gebhart/patrepeval huggingface dataset:
Thermodynamic and Kinetic Properties of Fatty Acid Interactions with Rat Liver Fatty Acid-binding Protein (1996)

Fatty acid-binding protein from rat liver (L-FABP) binds 2 fatty acids (FA) per protein, in contrast to FABPs from adipocyte, heart, and intestine, for which binding and structural studies are consistent with a single FA binding site. To understand better the unique characteristics of L-FABP, we have carried out equilibrium binding and kinetic measurements of long chain FA using the fluorescent probes of free fatty acids (FFA), ADIFAB and ADIFAB2, to monitor the concentration of FFA in the reaction of FA with L-FABP. We found that the dissociation constants (Kd) ranged from about 1 nM to 4 microM, being largest for myristate at 45 degrees C and smallest for oleate at 10 degrees C, and that 2 FA were bound per L-FABP for all temperatures and FA. The binding measurements also revealed that at temperatures below 37 degrees C, affinities for the two binding sites differ by between 5- and 20-fold but as the temperature was increased, the affinities converge toward equal values. Off-rate constants (koff) were similar for all FA and for temperatures between 10 and 45 degrees C, ranged from about 0.1 s-1 to 50 s-1. Moreover, for all FA, koff values for dissociation from both the high and low affinity sites were similar, indicating that binding affinity differences at the lower temperatures reflect lower on-rates for binding to the low affinity site. The temperature at which the affinities of the two sites become equivalent depends upon the FA; higher temperatures (45-50 degrees C) are required for the unsaturated FA and myristate than for the longer chain saturated FA (<37 degrees C). This transition from different to equivalent affinity binding sites at specific temperatures reflects a nonlinear van't Hoff behavior of the high affinity site, which in turn is a reflection of large heat capacity changes (between -0.6 and -1.2 kcal K-1 mol-1) that accompany FA binding to the high affinity site. These heat capacity changes, which are unique to L-FABP, do not appear to be correlated with a significant conformational change upon ligand binding. The differences between long chain saturated and unsaturated FA suggest that the conformation of FA bound to L-FABP may differ with both FA type and temperature, and that, in comparison to other FABPs, L-FABP may have distinctly different effects on saturated and unsaturated FA metabolism.
Clinical markers of post-Chikungunya chronic inflammatory joint disease: A Brazilian cohort (2023)

This cohort has provided important insights into the prognostic evaluation of CHIKF. Symptomatic sub-acute disease is a relevant predictor of evolution to chronic arthritis with synovitis, drawing attention to joint pain, edema, multiple articular involvement including small hand and feet joints as risk factors for chronification beyond three months, especially in women. Future studies are needed to accomplish the identification of accurate and early biomarkers of poor clinical prognosis, which would allow better understanding of the disease's evolution and improve patients' management, modifying CHIKF burden on global public health.
Stationary and moving target shadow characteristics in synthetic aperture radar (2014)

An occluded or dark region in synthetic aperture radar (SAR) imagery, known as a shadow, is created when incident radar energy is obstructed by a target with height from illuminating resolution cells immediately behind the target in the ground plane. Shadows depend on the physical dimensions and mobility of a target, platform and radar imaging parameters, and scene clutter. Target shadow dimensions and intensity can be important radar observables in SAR imagery for target detection, location, and tracking or even identification. Stationary target shadows can provide insight as to the physical dimensions of a target, while moving target shadows may show more accurately the location and motion of the target over time versus Doppler energy which may be shifted or smeared outside the scene. However, SAR shadows prove difficult to capture as a target or platform moves, since the quality of the no-return area may quickly be washed-out in a scene over many clutter resolution cells during an aperture. Prior work in the literature has been limited to describing partial shadow degradation effects from platform or target motion of vehicles such as static target shadow tip or interior degradation during an aperture, or shadow degradation due to target motion solely in cross-range. In this paper, we provide a more general formulation of SAR shadow dimensions and intensity for non-specific targets with an arbitrary motion.
Anti-CD40 Antibody Fused to CD40 Ligand Is a Superagonist Platform for Adjuvant Intrinsic DC-Targeting Vaccines (2022)

