gebhart/patrepeval huggingface dataset:
O4‐02‐02: TARGETING THE ALZHEIMER'S DISEASE‐ASSOCIATED RISK GENE, TREM2, WITH ANTISENSE OLIGONUCLEOTIDES (2018)

Genetic variants within the TREM2 gene show strong association with increased Alzheimer's disease (AD) risk. To enhance understanding of TREM2 loss, mice haploinsufficient or null for TREM2 have been crossed with amyloid beta (Aβ) depositing mouse models, yielding both positive and negative effects of TREM2 reduction on Aβ deposition. When crossed to mutant tau P301S mice, TREM2 deletion protected mice from neuronal degeneration. While these ongoing studies have identified important relationships between TREM2, microglia, and AD pathology, they are challenging to interpret in the context of disease progression and have the added complication of TREM2 absence from birth in both the CNS and periphery. We hypothesize that TREM2 reduction in AD models will be beneficial and lack adverse effects on tau, providing support for application of a TREM2 lowering strategy for patients. We developed antisense oligonucleotides (ASOs) that potently lower TREM2 mRNA throughout the brain. ASOs were administered to the lateral ventricle via a single bolus injection in APP/PS1 and TauP301S mice at 10 and 7 months of age, respectively. One month later, APP/PS1 mice were assessed for plaque deposition and microglial responses, and TauP301S mice were analyzed for tau pathology. TREM2-targeted ASO treatment in APP/PS1 mice substantially decreased TREM2 mRNA compared to control ASO treatment across multiple brain regions (p<0.01). When evaluated for Aβ, ASO-mediated TREM2 knockdown significantly reduced Aβ plaque deposition (p<0.001) and attenuated microglial association around plaque deposits (p<0.001). Treatment of TauP301S mice with TREM2-targeted ASO robustly decreased TREM2 mRNA (p<0.001) and was associated with significantly less phosphorylated tau reactivity within the hippocampus (p<0.05). These results confirm a role for TREM2 in mediating plaque deposition and tau phosphorylation and suggest that TREM2 lowering reduces pathological markers of neurodegeneration. While these data are seemingly contradictory to the presumption that TREM2 genetic variants confer a loss of function, we believe an ASO approach allows us to understand the timing of TREM2 action throughout disease progression, which may involve a time- or location-dependent role for TREM2. Overall, ASOs that target TREM2 will be highly informative on TREM2-mediated AD pathogenesis and may be effective at modulating disease.
Supplemental Table 2 from Identification of Anti-CA125 Antibody Responses in Ovarian Cancer Patients by a Novel Deep Sequence–Coupled Biopanning Platform (2023)

&lt;p&gt;Supplemental Table 2. DISGTNTSRA peptide alignment with CA125/MUC16 (accession # NP_078966). Amino acid position is indicated by numerical position and alignment indicates the sequence similarity of the peptide (top) to CA125/MUC16 (bottom).&lt;/p&gt;
Intercontinental Spread of Asian-Origin H5N8 to North America through Beringia by Migratory Birds (2015)

Phylogenetic network analysis and understanding of waterfowl migration patterns suggest that the Eurasian H5N8 clade 2.3.4.4 avian influenza virus emerged in late 2013 in China, spread in early 2014 to South Korea and Japan, and reached Siberia and Beringia by summer 2014 via migratory birds. Three genetically distinct subgroups emerged and subsequently spread along different flyways during fall 2014 into Europe, North America, and East Asia, respectively. All three subgroups reappeared in Japan, a wintering site for waterfowl from Eurasia and parts of North America.
Chemical constituents from leaves and trunk bark of Rinorea oblongifolia (Violaceae) (2019)

