gebhart/patrepeval huggingface dataset:
Macrophage Polarization and the Effect of MicroRNA-155 Administered in Water-in-Oil-in-Water Multiple Emulsion Formulations (2015)

The tumor microenvironment is composed of range of cells including macrophages that participate in sustaining tumor growth and invasion. Tumor-associated macrophages (TAM’s) polarized to the M2 or pro-tumoral phenotype are one such population of cells highly expressed in the tumor microenvironment. The expression of microRNA’s (miR’s) is often found to be dysregulated in TAM’s and hence exogenous delivery of miR provides a strategy for macrophage phenotypic modulation to attain improved anticancer activity. In this study, we assessed the use of multiple emulsions for the delivery of miR to achieve macrophage M1 repolarization. Water-in-oil-in-water (WOW) multiple emulsions (ME) were prepared using a two-step emulsification technique for encapsulation of miR-155 and cellular uptake, transfection efficiency, and repolarization capability of J774A.1 macrophages was assessed. The repolarized macrophages were co-cultured with SKOV3 ovarian cancer cells to assess the effect on macrophage morphology, motility and apoptosis of cancer cells. The ME showed enhanced uptake and expression of miR-155, which resulted in improved M1 polarization of J774A.1 cells. Co-culture studies with SKOV3 cells indicated an alteration in apoptotic profile. Holographic assessment of the co-cultured cells in real-time showed differences in motility and morphology of macrophages with miR-155 ME treated cells showing greater cellular interaction between the two phenotypes.
Design and Linearization of Class-E Power Amplifier for Nonconstant Envelope Modulation (2009)

This paper presents design and linearization techniques for a highly efficient, but nonlinear Class-E power amplifier (PA) applied to linear RF transmitters. To achieve maximum efficiency for Class-E PA operating above gigahertz frequencies, the proposed design theory modifies the classic Class-E condition and considers switch-on and switch-off resistances in deriving the analytical solution. For linearization, a digital envelope predistorter (DEP) is used to provide predistorted envelope modulation for the RF-input and supply-voltage signals fed to the Class-E PA. This DEP can successfully compensate for AM/AM and AM/PM distortions such that the Class-E PA, although classified as a switching-mode PA, can act as a linear PA. A cdma2000 1 times transmitter incorporating this Class-E PA and DEP is demonstrated to simultaneously achieve high efficiency and high modulation quality.
Diabetes mellitus risk for 102 drugs and drug combinations used in patients with bipolar disorder (2019)

There is an increased risk of diabetes mellitus associated with antipsychotic and psychotropic polypharmacy use in bipolar disorder. The evidence of a lower-than-baseline risk of DM with lamotrigine, oxcarbazepine, lithium, and bupropion monotherapy should be further investigated.
Selection of DNA Aptamers That Recognize α-Synuclein Oligomers Using a Competitive Screening Method (2012)

α-Synuclein (α-syn) oligomers are considered major molecules responsible for the onset of Parkinson's disease and dementia with Lewy bodies. α-Syn oligomers thus serve as an important target for the development of drugs and diagnostic tests for neurodegenerative diseases. In this paper we report on the identification of DNA aptamers that bind to soluble α-syn oligomers. A competitive screening method based on aptamer blotting was used for the selection of α-syn oligomer-specific aptamers. This approach resulted in the identification of eight aptamers that specifically bind to α-syn oligomers among α-syn monomers, oligomers, and fibrils. Interestingly, the aptamers also bound to amyloid β oligomers, which are strongly associated with the development of Alzheimer's disease. The results of this study support the hypothesis that amyloid oligomers share a common structure. Oligomer-binding aptamers may serve as powerful analytical tools for the design and development of drugs and diagnostic tests for neurodegenerative diseases.
False Positive Responses in Standard Automated Perimetry (2021)

Across 3 different standard automated perimetry thresholding algorithms, FP rates showed only weak associations with visual field test results, except in severe glaucoma. Current recommendations regarding acceptable FP ranges may require revision. GH or other analyses may be better suited than FP rates for identifying unreliable results in patients who frequently press the response button without having perceived stimuli.
Triplex hybridization of siRNA with bifacial glycopolymer nucleic acid enables hepatocyte targeted silencing (2019)