CD40 is a potent activating receptor expressed on antigen-presenting cells (APCs) of the immune system. CD40 regulates many aspects of B and T cell immunity <i>via</i> interaction with CD40L expressed on activated T cells. Targeting antigens to CD40 <i>via</i> agonistic anti-CD40 antibody fusions promotes both humoral and cellular immunity, but current anti-CD40 antibody-antigen vaccine prototypes require co-adjuvant administration for significant <i>in vivo</i> efficacy. This may be a consequence of dulling of anti-CD40 agonist activity <i>via</i> antigen fusion. We previously demonstrated that direct fusion of CD40L to anti-CD40 antibodies confers superagonist properties. Here we show that anti-CD40-CD40L-antigen fusion constructs retain strong agonist activity, particularly for activation of dendritic cells (DCs). Therefore, we tested anti-CD40-CD40L antibody fused to antigens for eliciting immune responses <i>in vitro</i> and <i>in vivo</i>. In PBMC cultures from HIV-1-infected donors, anti-CD40-CD40L fused to HIV-1 antigens preferentially expanded HIV-1-specific CD8<sup>+</sup> T cells <i>versus</i> CD4<sup>+</sup> T cells compared to analogous anti-CD40-antigen constructs. In normal donors, anti-CD40-CD40L-mediated delivery of Influenza M1 protein elicited M1-specific T cell expansion at lower doses compared to anti-CD40-mediated delivery. Also, on human myeloid-derived dendritic cells, anti-CD40-CD40L-melanoma gp100 peptide induced more sustained Class I antigen presentation compared to anti-CD40-gp100 peptide. In human CD40 transgenic mice, anti-CD40-CD40L-HIV-1 gp140 administered without adjuvant elicited superior antibody responses compared to anti-CD40-gp140 antigen without fused CD40L. In human CD40 mice, compared to the anti-CD40 vehicle, anti-CD40-CD40L delivery of Eα 52-68 peptide elicited proliferating of TCR I-Eα 52-68 CD4<sup>+</sup> T cells producing cytokine IFNγ. Also, compared to controls, only anti-CD40-CD40L-Cyclin D1 vaccination of human CD40 mice reduced implanted EO771.LMB breast tumor cell growth. These data demonstrate that human CD40-CD40L antibody fused to antigens maintains highly agonistic activity and generates immune responses distinct from existing low agonist anti-CD40 targeting formats. These advantages were <i>in vitro</i> skewing responses towards CD8<sup>+</sup> T cells, increased efficacy at low doses, and longevity of MHC Class I peptide display; and in mouse models, a more robust humoral response, more activated CD4<sup>+</sup> T cells, and control of tumor growth. Thus, the anti-CD40-CD40L format offers an alternate DC-targeting platform with unique properties, including intrinsic adjuvant activity.
Response to Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution” (2011)

Su et al . claim guanine-cytosine (GC) content variation can largely explain the observed tyrosine frequency variation, independent of adaptive evolution of cell-signaling complexity. We found that GC content variation, in the absence of selection for amino acid changes, can only maximally account for 38% of the observed tyrosine frequency variation. We also uncovered other mechanisms acting to reduce tyrosine phosphorylation that further support our previous proposal.
ChemInform Abstract: Enantioselective Synthesis of P‐Stereogenic Phosphinates and Phosphine Oxides by Molybdenum‐Catalyzed Asymmetric Ring‐Closing Metathesis. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
P1‐123: PROTEOMIC ANALYSIS OF ARCHIVED ALZHEIMER'S DISEASE BRAIN TISSUE USING LASER CAPTURE MICRODISSECTION AND LC‐MS (2014)

