gebhart/patrepeval huggingface dataset:
The role of polar interactions in the molecular recognition of CD40L with its receptor CD40 (1998)

CD40 Ligand (CD40L) is transiently expressed on the surface of T-cells and binds to CD40, which is expressed on the surface of B-cells. This binding event leads to the differentiation, proliferation, and isotype switching of the B-cells. The physiological importance of CD40L has been demonstrated by the fact that expression of defective CD40L protein causes an immunodeficiency state characterized by high IgM and low IgG serum levels, indicating faulty T-cell dependent B-cell activation. To understand the structural basis for CD40L/CD40 association, we have used a combination of molecular modeling, mutagenesis, and X-ray crystallography. The structure of the extracellular region of CD40L was determined by protein crystallography, while the CD40 receptor was built using homology modeling based upon a novel alignment of the TNF receptor superfamily, and using the X-ray structure of the TNF receptor as a template. The model shows that the interface of the complex is composed of charged residues, with CD40L presenting basic side chains (K143, R203, R207), and CD40 presenting acidic side chains (D84, E114, E117). These residues were studied experimentally through site-directed mutagenesis, and also theoretically using electrostatic calculations with the program Delphi. The mutagenesis data explored the role of the charged residues in both CD40L and CD40 by switching to Ala (K143A, R203A, R207A of CD40L, and E74A, D84A, E114A, E117A of CD40), charge reversal (K143E, R203E, R207E of CD40L, and D84R, E114R, E117R of CD40), mutation to a polar residue (K143N, R207N, R207Q of CD40L, and D84N, E117N of CD40), and for the basic side chains in CD40L, isosteric substitution to a hydrophobic side chain (R203M, R207M). All the charge-reversal mutants and the majority of the Met and Ala substitutions led to loss of binding, suggesting that charged interactions stabilize the complex. This was supported by the Delphi calculations which confirmed that the CD40/CD40L residue pairs E74-R203, D84-R207, and E117-R207 had a net stabilizing effect on the complex. However, the substitution of hydrophilic side chains at several of the positions was tolerated, which suggests that although charged interactions stabilize the complex, charge per se is not crucial at all positions. Finally, we compared the electrostatic surface of TNF/TNFR with CD40L/CD40 and have identified a set of polar interactions surrounded by a wall of hydrophobic residues that appear to be similar but inverted between the two complexes.
YerbaBuena: Securing Deep Learning Inference Data via Enclave-based Ternary Model Partitioning (2018)

Deploying and serving deep learning (DL) models in the public cloud facilitates the process to bootstrap artificial intelligence (AI) services. Yet, preserving the confidentiality of sensitive input data remains a concern to most service users. Accidental disclosures of user input data may breach increasingly stringent data protection regulations and inflict reputation damage. In this paper, we systematically investigate the life cycles of input data in deep learning image classification pipelines and further identify the potential places for information disclosures. Based on the discovered insights, we build YerbaBuena, an enclave-based model serving system to protect the confidentiality and integrity of user input data. To accommodate the performance and capacity limitations of today's enclave technology, we employ a Ternary Model Partitioning strategy that allows service users to securely partition their proprietary DL models on local machines. Therefore, we can (I) enclose sensitive computation in a secure enclave to mitigate input information disclosures and (II) delegate non-sensitive workloads to run out of enclave with hardware-assisted DL acceleration. Our comprehensive partitioning analysis and workload measurement demonstrate how users can automatically determine the optimal partitioning for their models, thus to maximize confidentiality guarantees with low performance costs.
Enhanced immunogenicity of CTL antigens through mutation of the CD8 binding MHC class I invariant region (2007)