In this manuscript, we demonstrate the utility of polyacrylates modified with both an artificial base-triple and a sugar (GalNAc) to serve as an siRNA packaging and delivery platform to hepatocytes in culture and in vivo (mice). This work is based upon our previously published finding that base-triple modified polyacrylates can triplex hybridize with oligo T/U DNA/RNA and deliver luciferase-targeted siRNA to HeLa cells engineered to express luciferase (JACS 2015). Herein, we expand on the scope of this work by employing a well-established liver-targeting ligand (GalNAc) to silence an endogenous human target, ApoB, the primary protein component of low density lipoprotein. Our platform was found to be effective in both hepatocyte (HepG2) cell culture as well as in an animal model of cardiac disease that features elevated ApoB levels. This manuscript thus validates the use of a synthetic platform that is designed to integrate both packaging via triplex hybridization with tissue-targeting ligand display. This enabling method could be useful as a new, convenient siRNA platform that accessible through scalable synthesis. Further, this platform would improve the efficiency of screening siRNA sequences for silencing efficacy using the identical glycopolymer carrier, thus alleviating the need for covalent ligand modification of each RNA substrate as typical for competing technologies.
Optical diagnostics of dusty plasmas during nanoparticle growth (2016)

International audience
Evaluating the Patient with LV Dysfunction for Potential Revascularization (2008)

This chapter contains sections titled: Physiological Basis of Viability Imaging Techniques The “Ideal” Technique Common Assumptions and Clinical Implications Conclusions References
Der Weak-Link-Ansatz zur Synthese anorganischer Makrocyclen (1998)

Homo-Dimetall-Makrocyclen wurden aus flexiblen Liganden nach einer neuen Methode, die als Weak-Link-Ansatz bezeichnet wird, in hohen Ausbeuten hergestellt [Gl. (a)]. Kleine aromatische Moleküle können wegen ihrer Wechselwirkungen mit den beiden Rh-Zentren des Makrocyclus innerhalb des Käfigs eingelagert und ausgerichtet werden.
Identification of Novel and Widely Expressed Cancer/Testis Gene Isoforms That Elicit Spontaneous Cytotoxic T-Lymphocyte Reactivity to Melanoma (2004)

Multiple isoforms (TAG-1, TAG-2a, TAG-2b, and TAG-2c) of a novel cancer/testis antigen gene have been identified and are expressed in 84-88% of melanoma cell lines tested. The tumor antigen (TAG) genes are also expressed in K562, a myelogenous leukemia cell line, and they have homology to two chronic myelogenous leukemia-derived clones and a hepatocellular carcinoma clone in the human expressed sequence tags (EST) database, thus indicating that their expression is not restricted to melanomas. In contrast to the fact that many cancer/testis antigens are poorly immunogenic, the TAG-derived peptide, RLSNRLLLR, is recognized by HLA-A3-restricted, melanoma-specific CTLs that were obtained from a melanoma patient with spontaneous reactivity to the peptide. Unlike most cancer/testis antigen genes which are located on the X chromosome, the TAG genes are located on chromosome 5. The genes have the additional unusual features of being coded for in an open reading frame that is initiated by one of three nonstandard initiation codons, and the sequence coding the RLSNRLLLR peptide crosses an exon-exon boundary. The properties of the TAG antigens indicate that they are excellent vaccine candidates for the treatment of melanoma and perhaps other cancers.
Duplexing, resource allocation and inter‐cell coordination: design recommendations for next generation wireless systems (2005)

Abstract Coexistence of different access technologies, hierarchical cellular deployment, a wide variety of data services, requirements for transparent operation across different technologies, adaptivity to varying network conditions and mobility and quality of service (QoS) constraints introduce a number of challenges in the design of future generation systems and the specification of new air interfaces, such as efficiency and flexibility in the utilization of spectrum, dynamic resource allocation and exploitation of the multiuser diversity and reconfigurable interference management and inter‐cell coordination. In this paper, three critical issues for the design of next generation systems are addressed: (i) duplexing, (ii) scheduling and resource allocation and (iii) interference and inter‐cell coordination. A number of research directions are presented, which constitute promising potential candidates for next generation systems specification. Copyright © 2005 John Wiley &amp; Sons, Ltd.
The effects of active queue management on web performance (2003)

