelial Cell Metabolism is Controlled by the Flow-induced Long Non-coding Rna Lncflow2 (2017)

Introduction: The majority of the human transcriptome consists of non-coding transcripts which may exert regulatory effects on epigenetic and transcriptional processes. Since laminar flow is an important atheroprotective regulator, we analysed its impact on the expression of long non-coding RNAs (lncRNA) in human endothelial cells (EC) by RNA deep sequencing. Among the significantly up-regulated lncRNAs, we confirmed a 3-fold up-regulation of lncflow2 by laminar flow (p Results: Silencing of lncflow2 by GapmeRs reduced sprout formation of ECs (34.7 % reduction, p
High open-circuit voltage values on fine-grained thin-film polysilicon solar cells (2006)

Grain boundaries are known to be the main limiting factor for a high performance of polysilicon solar cells. Defects at these grain boundaries serve as recombination centers for minority and majority carriers. Grain boundaries are also known to be paths for enhanced hydrogen diffusion, which results in passivation of part of the defects. In this paper, we show that grain boundaries are also paths for an enhanced phosphorus diffusion that limits the effect of hydrogen passivation. Phosphorus spikes along the grain boundaries enhance the junction area and determine the collection and the recombination volumes. Avoiding this preferential diffusion of phosphorus atoms during emitter formation, we obtained open-circuit voltages (Voc) up to 536mV on polysilicon material with a grain size of only 0.2μm. These high Voc values can only be accounted for by theory if a much smaller grain boundary recombination velocity is assumed than what was previously accepted for p-n junctions on fine-grained polysilicon solar cells.
Passive Operating On-chip Plasma Isolation From Whole Blood (2007)

In clinical chemistry, a necessary step performed is the isolation of plasma from whole blood, and effective sample preparation techniques are needed for the development of miniaturized clinical diagnostic devices. This study demonstrates the use of passive microfluidic devices, which operating entirely on capillary action, for on-chip isolation of plasma from whole blood. Using these devices, several to several tens nanoliter volumes of plasma were effectively separated from a single drop of whole blood in 2 minutes. This study may have broad implications in the design of lab-on-a-chip devices for bioanalytical applications.
Complicated Clinical Course in Incipient Gigantism Due to Treatment-resistant Aryl Hydrocarbon Receptor–Interacting Protein–mutated Pediatric Somatotropinoma (2021)

We identified a novel pathologic <i>AIP</i> mutation that was associated with incipient acrogigantism in an extremely young patient who had a complicated course of disease. Growth acceleration can be masked due to failure to thrive. Tumoral growth hormone release in vivo may be predicted with in vitro exposure to somatostatin receptor analogs, as it cannot be assumed that all <i>AIP</i>-mutated somatotropinomas respond well to pasireotide.
Supporting distributed feed-following apps over edge devices (2013)

In feed-following applications such as Twitter and Facebook, users (consumers) follow a large number of other users (producers) to get personalized feeds, generated by blending producers- feeds. With the proliferation of Cloud-connected smart edge devices such as smartphones, producers and consumers of many feed-following applications reside on edge devices and the Cloud. An important design goal of such applications is to minimize communication (and energy) overhead of edge devices. In this paper, we abstract distributed feed-following applications as a view maintenance problem, with the goal of optimally placing the views on edge devices and in the Cloud to minimize communication overhead between edge devices and the Cloud. The view placement problem for general network topology is NP Hard; however, we show that for the special case of Cloud-edge topology, locally optimal solutions yield a globally optimal view placement solution. Based on this powerful result, we propose view placement algorithms that are highly efficient, yet provably minimize global network cost. Compared to existing works on feed-following applications, our algorithms are more general--they support views with selection, projection, correlation (join) and arbitrary black-box operators, and can even refer to other views. We have implemented our algorithms within a distributed feed-following architecture over real smartphones and the Cloud. Experiments over real datasets indicate that our algorithms are highly scalable and orders-of-magnitude more efficient than existing strategies for optimal placement. Further, our results show that optimal placements generated by our algorithms are often several factors better than simpler schemes.
Asymmetric Eschenmoser−Claisen Rearrangement for Anti-β-Substituted γ,δ-Unsaturated Amino Acids (2007)

Optically active anti-beta-substituted gamma,delta-unsaturated amino acids are important synthetic building blocks in organic synthesis and for peptidomimetics. A novel asymmetric Eschenmoser-Claisen rearrangement with use of a C2-symmetric chiral auxiliary was developed to generate this type of amino acid. Excellent diastereoselectivities and high enantioselectivities (87-93% ee) were obtained after the chiral auxiliary was removed via iodolactonization/zinc reduction.
Distinct Reactivity of Mono- and Bis-NHC Silver Complexes: Carbene Donors versus Carbene–Halide Exchange Reagents (2011)

The synthesis of N-heterocyclic carbene (NHC) complexes of silver is an established technique for their use as carbene transfer reagents. While it is known that both mono-NHC Ag(I) and bis-NHC Ag(I) complexes are accessible, different reactivities of these species have not been explored synthetically. Whereas the commonly used mono-NHC Ag(I) complexes act as NHC donors only, we found that a bis-NHC Ag(I) complex was capable of transferring one carbene under halide abstraction. This is exemplified in the transformation of P–Cl compounds into the respective imidazolium–phosphines by a bis-NHC Ag(I) complex but not by its corresponding mono-NHC Ag(I) complex. When the bis-NHC Ag(I) complex was allowed to react with [M(cod)Cl]2 (M = Rh, Ir), both NHCs were transferred under chloride abstraction to give [M(cod)(NHC)2]+ exclusively, a reaction which is reported to stop at [M(cod)Cl(NHC)] even with an excess of mono-NHC Ag(I) complex in the presence of AgPF6.
The Use of Cytokine Knockouts to Study Host Defense Against Infection (2003)