CD8(+) cytotoxic T lymphocytes (CTL) are key determinants of immunity to intracellular pathogens and neoplastic cells. Recognition of specific antigens in the form of peptide-MHC class I complexes (pMHCI) presented on the target cell surface is mediated by T cell receptor (TCR) engagement. The CD8 coreceptor binds to invariant domains of pMHCI and facilitates antigen recognition. Here, we investigate the biological effects of a Q115E substitution in the alpha2 domain of human leukocyte antigen (HLA)-A*0201 that enhances CD8 binding by approximately 50% without altering TCR/pMHCI interactions. Soluble and cell surface-expressed forms of Q115E HLA-A*0201 exhibit enhanced recognition by CTL without loss of specificity. These CD8-enhanced antigens induce greater CD3 zeta chain phosphorylation in cognate CTL leading to substantial increases in cytokine production, proliferation and priming of naive T cells. This effect provides a fundamental new mechanism with which to enhance cellular immunity to specific T cell antigens.
Locking characteristics of a subharmonically hybrid mode-locked multisection semiconductor laser (1996)

Locking characteristics of a subharmonically hybrid mode-locked (SH-ML) semiconductor laser are investigated experimentally. The locking bandwidths under the second- and third-order SH-ML operation, as well as under fundamental hybrid mode-locking (FH-ML) condition, are characterized with a variety of microwave power and reverse bias voltage applied to the saturable absorber of the laser. Unique locking characteristics are observed for the third-order SH-ML where the locking bandwidth increases with increasing reverse bias, which is opposite to the FH-ML case. This leads to a locking bandwidth of 56 MHz, 2.3 times broader than that for the FH-ML under the shortest pulse condition.
Effect of Feeding Various Concentrations of Shea Oil on Some Biochemical Parameters in Normal Albino Rat (2012)

The effect of feeding various concentration of Shea oil on some Biochemical parameters was studied. Twenty five (25) adult rats weighing between 150g to 240 g where divided into five (5) groups of 5 rats each. Group I Control was given growers Marsh and water ad libitum. Groups II, III, IV, V were given 250mg, 500mg, 1000mg, 1500mg (wet weight) of Shea oil respectively in addition to growers marsh and water ad libitum. The feeding and intubation lasted for 28days after which the rats were sacrificed and blood samples were collected. The blood samples were assayed for Biochemical parameters; lipid profile, Glucose, Total protein and Albumin usin and effect is dose standard methods. The results showed significant decrease in the Lipid profile and Albumin (P 0.05). The results also showed insignificant decrease and increase in Total protein and Glucose respectively when comparison was made between the test groups and control and within the test groups only. In conclusion, Shea oil has hypolipideamic effect which is dose dependent and can be used in therapeutic treatment of lipid related problems such as arteriosclerosis, coronary heart disease and obesity.
Homodyne Digitally Assisted and Spurious-Free Mixerless Direct Carrier Modulator With High Carrier Leakage Suppression (2017)

In this paper, a new method to design a digitally assisted and spurious-free direct carrier mixerless modulator based on the six-port correlator is proposed. The calibration of the modulator based on modified Cartesian memory polynomial (MCMP) is used to linearize and mitigate hardware impairment of the whole system. The modulation and the up conversion are performed by using the variable loads controlled by the differential in-phase and quadrature-phase baseband voltages together with common-mode voltages. The proposed MCMP is able to compensate for nonlinearity, frequency responses, residual carrier leakage, crosstalk between the in-phase and the quadrature-phase data. The proof-of-concept of digitally assisted mixerless modulator is developed and its performance is assessed at 2.6 GHz with modern communication signals. The error vector magnitudes between the input ideal baseband signals and the up-converted radio frequency signals are all between 2% and 4%. The residual carrier leakage, which remains present after imperfect suppression through hardware means, degrades the overall system performance and it can be suppressed completely by means of the proposed memory polynomial model.
Formation of the totally degenerate bicyclo[3.2.2]nonatrienyl radical by electron transfer (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFormation of the totally degenerate bicyclo[3.2.2]nonatrienyl radical by electron transferWilliam N. WashburnCite this: J. Am. Chem. Soc. 1978, 100, 19, 6235–6236Publication Date (Print):September 1, 1978Publication History Published online1 May 2002Published inissue 1 September 1978https://pubs.acs.org/doi/10.1021/ja00487a048https://doi.org/10.1021/ja00487a048research-articleACS PublicationsRequest reuse permissionsArticle Views61Altmetric-Citations5LEARN 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
Advanced Synthesis of Reflectarrays using a Spherical Mapping of the 2nd Order Phoenix Cell (2019)