Genome-wide association studies (GWAS) have identified novel genes that are associated with increased risk for Alzheimer's disease (AD), suggesting that a variety of protein pathways are likely to be involved in the development of late onset AD. However, it is not yet known how these pathways participate in the pathogenesis of AD. Therefore the aim of this study was to use an unbiased proteomic approach to examine localized protein changes in the AD brain at different stages of disease progression. 8μm paraffin-embedded formalin fixed brain sections of the hippocampus and entorhinal cortex from individuals with early AD, advanced AD and aged matched controls were used. Specific disease-associated structures, such as amyloid plaques or degenerating neurons in the entorhinal cortex, were collected using laser capture microdissection. Amyloid plaques were either identified using immunohistochemistry for 6E10/4G8 or by Thioflavin S staining and neurons were identified by cresyl violet staining. At least 500 plaques or 1000 neurons were collected per sample to ensure an adequate starting protein amount. Quantitative, label-free LC-MS was then performed on samples to identify all proteins in the specific brain structures. Preliminary results show that LC-MS can be successfully performed using a small starting amount of protein from archived, paraffin embedded brain tissue. Immunohistochemistry or histological staining did not interfere with protein detection using LC-MS. Furthermore, LC-MS successfully identified many proteins in these samples that have been previously associated with AD including tau, apolipoprotein E, complement C1q, neuroligin and heat shock proteins. Studies are ongoing to determine which proteins have altered expression in AD tissue from patients at early versus late stages of disease and tissue from normal age-matched controls. The combined use of laser capture microdissection and LC-MS to characterize proteins in specific brain structures or cell types has great promise for future studies. Future results using this technique will complement those from GWAS studies, potentially identifying protein pathways uniquely expressed or altered in AD. The function of these identified proteins and consequences of expression in AD can then be pursued in further research and could provide novel therapeutic targets.
Synthesis of uniformly dispersed anatase nanoparticles inside mesoporous silica thin films via controlled breakup and crystallization of amorphous TiO2 deposited using atomic layer deposition (2013)

Amorphous titanium dioxide was introduced into the pores of mesoporous silica thin films with 75% porosity and 12 nm average pore diameter via Atomic Layer Deposition (ALD) using alternating pulses of tetrakis(dimethylamino)titanium and water. Calcination provoked fragmentation of the deposited amorphous TiO2 phase and its crystallization into anatase nanoparticles inside the nanoporous film. The narrow particle size distribution of 4 ± 2 nm and the uniform dispersion of the particles over the mesoporous silica support were uniquely revealed using electron tomography. These anatase nanoparticle bearing films showed photocatalytic activity in methylene blue degradation. This new synthesis procedure of the anatase nanophase in mesoporous silica films using ALD is a convenient fabrication method of photocatalytic coatings amenable to application on very small as well as very large surfaces.
Morphogenetic and proliferative responses to heregulin of mammary epithelial cells in vitro are dependent on HER2 and HER3 and differ from the responses to HER2 homodimerisation or hepatocyte growth factor. (2000)

The effects of heregulin on the cell line HB2, derived from immortalised human luminal mammary epithelial cells, have been examined. HB2 cells, which normally form smooth spherical colonies in collagen gels, exhibited a striking heregulin-induced morphological change to colonies projecting a large number of spiky branches. A mitogenic effect of heregulin on HB2 cells was also seen, which was more pronounced on collagen than on plastic, whereas cell motility was unaffected. HB2 cells were found to express the heregulin receptor subunits HER2 and HER3, but not HER4. Treatment of HB2 cells with heregulin also induced tyrosine phosphorylation of a band shown by immunoprecipitation to contain HER3. Using specific receptor-blocking antibodies, it was found that both the morphogenetic and proliferative responses of heregulin in HB2 cells were mediated by HER2 and HER3. To compare the effects of HER2 in heregulin signaling to heregulin-independent HER2 homodimerisation (thought to be a carcinoma-associated event), HB2 cells were transfected with the trk-neu hybrid receptor which could be induced to form homodimers by NGF. Although activated HER2 homodimers induced proliferation in the HB2 transfectants in collagen, a morphological response in collagen was not seen, suggesting that HER3 signaling is important for morphogenesis in this cell type.
An Experimental CMOS Photon Detector with 0.5e- RMS Temporal Noise and 15μm pitch Active Sensor Pixels (2018)