Two new coruleoellagic acid derivatives, 3,4',5,5',-tetramethylcoruleoellagic acid <b>(1)</b>; 3',4,4',5,5'-pentamethylcoruleoellagic acid <b>(2)</b> and a new friedelane-type triterpene derivative rinol <b>(5)</b>, were isolated from leaves and trunk bark of <i>Rinorea oblongifolia</i> (Violaceae) along with seven known compounds including 3,3',4,4',5'-pentamethylcoruleoellagic acid <b>(3)</b>, hexamethylcoruleoellagic acid <b>(4),</b> 28-hydroxyfriedelin <b>(6),</b> friedelin <b>(7),</b> friedelan-3-ol <b>(8),</b> scopoletin <b>(9)</b> and β-sitosterol-3-<i>O</i>-β-D-glucopyranoside <b>(10).</b> Their structures were elucidated by means of spectroscopic methods including IR, 1D and 2D NMR in conjunction with mass spectrometry. Crude extracts of leaves and trunk bark as well as compounds <b>1-4</b> were evaluated for their antibacterial activities against 7 pathogenic bacterial strains (<i>Streptococcus pneumoniae</i> ATCC49619, <i>Staphylococcus aureus</i> ATCC 43300, <i>Klepsiella pneumoniae</i> ATCC 700603, <i>Haemophilus influenza</i> ATCC 49247, <i>Escherichia coli</i> ATCC 25922, <i>Pseudomonas aeruginosa</i> HM601, <i>Staphylococcus aureus</i> BAA 977). Compound <b>(3)</b> displayed noteworthy activity against <i>Haemophilus influenza</i> with MIC value of 9.38 µg/mL.
Symbiotic Cognitive Computing (2016)

IBM Research is engaged in a research program in symbiotic cognitive computing to investigate how to embed cognitive computing in physical spaces. This article proposes five key principles of symbiotic cognitive computing: context, connection, representation, modularity, and adaptation, along with the requirements that flow from these principles. We describe how these principles are applied in a particular symbiotic cognitive computing environment and in an illustrative application for strategic decision making. Our results suggest that these principles and the associated software architecture provide a solid foundation for building applications where people and intelligent agents work together in a shared physical and computational environment. We conclude with a list of challenges that lie ahead.
Supplementary Table C from Coordinated Regulation of Cell Cycle Transcripts by p53-Inducible microRNAs, miR-192 and miR-215 (2023)

Supplementary Table C from Coordinated Regulation of Cell Cycle Transcripts by p53-Inducible microRNAs, miR-192 and miR-215
Two‐Dimensional Materials for Beyond‐Lithium‐Ion Batteries (2016)

Lithium‐ion batteries (LIBs) have dominated the portable electronics industry and solid‐state electrochemical research and development for the past two decades. In light of possible concerns over the cost and future availability of lithium, sodium‐ion batteries (SIBs) and other new technologies have emerged as candidates for large‐scale stationary energy storage. Research in these technologies has increased dramatically with a focus on the development of new materials for both the positive and negative electrodes that can enhance the cycling stability, rate capability, and energy density. Two‐dimensional (2D) materials are showing promise for many energy‐related applications and particularly for energy storage, because of the efficient ion transport between the layers and the large surface areas available for improved ion adsorption and faster surface redox reactions. Recent research highlights on the use of 2D materials in these future ‘beyond‐lithium‐ion’ battery systems are reviewed, and strategies to address challenges are discussed as well as their prospects.
Wide Dynamic Range CMOS Image Sensors for High Quality Digital Camera, Security, Automotive and Medical Applications (2006)

Wide dynamic range (DR) CMOS image sensors featuring a lateral overflow integration capacitor in a pixel, which locates next to the floating diffusion and integrates the overflow photoelectrons from the fully depleted photodiode in the same integration term, have been developed. The DR has been extended to 100 dB in a single exposure by adding the minimum number of the circuit elements to the four transistors type CMOS image sensor, with a high sensitivity, a high S/N ratio and a superior moving image quality. The hyper DR extension over 200 dB, with the equivalent light intensity ranging from 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> 1x to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> 1x has also been achieved by the combination of the voltage readout operations of the above mentioned lateral overflow integration in multiple exposures and the current readout operation of amplifying the photodiode current. The S/N ratio dominated by all the noise components including the photon shot noise exceeds 40 dB in any switching point from low light to bright light.
Real‐time Monitoring of Force Response Measured in Mechanically Stimulated Tissue‐Engineered Cartilage (2009)