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Subiculum fiber degeneration within the fornix white matter tract in 5xFAD mice (2022)

Abstract Background Alzheimer’s disease (AD) is a progressive neurodegenerative disease that affects all components of the neurovascular unit. The hallmark pathology of AD, amyloid plaques and tau neurofibrillary tangles, aggregate within gray matter areas and spread across neural networks. Although AD pathology is scarce within white matter brain regions, white matter abnormalities have been observed in AD patients using diffusion tensor imaging (DTI; Sachdev et al 2013) and white matter tracts are putative therapeutic targets for deep brain stimulation (Lam et al 2020). Particularly, the fornix is a white matter tract which connects the hippocampus to brain regions of the classic Papez circuit and Default Mode Network (DMN). A recent whole brain analysis using transgenic 5xFAD/Thy1‐GFP mouse (Zhang et al 2020) found evidence of fornix degeneration and dystrophic axon terminals within the mammillary body (a major SUB target) occurring as early as 2 months of age. However, due to the broad expression of GFP under the Thy1 promotor, it is difficult to determine the origin of axon fibers and further characterize if other SUB pathways are also affected. Method To investigate white matter changes in AD and further characterize SUB axon degeneration, we performed triple anterograde tract‐tracing of SUB axon fibers and post‐mortem DTI tractography imaging within the same 8‐9 mo. old 5xFAD mice. Result DTI imaging revealed a significant decrease in fiber density of the fornix white matter tract in 5xFAD mice. Quantification of tracer‐labeled fluorescent fiber density in the 5xFAD mice vs control mice also revealed significant degeneration of SUB fibers within the fornix white matter as well as downstream SUB targets including mammillary body, retrosplenial cortex, and anterior thalamus. Furthermore, SUB axon terminals in 5xFAD mice appeared dystrophic and terminal field topography was disrupted. Conclusion DTI imaging and anatomical tract tracing approaches reveal white matter degeneration in 5xFAD mice and the fornix/SUB fibers are particularly vulnerable in AD. Diminished SUB input to brain regions of the Papez circuit/DMN likely leads to neural network dysfunction. Whether amyloid pathology, neurovascular dysfunction, or inflammatory response in the 5xFAD mouse contributes to white matter degeneration remains to be determined by future studies.
Supplementary Figure 2 from Combination Immunotherapy after ASCT for Multiple Myeloma Using MAGE-A3/Poly-ICLC Immunizations Followed by Adoptive Transfer of Vaccine-Primed and Costimulated Autologous T Cells (2023)

&lt;p&gt;PDF file - 1065KB, Supplemental Data for Figure 4.&lt;/p&gt;
ChemInform Abstract: Codoping in SnTe: Enhancement of Thermoelectric Performance Through Synergy of Resonance Levels and Band Convergence. (2015)

Abstract The thermoelectric performance of p‐type SnTe is enhanced over a broad temperature range with a peak ZT (figure of merit) value of ≈1.4 at 923 K via In/Cd co‐doping and CdS nanostructuring.
Rapid Telomere Shortening in Children (1999)