This is the first reported non-electron-multiplying CMOS Image Sensor (CIS) photon-detector for replacing Photo Multiplier Tubes (PMT). 15jum pitch active sensor pixels with complete charge transfer and readout noise of 0.5 e-RMS are arrayed and their digital outputs are summed to detect micro light pulses. Successful proof of radiation counting is demonstrated.
Surfactant/Nonionic Polymer Interaction. A NMR Diffusometry and NMR Electrophoretic Investigation (2004)

The interaction between the nonionic polymer poly(ethylene oxide) (PEO) of molecular weight 20,000 and surfactants of various types [sodium dodecyl sulfate (SDS), dodecyl trimethylammonium bromide, octyl beta-D-glucoside, and potassium laurate] has been investigated in an aqueous solution at 25 degrees C by 1H NMR pulsed-gradient spin-echo self-diffusion techniques. The SDS/PEO study was further complemented by component-resolved 1H NMR-based studies of the electrophoretic mobility of PEO and the alkyl part of SDS under the same measurement conditions. Through such combined studies, a much more complete picture of the binding and aggregation processes becomes accessible.
<title>PDT of the endometrium using ALA</title> (1997)

There is a widely recognized need for new approaches to effect endometrial ablation as an alternative to hysterectomy for treatment of menorrhagia. Photodynamic therapy (PDT) offers one such approach. We have investigated the use of 5-aminolaevulinic acid (ALA)-based PDT of the endometrium in model systems and in a series of patients. In all of this work, the ALA was administrated directly into the uterine cavity to reduce any possibility of systemic photosensitization. In a series of experiments in perfused ex vivo uteri, ALA was introduced into the cavity and protoporphyrin formation was measured in the endometrium, the underlying myometrium and the perfusate. ALA transfer into the perfusate was also measured. This work demonstrated that protoporphyrin formation in the endometrium was approximately ten fold that in the underlying myometrium and that systemic photosensitization would be unlikely to result form transfer of administered ALA from the uterus into the circulation. Similar results were found in studies carried out in vivo, where ALA was administered to patients scheduled for hysterectomy. Using a specially designed light source, the first patients have now been treated by giving intrauterine ALA followed by laser light. Two series of treatments - 10 in all - have been carried out. Eight patients have one year follow up. A reduction in measured menstrual blood loss was demonstrated in all but one patient. Complete symptomatic relief was obtained in tow women who did not require further treatment.
Functional genomic analysis of systemic cell division regulation in legumes (2009)

\n\t\t\t\t\tLegumes develop root nodules from pluripotent stem cells in the rootpericycle in response to mitogenic activation by a decorated chitin-likenodulation factor synthesized in Rhizobium bacteria. The soybean genes encoding the receptor for such signals were cloned using map-based cloning approaches. Pluripotent cells in the root pericycle and the outer or inner cortex undergo repeated cell divisions to initiate a composite nodule primordium that develops to a functional nitrogen-fixing nodule. The process itself is autoregulated, leading to the characteristic nodulation of the upper root system. Autoregulation of nodulation (AON) in all legumes is controlled in part by a leucine-rich repeat receptor kinase gene (GmNARK). Mutations of GmNARK, and its other legume orthologues, result in abundant nodulation caused by the loss of a yet-undefined negative nodulation repressor system. AON receptor kinases are involved in perception of a long distance, root-derived signal, to negatively control nodule proliferation. GmNARK and LjHAR1 are expressed in phloem parenchyma. GmNARK kinase domain interacts with Kinase Associated Protein Phosphatase (KAPP). NARK gene expression did not mirror biological NARK activity in nodulation control, as q-RT-PCR in soybean revealed high NARK expression in roots, root tips, leaves, petioles, stems and hypocotyls, while shoot and root apical meristems were devoid of NARK RNA. High through-put transcript analysis in soybean leaf and root indicated that major genes involved in JA synthesis or response are preferentially down-regulated in leaf but not root of wild type, but not NARK mutants, suggesting that AON signaling may in part be controlled by events relating to hormone metabolism. Ethylene and abscisic acid insensitive mutants of L. japonicus are described. Nodulation in legumes has significance to global economies and ecologies, as the nitrogen input into the biosphere allows food, feed and biofuel production without the inherent costs associated with nitrogen fertilization [1]. Nodulation involves the production of a new organ capable of nitrogen fixation [2] and as such is an excellent system to study plant &amp;ndash; microbe interaction, plant development, long distance signaling and functional genomics of stem cell proliferation [3, 4]. Concerted international effort over the last 20 years, using a combination of induced mutagenesis followed by gene discovery (forward genetics), and molecular/biochemical approaches revealed a complex developmental pathway that &amp;lsquo;loans&amp;rsquo; genetic programs from various sources and orchestrates these into a novel contribution. We report our laboratory&amp;rsquo;s contribution to the present analysis in the field.\n\t\t\t\t
A Novel Frame Design for Non-Terrestrial Network Based Integrated Sensing and Communication (2022)