Mechanical stimulation improves tissue-engineered cartilage development both in terms of biochemical composition and structural properties. However, the link between the compositional changes attributed to mechanical stimulation and the changing structural properties of the engineered cartilage is poorly understood. We hypothesize that transient events associated with construct stiffening can be documented and used to understand milestones in construct development. To do this, we designed and built a mechanical stimulation bioreactor that can continuously record the force response of the engineered construct in real time. This study documents the transient changes of the stiffness of tissue-engineered cartilage constructs over the first 14 days of their development under cyclic loading. Compressive strain stimulation (15%, 1 Hz) was applied to poly(ethylene glycol) (PEG) hydrogels seeded with primary articular chondrocytes. The average compressive modulus of strain-stimulated constructs was 12.7 +/- 1.45 kPa after 2 weeks, significantly greater (P < 0.01) than the average compressive moduli of both unstimulated constructs (10.7 +/- 0.94 kPa) and nonviable stimulated constructs (11.2 +/- 0.91 kPa). The system was able to document that nearly all of the stiffness increase occurred over the last 2 days of the experiment, where live-cell constructs demonstrated a rapid 20% increase in force response. The system's ability to track significant increases in stiffness over time was also confirmed by Instron testing. These results present a novel view of the early mechanical development of tissue-engineering cartilage constructs and suggest that the real-time monitoring of force response may be used to noninvasively track the development of engineered tissue.
TX-004HR vaginal estradiol has negligible to very low systemic absorption of estradiol (2016)

Vaginal TX-004HR resulted in negligible to very low systemic absorption of estradiol. No statistical differences in estradiol PK parameters were observed on day 14 with 4 and 10 μg, and only minor increases were observed with 25 μg (within the normal postmenopausal range). This PK substudy, in conjunction with the primary efficacy results, demonstrated that TX-004HR provided local benefits of estradiol with limited systemic exposure.
Deadbeat direct torque and flux control of interior permanent magnet machines with discrete time stator current and stator flux linkage observer (2009)

This paper presents a discrete time deadbeat-direct torque and flux controller (DB-DTFC) for interior permanent magnet synchronous machines (IPMSMs). A Gopinath-style discrete time flux linkage observer is developed which contains two different flux estimation methods based on current and voltage models for flux linkage. This observer produces correctly estimated flux linkages needed for accurate DB-DTFC implementation. In order to eliminate the sampling delay due to a characteristic of digital control computation, a complex vector model-based rotor reference frame current observer is also developed. Combining the discrete time current and flux linkage observers, the correct single time step (deadbeat) air-gap torque and stator flux linkage control at the (constant) switching frequency is achieved and experimentally evaluated.
Movie 5 from HER2 Isoforms Uniquely Program Intratumor Heterogeneity and Predetermine Breast Cancer Trajectories During the Occult Tumorigenic Phase (2023)

&lt;p&gt;d16HER2 mammary intraepithelial neoplasm. d16HER2 shown in magenta. Krt14 antibody staining shown in green.&lt;/p&gt;
Thermodynamics and premelting conformational changes of phased (dA)5 tracts (1993)

Using synthetic 45 bp long DNAs of known sequences, we have studied (i) the unusual structure that the phased A-tracts have at temperatures below 37 degrees C, (ii) the thermodynamics of the loss of that aberrant structure well below the duplex melting temperature, and (iii) the conformational changes that occur with temperature. Using temperature-dependent circular dichroism, we detect a low-temperature structural transition in a 45-mer duplex with four segments of phased (dA)5 tracks separated by five segments of five randomized G-C pairs, but none in the corresponding isomeric random sequence 45-mer duplex. Differential scanning calorimetry measurements reveal the enthalpy of this preglobal melting transition to be 3.5 kcal/mol.AT pair or 4.4 kcal/mol.AA step. The integrated enthalpy change for this helix-to-helix intramolecular event only is about 16% of the global duplex-to-single-strands melting enthalpy and is relatively broad compared to the global melting event (about 30 vs 15 degrees C for the full width at half maxima). Electric birefringence decay measurements show that the phased 45 bp duplex has a rotational time constant of 100 ns at 5 degrees C which increases to 220 ns above 40 degrees C. Simple modeling of the dynamics within the junction model for bending yields that the bend per A-tract is 42 degrees at 5 degrees C, decreasing to 0 degrees above 40 degrees C. We suggest that this sequence-dependent structure which "melts" at physiological temperatures may be relevant to DNA topology and function.
Abstract 125: Silicone Implant Shells Increase The Rate Of Proliferation Of Patient-derived BIA-ALCL Cells But Not Primary T Cells In An Engineered Biomimetic Patient-derived Breast Tissue (2020)