Telomere shortening may reflect the total number of divisions experienced by a somatic cell and is associated with replicative senescence. We found that the average rate of telomere shortening in peripheral blood mononuclear cells (PBMCs) obtained longitudinally from nine different infants during the first 3 years of life (270 bp per year) is more than fourfold higher than in adults and does not correlate with telomerase activity. These results show that the rate of telomere loss changes during ontogeny, suggesting the existence of periods of accelerated cell division. Because human immunodeficiency virus (HIV) preferentially infects actively dividing cells, our observation suggesting accelerated cell division in children may provide an explanation for some of the distinctive pathogenic features of the HIV disease in infants, including higher viral loads and more rapid progression to acquired immunodeficiency syndrome (AIDS).
Hydrogen Peroxide Decomposition in Ammonia Solutions (1998)

The decomposition of in ammonia hydroxide peroxide mixtures (APM) have been studied as a function of metal‐ion weight concentration (0.1‐10 ppb range) and temperature. It has been found that the uncatalyzed self‐decomposition of is second order with an activation energy of 170 (±10) kJ/mol. Additionally, copper ions, which form mononuclear ammonia complexes catalyze the decomposition. Superimposed on the uncatalyzed reaction, a first order copper‐ion catalyzed decomposition with an activation energy of 84 (±2) kJ/mol has been measured. The iron‐ion catalyzed reaction is a mixture of first and second order. Due to the insolubility of Fe(III) it aggregates to large clusters or colloid particles. Higher concentrations of the large clusters shift the reaction kinetics from first order to second order. The first and second order iron‐ion catalyzed decomposition reactions have similar activation energies [65 (±4) and 71 (±4) kJ/mol] suggesting a similar primary reaction step. Furthermore, the effect of complexing agents has been evaluated. Substoichiometric amounts of diethylenetriamine‐NNN'N''N''‐penta(methylphosphonic) acid break down these iron clusters favoring the first order reaction at the expense of the second order reaction. Superstoichiometric amounts of the complexing agent completely inactivate the iron ions, but had no effect on the copper‐ion catalyzed decomposition reaction. © 1999 The Electrochemical Society. All rights reserved.
KSHV Viral Protein Kinase Interacts with USP9X to Modulate the Viral Lifecycle (2023)

Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi sarcoma (KS), the plasmablastic form of multicentric Castleman's disease, and primary effusion lymphoma. In sub-Saharan Africa, KS is the most common HIV-related malignancy and one of the most common childhood cancers. Immunosuppressed patients, including HIV-infected patients, are more prone to KSHV-associated disease. KSHV encodes a viral protein kinase (vPK) that is expressed from ORF36. KSHV vPK contributes to the optimal production of infectious viral progeny and upregulation of protein synthesis. To elucidate the interactions of vPK with cellular proteins in KSHV-infected cells, we used a bottom-up proteomics approach and identified host protein ubiquitin-specific peptidase 9X-linked (USP9X) as a potential interactor of vPK. Subsequently, we validated this interaction using a co-immunoprecipitation assay. We report that both the ubiquitin-like and the catalytic domains of USP9X are important for association with vPK. To uncover the biological relevance of the USP9X/vPK interaction, we investigated whether the knockdown of USP9X would modulate viral reactivation. Our data suggest that depletion of USP9X inhibits both viral reactivation and the production of infectious virions. Understanding how USP9X influences the reactivation of KSHV will provide insights into how cellular deubiquitinases regulate viral kinase activity and how viruses co-opt cellular deubiquitinases to propagate infection. Hence, characterizing the roles of USP9X and vPK during KSHV infection constitutes a first step toward identifying a potentially critical interaction that could be targeted by future therapeutics. <b>IMPORTANCE</b> Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi sarcoma (KS), the plasmablastic form of multicentric Castleman's disease, and primary effusion lymphoma. In sub-Saharan Africa, KS is the most common HIV-related malignancy. KSHV encodes a viral protein kinase (vPK) that aids viral replication. To elucidate the interactions of vPK with cellular proteins in KSHV-infected cells, we used an affinity purification approach and identified host protein ubiquitin-specific peptidase 9X-linked (USP9X) as a potential interactor of vPK. Depletion of USP9X inhibits both viral reactivation and the production of infectious virions. Overall, our data suggest a proviral role for USP9X.
Average Minimum Distances of periodic point sets (2020)