We present an empirical study of the effects of active queue management (AQM) on the distribution of response times experienced by a population of web users. Three prominent AQM schemes are considered: the Proportional Integrator (PI) controller, the Random Exponential Marking (REM) controller, and Adaptive Random Early Detection (ARED). The effects of these AQM schemes were studied alone and in combination with Explicit Congestion Notification (ECN). Our major results are:
Supplementary Materials and Methods, Figures S1-S7, Table S1 from Bioengineered Implantable Scaffolds as a Tool to Study Stromal-Derived Factors in Metastatic Cancer Models (2023)

&lt;p&gt;Supplementary Materials and Methods, Figures S1-S7, Table S1. Supplementary Materials and Methods. Porous hydrogel scaffold fabrication; 3D culture of primary human bone marrow stromal cells; In vitro invasion assay; In vitro proliferation assay. Supplementary Figure S1. In vitro PC-3 cell invasion and proliferation assays. Supplementary Figure S2. Human BMSC survival in vivo and marrow-like microenvironment formation in scaffolds 4 weeks after subdermal implantation in NSG mice. Supplementary Figure S3. Longitudinal bioluminescence monitoring of human tumor xenografts. Supplementary Figure S4. Histological analysis of PC-3 cells. Supplementary Figure S5. Ex vivo monitoring of DU-145 and MDA-231 #1833 cell engraftment in explanted scaffolds. Supplementary Figure S6. Metastasis development in DU-145 and MDA-231 #1833 xenograft models after scaffold transplantation. Supplementary Figure S7. Effect of IL-1Ra and IL-1b on PC-3 cell growth. Supplementary Table S1. Comprehensive list of genes interrogated by the Mouse Tumor Metastasis RT2 Profiler PCR Array.&lt;/p&gt;
Herbicides, Asulam (2002)

Abstract The herbicidal properties of asulam (methyl 4‐aminobenzenesulfonylcarbamate) were first described in 1965. It is used alone or in mixtures to control docks ( Rumex spp.) and bracken ( Pteridium aquilinum ) in pastures, forestry, and orchards; wild oats ( Avena fatua ) in flax; and annual and perennial grasses and broad‐leaved weeds in spinach, oilseed poppies, and alfalfa. It is also used to control annual and perennial grasses, such as johnsongrass ( Sorghum halepense ) in sugarcane and annual grasses and broad‐leaved weeds in plantation crops. The physicochemical properties of asulam favor high phloem mobility, which contributes to the herbicidal activity against perennial weeds. The mode of action of asulam is unique for herbicides. It is an inhibitor of folic acid biosynthesis similar to the sulfonamide antimicrobial drugs, which are competitive inhibitors of 7,8‐dihydropteroate synthase (DHPS). The mechanism of selectivity to asulam is reported as having greater metabolic degradation in tolerant species. Asulam has a very low environmental, ecotoxicological, and toxicological impact. It is rapidly degraded in soil and possesses very low acute and chronic toxicity.
Adrenomedullin in the central nervous system (2002)

Adrenomedullin (AM) is a novel vasodilator peptide first purified from human pheochromocytoma by tracing its capacity to stimulate cAMP production in platelets. AM immunoreactivity is widely distributed in the central nervous system (CNS) and in the rat has been demonstrated by immunohistochemical techniques to be present in many neurons throughout the brain and spinal cord, as well as in some vascular endothelial cells and perivascular glial cells. Electron microscopy shows that the immunoreactivity is located mainly in the neuronal cytoplasm, but also occurs in the cell nucleus in some cells of the caudate putamen and olfactory tubercle. Biochemical analyses suggest that higher molecular forms, presumably precursor forms, may predominate over fully processed AM in some brain areas. The expression of AM immunoreactivity is increased in cortical neurons, endothelial cells, and perivascular processes after a simulation of ischemia by oxygen and glucose deprivation. Immunohistochemical, electrophysiological, and pharmacological studies suggest that AM in the CNS can act as a neurotransmitter, neuromodulator, or neurohormone, or as a cytoprotective factor in ischemic/hypoxic conditions, in addition to its vasodilator role.
First Pilot of Borehole to Surface Electromagnetic in Saudi Arabia - A New Technology to Enhance Reservoir Mapping & Monitoring (2011)