Purpose: The pathogenesis of breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) remains poorly understood. Our lab has demonstrated the power of studying BIA-ALCL behavior in a high-fidelity tissue engineered ex vivo biomimetic, three-dimensional model. Herein we use this model to compare the effect of silicone implant shell on proliferation of patient-derived BIA-ALCL cells to patient-derived T progenitor cells (from which ALCL originates) within the breast microenvironment. Methods: Patient-derived breast tissue was processed for its component adipocytes, ductal organoids, and stromal vascular fraction. These were suspended within 50 µl of 0.3% type I collagen matrix, to which was added 200,000 cells/mL of either patient-derived BIA-ALCL cells or T progenitor cells. These were then plated into 6mm wells. As a control, both BIA-ALCL and T progenitor cells were suspended within type I collagen alone at the same seeding density without breast components. Before plating, wells were lined circumferentially with either textured, smooth, or no implant shell. These were 1cm by 2cm pieces dissected from the whole implant. Wells were imaged using confocal microscopy over 8 days. Results: Unstimulated T progenitor cell count showed no significant increase in any of the conditions tested. The change in cell count over 8 days was 3.85% in each condition (p =0.3352). A Tukey’s multiple comparison test comparing each condition to each other additionally revealed no significant increase in cell count over 8 days for all conditions. The mean difference in cell count between days 0 and 4 was 214.1 cells (p = 0.559, 95% CI [-244.5, 672.6]), and between days 0 and 6 it was 229.1 cells (p =0.343, 95% CI [-148.8, 607.0]). This can be compared to previous studies by our group where proliferation of BIA-ALCL cells was found to be significantly more robust in the biomimetic platform compared to collagen-only groups, regardless of implant shell type (p < 0.01). BIA-ALCL cells grew nearly 30% faster in textured and smooth shell biomimetic groups compared to biomimetic wells lacking implant shell. Conclusion: Within a tissue-engineered 3D model of the breast microenvironment, unstimulated T progenitor cells showed no significant increase in proliferation regardless of the presence or absence of implant shell. Comparatively, BIA-ALCL cells proliferated more robustly in the presence of textured and smooth implant shell. Our data suggest that silicone implant shell has a significant and quantifiable effect on cell proliferation among pathologic BIA-ALCL cells, but not their precursor T cells. Thus, these data suggest that breast implant silicone shell alone is not a sufficient stimulus for T cell proliferation within the breast microenvironment, and imply that co-stimulatory factors are required. Further investigation into possible co-stimulatory factors are currently underway using our high-fidelity ex vivo model of the breast microenvironment.
Next Generation Copper Mediators for the Efficient Production of 18F‐Labeled Aromatics (2022)

Cu-mediated radiofluorination is a versatile tool for the preparation of <sup>18</sup> F-labeled (hetero)aromatics. In this work, we systematically evaluated a series of complexes and identified several generally applicable mediators for highly efficient radiofluorination of aryl boronic and stannyl substrates. Utilization of these mediators in nBuOH/DMI or DMI significantly improved <sup>18</sup> F-labeling yields despite use of lower precursor amounts. Impressively, application of 2.5 μmol aryl boronic acids was sufficient to achieve <sup>18</sup> F-labeling yields of up to 75 %. The practicality of the novel mediators was demonstrated by efficient production of five PET-tracers and transfer of the method to an automated radiosynthesis module. In addition, (S)-3-[<sup>18</sup> F]FPhe and 6-[<sup>18</sup> F]FDOPA were prepared in activity yields of 23±1 % and 30±3 % using only 2.5 μmol of the corresponding boronic acid or trimethylstannyl precursor.
ChemInform Abstract: Use of [4,6‐Di‐14C]‐5′‐DMT‐thymidine Phosphoramidite Reagent for the Radiolabeling of Synthetic Oligonucleotides (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.
Spectroscopy and photochemistry of binuclear iridium(I) complexes (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpectroscopy and photochemistry of binuclear iridium(I) complexesJanet L. Marshall, Stephen R. Stobart, and Harry B. GrayCite this: J. Am. Chem. Soc. 1984, 106, 10, 3027–3029Publication Date (Print):May 1, 1984Publication History Published online1 May 2002Published inissue 1 May 1984https://pubs.acs.org/doi/10.1021/ja00322a045https://doi.org/10.1021/ja00322a045research-articleACS PublicationsRequest reuse permissionsArticle Views495Altmetric-Citations62LEARN 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
A “One‐Pot” Microwave‐Mediated Synthesis of the Basic Canthine Skeleton: Expedient Access to Unnatural β‐Carboline Alkaloids. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Beam with Adaptive Divergence Angle in Free-Space Optical Communications\n for High-Speed Trains (2018)