Periodic sets of points model all solid crystalline materials (crystals) by representing atoms as labeled points. Crystal structures are determined in a rigid form and are considered up to rigid motions or isometries. Modern tools of Crystal Structure Prediction output thousands of simulated structures, though only few of them can be really synthesized. The first obstacle is the presence of many near duplicate structures that can not be efficiently recognized on the fly by past tools. To continuously quantify a similarity between periodic sets, their isometry invariants should be continuous under perturbations when all discrete invariants such as symmetry groups can break down. This paper studies the isometry classification problem for periodic sets with the new continuity requirement and introduces the Average Minimum Distances, which form an infinite sequence of continuous isometry invariants. Their asymptotic behaviour for a wide class of sets is explicitly described in terms of a point packing coefficient. All results are illustrated by experiments on large datasets of crystals.
Catalyst-Controlled Regioselective Suzuki Couplings at Both Positions of Dihaloimidazoles, Dihalooxazoles, and Dihalothiazoles (2010)

Various dihaloazoles can be monoarylated at a single C-X bond with high selectivity via Suzuki coupling. By changing the palladium catalyst employed, the selectivity can be switched for some dihaloazoles, allowing for Suzuki coupling at the other, traditionally less reactive C-X bond. These conditions are applicable to coupling of a wide variety of aryl-, heteroaryl-, cyclopropyl-, and vinylboronic acids with high selectivities and enable the rapid construction of diverse arrays of diarylazoles in a modular fashion.
AMFinder training dataset (2021)

Soil fungi establish mutualistic interactions with the roots of most vascular land plants. Arbuscular mycorrhizal (AM) fungi are among the most extensively characterised mycobionts to date. The software AMFinder allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks. <strong>This dataset contains ink-stained root images used for AMFinder training.</strong>
Nonlocal Optical Pump-THz Probe in the Near Field (2020)

We demonstrate the first “nonlocal” nanoscale NIR-pump THz-probe measurements of semi-insulating GaAs using a scattering-type scanning near-field microscopy technique. We observe temporal shifts in the photoexcitation response which correspond to lateral offsets in the pump spot.
Assessment of Bromodomain Target Engagement by a Series of BI2536 Analogues with Miniaturized BET‐BRET (2016)

Evaluating the engagement of a small molecule ligand with a protein target in cells provides useful information for chemical probe optimization and pharmaceutical development. While several techniques exist that can be performed in a low-throughput manner, systematic evaluation of large compound libraries remains a challenge. In-cell engagement measurements are especially useful when evaluating compound classes suspected to target multiple cellular factors. In this study we used a bioluminescent resonant energy transfer assay to assess bromodomain engagement by a compound series containing bromodomain- and kinase-biasing polypharmacophores based on the known dual BRD4 bromodomain/PLK1 kinase inhibitor BI2536. With this assay, we discovered several novel agents with bromodomain-selective specificity profiles and cellular activity. Thus, this platform aids in distinguishing molecules whose cellular activity is difficult to assess due to polypharmacologic effects.
ChemInform Abstract: Geminal Substituent Effects. Part 4. The Dependence of the Inverse Anomeric Effect of Geminal Cyano Groups on the Structure. (1991)

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.
200-fs pulse generation from a GaInN semiconductor laser diode passively mode-locked in a dispersion-compensated external cavity (2012)

We have demonstrated passively mode-locked operation of a GaInN bisectional laser diode in a dispersion-compensated external cavity. With negative group velocity dispersion in the external cavity, we obtained femtosecond optical pulses after spectral filtering with a bandpass filter. The pulse duration was as short as 200 fs with a time-bandwidth product of 0.41. This is the shortest pulse ever reported for a mode-locked GaInN laser diode.