The sequencing of the human genome has revealed the existence of a large number of new members of the various cytokine families and has raised the perennial issue of how cytokines function to benefit human evolution. Usually duplication or redundancy of a gene suggests that it functions to assist the survival of the species. In the case of the proinflammatory cytokines, their role in the survival of the host is less clear since this class of cytokines is clearly implicated in host defense mechanisms against infection as well as the pathogenic processes of several diseases. The interleukin-1 (IL-1) and tumor necrosis factor (TNF) families of proinflammatory cytokines have been studied in great detail for their roles in disease; however, studies on their roles in host defense against infection are limited to a few organisms and models. However, it remains likely that these cytokines contribute to host defense mechanisms using the very same molecular and cellular pathways involved in chronic inflammation, tissue destruction, and tissue remodeling. How does one reconcile the existence of two opposing outcomes for the host—one clearly not in the interest of survival and another vital to the host in order to survive even a minor invasion by a microbe? In each case, identical molecular mechanisms are at work. For example, the processes for emigration of neutrophils into tissues to engulf microorganisms via an increase in endothelial adhesion molecules and chemokine production are the same for the host whether in infected tissue or an inflamed joint. On closer examination, the production and activity of proinflammatory cytokines reveal several levels of regulation, which may explain these seemingly discordant roles for the host. For routine infection or injury, cytokines such as IL-1β and TNF-α are transiently expressed and secreted, their activities are modulated by coproduction of naturally occurring antiinflammatory cytokines, and the levels of production fall rapidly. Thus, IL-1β and TNF-α turn on and off rapidly during infection. In contrast, the production of these same cytokines in chronic inflammatory diseases such as rheumatoid arthritis and inflammatory bowel disease fails to cease. Cytokine production in host defense is regulated, whereas in chronic disease it is dysregulated.
ChemInform Abstract: Syn‐Selective Michael Addition of Amines to Bis‐enones: Synthesis of 1, 3,4,7‐Tetrasubstituted (4R,5S,6S,7R)‐Hexahydro‐5,6‐dihydroxy‐2H‐1,3‐ diazepin‐2‐ones. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Synthesis, Characterization and Dye Removal Capability of Conducting Polypyrrole/Mn0.8Zn0.2Fe2O4/Graphite Oxide Ternary Composites (2022)

Herein, ternary composites from polypyrrole (PPy), Mn0.8Zn0.2Fe2O4 (MZF), and graphite oxide (GO) were prepared to remove acid red dye (AR1) from wastewater. MZF was synthesized using spent Zn–C batteries, acid leaching, and sucrose auto-combustion processes; GO was prepared via oxidation and exfoliation of graphite. The composites were prepared by adding MZF and GO during the in-situ polymerization of pyrrole. Different PPy/MZF/GO (PMG) composites were prepared by changing the weight ratios of the PPy, MZF, and GO. We investigated the prepared composites’ structural, magnetic, and electrical/dielectric properties. We evaluated different experimental conditions’ influences on dye removal performance, such as pH, dosage, dye concentration, temperature, and contact time. XRD, FT-IR, and magnetic properties indicated that PPy completely coated the other contents. The electrical/dielectric properties improved while increasing the GO ratio. The PMG at GO content 50 wt.% (PMG50) showed the most efficient ratio for better removing AR1 from wastewater.
[Role of the lip-bumper in nonextraction orthodontic therapy: clinical-statistical study]. (1990)

The purpose of this study is to investigate the morphologic and dimensional changes of lower arch that might occur in patients undergoing treatment with the lip-bumper. After a brief examination of the clinical applications of lip-bumper, we report the results of a research concerning 20 children in the mixed dentition period. The effect of this simple orthodontic appliance has been an expansion of the mandibular dental arch, with a real increase of arch length and transverse dimension. Therefore the lip-bumper can be used in non-extraction treatment of malocclusion, in order to obtain a space recovery in lower arch.
KELOIDS: TIME TO DISPEL THE MYTHS? (1999)

Fong, Eileen P. M.B.B.S., F.R.C.S.; Chye, Lim Thiam M.B.B.S., F.R.C.S., F.A.M.(Sing.); Tan, Walter T. L. M.B.B.S., F.R.C.S., F.R.A.C.S., F.A.M.(Sing.) Author Information
Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles (2020)

SARS-CoV-2 spike (S) mediates entry into cells and is critical for vaccine development against COVID-19. S is synthesized as a precursor, processed into S1 and S2 by furin proteases, and activated for fusion when human angiotensin-converting enzyme 2 (hACE2) engages the receptor-binding domain (RBD) and when the N-terminus of S2 is proteolytically processed. Structures of soluble ectodomains and native virus particles have revealed distinct conformations of S, including a closed trimer with all RBD oriented downward, trimers with one or two RBDs up, and hACE2-stabilized conformations with up to three RBD oriented up. Real-time information that connects these structures, however, has been lacking. Here we apply single-molecule Forster Resonance Energy Transfer (smFRET) imaging to observe conformational dynamics of S on virus particles. Virus-associated S dynamically samples at least four distinct conformational states. In response to hACE2, S opens into the hACE2-bound S conformation through at least one on-path intermediate, with trypsin partially activating S. Conformational preferences of convalescent patient plasma and monoclonal antibodies suggest mechanisms of neutralization involving either direct competition with hACE2 for binding to RBD or allosteric interference with conformational changes required for entry. Our findings inform on mechanisms of S recognition and on conformations for immunogen design.