The first Borehole to Surface Electromagnetic (BSEM) pilot field survey in Saudi Arabia — to identify oil and water bearing reservoir layers in an oilfield water injection transition zone — was successfully completed. The objective of a BSEM survey is to obtain resistivity and induced polarization (IP) maps based on an acquisition grid at the surface that covers a few kilometers around the transmitter well. The survey reveals oil and water bearing zones in the investigated reservoir layers. In this pilot field test, BSEM showed the potential to map water-front movements, in an area of about 4 km from the single well surveyed, evaluate the sweep efficiency, eventually identify bypassed-lagged oil zones and monitor the fluid displacements, if surveys are repeated in time. Furthermore, in addition to reservoir monitoring, BSEM can be very useful in non-diagnosed areas like exploration fields.
FUROSHIKI: Augmented Reality Media That Conveys Japanese Traditional Culture (2019)

Furoshiki is a traditional culture of Japan which has prevailed in its everyday life and is widely used even today. In this paper, we propose a system through which users can be, while getting interested, exposed including to Japanese wrapping culture and attitude of dealing with things with care by augmenting an act to “wrap” with a piece of Japanese traditional furoshiki using the image-recognition technique and the motion-image projection technique.
Gal-Gal pyelonephritis Escherichia coli pili linear immunogenic and antigenic epitopes. (1985)

The linear immunogenic and antigenic structure of E. coli Gal-Gal pili from the recombinant strain HU 849 was investigated with nine synthetic peptides corresponding to regions of the pilus sequence predicted to contain hydrophilic beta-turns. Five peptides, as bovine serum albumin conjugates, were found by anti-HU 849 pilus serum and were thus designated "immunogenic epitopes." Peptides corresponding to R 25-38, R 38-50, and R 48-61 (which jointly comprise the single intramolecular disulfide loop), and R 103-116, were bound in low titer. A prominent immunogenic epitope was specified by a peptide corresponding to R 65-75. Four peptides, as thyroglobulin conjugates, elicited antisera in rabbits that bound intact HU 849 pili. These were designated "antigenic epitopes." Two prominent antigenic epitopes were localized to peptides corresponding to R 5-12 and R 93-104, whereas peptides corresponding to R 65-75 and R 119-131 represented two minor antigenic epitopes. None of the peptide antisera bound Gal-Gal pili from heterologous strains except anti-R 93-104 and anti-R 5-12. In 8 of the 10 Gal-Gal-binding pyelonephritis isolates tested, anti-R 5-12 detected a protein with an apparent molecular weight of 18,000 co-migrating with several Gal-Gal pili. Anti-R 93-104 detected a corresponding protein in 4 of 8 fecal and 7 of 12 pyelonephritis Gal-Gal-binding isolates; however, it also bound apparently unrelated proteins of higher molecular weight.
Differential Dependence On Aerobic Glycolysis In Normal and Malignant Hematopoietic Stem and Progenitor Cells To Sustain Daughter Cell Production (2013)

Abstract How glucose is metabolized can influence cell function, but whether differences in glucose metabolism reflect, or dictate, cell state is not clear and is of particular interest given the association of cancer with aerobic glycolysis. Studies on cancer cell lines have indicated that increased glucose uptake with lactate production regardless of oxygen concentration, a phenomenon also known as the Warburg effect, is promoted in part by expression of the M2 isoform of pyruvate kinase (PKM2) and the muscle form of lactate dehydrogenase A (LDHA). Normal somatic cells thought to also preferentially use glycolytic metabolism are tissue stem cells, particularly the self-renewing hematopoietic stem cells (HSC) resident in the hypoxic microenvironment of the bone marrow. It remains to be defined, however whether proliferating hematopoietic progenitor cells rely on aerobic glycolysis and whether malignant and normal hematopoietic cells are dependent on the same metabolic regulation. We observed that PKM2 and LDHA are the predominant isoforms expressed by all BM hematopoietic cells. To further understand the role of glycolytic metabolism in hematopoiesis and hematological malignancy, we utilized a mouse strain that allows conditional deletion of the PKM2 specific exon 10. Deletion of PKM2 in hematopoetic cells leads to expression of PKM1, accompanied with partial inhibition of lactate production and decreased glycolytic intermediates in the hematopoietic stem/progenitor cell (HSPC) population. Loss of PKM2 compromises the long-term repopulation capacity of HSPCs as revealed by serial transplantation assay. Interestingly, the repopulating defects resulting from PKM2 depletion appear to involve progenitors, perhaps due to inadequate biomass generation necessary for robust cell proliferation. To confirm that the effect of PKM2 deletion on HSPC function is due to metabolic changes rather than other putative PKM2 functions, we engineered a mouse strain that allowed conditional knockout of LDHA to more potently impair aerobic glycolysis. LDHA deletion completely inhibited lactate production, enhanced ROS levels in hematopoietic cells and impaired long-term BM repopulating activity. In contrast to PKM2 deletion that affects progenitor but not stem cells, LDHA depletion impacts both stem cell maintenance and progenitor cell proliferation. Deletion of either PKM2 or LDHA markedly suppressed leukemia initiation by either putative stem cell (BCR-ABL) or progenitor (MLL-AF9) transforming alleles. Therefore, modulating aeroblic glycolysis has effects on normal hematopoietic cells that depend upon cell state and negatively impacts leukemic growth regardless of cell state. The differential sensitivity of normal and malignant cells to modulation of aerobic glycolysis suggests a potential therapeutic opportunity for leukemia intervention. Disclosures: No relevant conflicts of interest to declare.
Molecular Characterization of BK and JC Viruses Circulating among Potential Kidney Donors in Kuwait (2013)