In this paper, a novel frame design is proposed which realizes integrated sensing and communication (ISAC) while developing synergy among non-terrestrial (NTN) and terrestrial networks. Conventional time division duplexing (TDD) based systems suffer from high latency in sensing and communication performance which further aggravates with the increasing distance between transmitter and receiver as in the case of NTN. Therefore, to overcome the issue of latency, a spectrum efficient frame design is proposed that exploits the waiting period of a pulsed radar to perform interference free communication and sensing. The communication transmitter and radar transceiver embedded in high altitude platforms (HAPs) uses pulsed radar for sensing. Due to high altitudes, the target echo is reached at the HAPS after a long delay. This delay time is exploited to embed fixed and opportunistic communication in the proposed ISAC frame design. The numerical analysis explains spectrum efficiency of the proposed frame design compared to TDD mode of JRC systems, with reliable communication and accurate target detection.
Double-layer graphene for enhanced tunable infrared plasmonics (2017)

Graphene is emerging as a promising material for photonic applications owing to its unique optoelectronic properties. Graphene supports tunable, long-lived and extremely confined plasmons that have great potential for applications such as biosensing and optical communications. However, in order to excite plasmonic resonances in graphene, this material requires a high doping level, which is challenging to achieve without degrading carrier mobility and stability. Here, we demonstrate that the infrared plasmonic response of a graphene multilayer stack is analogous to that of a highly doped single layer of graphene, preserving mobility and supporting plasmonic resonances with higher oscillator strength than previously explored single-layer devices. Particularly, we find that the optically equivalent carrier density in multilayer graphene is larger than the sum of those in the individual layers. Furthermore, electrostatic biasing in multilayer graphene is enhanced with respect to single layer due to the redistribution of carriers over different layers, thus extending the spectral tuning range of the plasmonic structure. The superior effective doping and improved tunability of multilayer graphene stacks should enable a plethora of future infrared plasmonic devices with high optical performance and wide tunability.
Transformation of Human Mesenchymal Stem Cells in Radiation Carcinogenesis: Long-Term Effect of Ionizing Radiation (2008)

Increasing evidence on cancer stem cells suggest that stem cells are susceptive to carcinogenesis and consequently can be the origin of many cancers. We have recently established a telomerase-transduced human mesenchymal stem cell line and subsequently irradiated this in order to achieve malignant transformation. In the present study, we analyzed the long-term effect of ionizing radiation on these cells and investigate whether radiation can trigger tumor development. The cells were irradiated with a low (2.5 Gy) and a high (15 Gy) dose of gamma-rays and followed for up to 6 months after radiation. A subclone of the cells irradiated with 2.5 Gy of gamma-rays formed tumors after implantation to severe combined immunodeficiency mice. During the process of transformation, the cells showed accelerated telomere shortening, increased levels of anaphase bridges and a shift from balanced to unbalanced translocations. The tumor suppressor genes p53 and p21(CIP1) functioned normally throughout the study. Our observations indicate that radiation destabilized the telomeres and that the presence of uncapped telomeres initiated fusion-break-fusion cycles, resulting in increased chromosomal instability and tumor formation. Thus, bone marrow-derived human mesenchymal stem cells are capable of exhibiting a malignant phenotype.