In this paper, we propose an adaptive beam that adapts its divergence angle\naccording to the receiver aperture diameter and the communication distance to\nimprove the received power and ease the alignment between the communicating\noptical transceivers in a free-space optical communications (FSOC) system for\nhigh-speed trains (HSTs). We compare the received power, signal-to-noise ratio,\nbit error rate, and the maximum communication distance of the proposed adaptive\nbeam with a beam that uses a fixed divergence angle of 1 mrad. The proposed\nadaptive beam yields a higher received power with an increase of 33 dB in\naverage over the fixed-divergence beam under varying visibility conditions and\ndistance. Moreover, the proposed adaptive divergence angle extends the\ncommunication distance of a FSOC system for HSTs to about three times under\ndifferent visibility conditions as compared to a fixed divergence beam. We also\npropose a new ground transceiver placement that places the ground transceivers\nof a FSOC system for HSTs on gantries placed above the train passage instead of\nplacing them next to track. The proposed transceiver placement provides a\nreceived-power increase of 3.8 dB in average over the conventional placement of\nground-station transceivers next to the track.\n
Antimicrobial Photoinactivation Using Visible Light Plus Water-Filtered Infrared-A (VIS + wIRA) and Hypericum Perforatum Modifies In Situ Oral Biofilms (2019)

Due to increasing antibiotic resistance, the application of antimicrobial photodynamic therapy (aPDT) is gaining increasing popularity in dentistry. The aim of this study was to investigate the antimicrobial effects of aPDT using visible light (VIS) and water-filtered infrared-A (wIRA) in combination with a Hypericum perforatum extract on in situ oral biofilms. The chemical composition of H. perforatum extract was analyzed using ultra-high-performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS). To obtain initial and mature oral biofilms in situ, intraoral devices with fixed bovine enamel slabs (BES) were carried by six healthy volunteers for two hours and three days, respectively. The ex situ exposure of biofilms to VIS + wIRA (200 mWcm<sup>-2</sup>) and H. perforatum (32 mg ml<sup>-1</sup>, non-rinsed or rinsed prior to aPDT after 2-min preincubation) lasted for five minutes. Biofilm treatment with 0.2% chlorhexidine gluconate solution (CHX) served as a positive control, while untreated biofilms served as a negative control. The colony-forming units (CFU) of the aPDT-treated biofilms were quantified, and the surviving microorganisms were identified using MALDI-TOF biochemical tests as well as 16 S rDNA-sequencing. We could show that the H. perforatum extract had significant photoactivation potential at a concentration of 32 mg ml<sup>-1</sup>. When aPDT was carried out in the presence of H. perforatum, all biofilms (100%) were completely eradicated (p = 0.0001). When H. perforatum was rinsed off prior to aPDT, more than 92% of the initial viable bacterial count and 13% of the mature oral biofilm were killed. Overall, the microbial composition in initial and mature biofilms was substantially altered after aPDT, inducing a shift in the synthesis of the microbial community. In conclusion, H. perforatum-mediated aPDT using VIS + wIRA interferes with oral biofilms, resulting in their elimination or the substantial alteration of microbial diversity and richness. The present results support the evaluation of H. perforatum-mediated aPDT for the adjunctive treatment of biofilm-associated oral diseases.