BK and JC polyomaviruses can be associated with nephropathy following renal transplantation. The aim of this study was to determine the prevalence, load, and genotypes of BK and JC viruses circulated in potential kidney donors in Kuwait. The detection of polyomavirus DNA was carried out in serum and urine samples of 165 potential kidney donors. Seventy (42%) individuals were tested positive for polyomavirus DNA, of whom 20 (12%) had detectable polyomavirus DNA in their serum samples, 40 (24%) in their urine samples, and 10 (6%) in both serum and urine samples. In the group of polyomavirus-positive patients, JC DNA could be detected in 78% of urine samples and 11% of serum samples, whereas BK DNA could be detected in 7% of urine samples and 3% of serum samples. The median polyomaviral load was low. The detected BK sequences in Kuwaiti adults formed new clusters sharing common ancestor with subgroups Ib1 and IVc, which are prevalent in Asia and Europe. Additionally, around half of the detected JCV sequences in Kuwaiti adults formed new clusters within the African subtype 3. Our results suggest high rate of polyomavirus shedding among healthy adults in Kuwait that can jeopardize their suitability for kidney donation.
Graphene based Ultra-Thin Flat Lenses (2015)

Flat lenses when compared to curved surface lenses have the advantages of being aberration free, and they offer a compact design necessary for a myriad of electro-optical applications. In this paper we present flat and ultrathin lenses based on graphene, the worlds thinnest known material. Monolayers and multilayers of graphene were fabricated into Fresnel zones to produce Fresnel zone plates, which utilize the reflection and transmission properties of graphene for their operation. The working of the lenses and their performance in the visible and terahertz regimes were analyzed computationally. Experimental measurements were also performed to characterize the lens in the visible regime, and a good agreement was obtained with the simulations. This work demonstrates the principle of atom-thick graphene-based lenses, with perspectives for ultracompact integration.
Tryptophan and kynurenines in neurodegenerative disease (2019)

There is mounting evidence that there exists a connection between abnormal tryptophan metabolism and neurodegenerative diseases. The relationship between tryptophan and kynurenines in 48 age-matched normal and Alzheimer’s disease human brain tissues was investigated using label-free fluorescence spectroscopy.
Mouse placental macrophages have a decreased ability to present antigen. (1993)

Large numbers of macrophages can be found in an animal's uteroplacental unit. This high concentration of macrophages suggests they must play an important role during placental development. To gain a better understanding of the functional capacity of placental macrophages, we have obtained a highly enriched placental macrophage culture and have derived several cell lines from this population. Both placental macrophages and cell lines show colony-stimulating factor 1-dependent growth, express Fc receptors, and can perform Fc-receptor-mediated phagocytosis. In addition, they express macrophage markers Mac-1, F4/80, and CD14. Although placental macrophages express major histocompatibility complex class II molecules constitutively, they display a decreased ability to present protein antigens to T cells. Since primary fetal liver macrophages of the same gestational stage also show a decreased ability to present antigens, this phenomenon may reflect a developmental stage of macrophages.
Thickness determination for silicon-on-insulator structures (1986)

Optical interference at the interfaces of a silicon-on-insulator structure has been used for rapid, nondestructive determination of the silicon and oxide layer thicknesses. The technique is useful for determining the layer thicknesses for wafers in which devices and circuits are subsequently fabricated, especially for very thin silicon films in which the device characteristics depend strongly on the silicon thickness.