gebhart/patrepeval huggingface dataset:
Enhancement of Macrophage Colony-Stimulating Factor–Induced Growth and Differentiation of Human Monocytes by Interleukin-10 (1997)

Interleukin-10 (IL-10) has been reported to be a negative cytokine for monocytes/macrophages. In the present study, we showed that IL-10 is rather a positive cytokine and augments the growth and differentiation of human monocytes stimulated with macrophage colony-stimulating factor (M-CSF ). Highly purified adherent human monocytes were cultured for 7 days with M-CSF in the presence or absence of IL-10. The number of recovered cells increased in the culture of monocytes with M-CSF + IL-10 compared to the culture with M-CSF alone. IL-10 alone was not enough to maintain the survival and differentiation of monocytes into macrophages. Morphological change cultured in M-CSF was also accelerated by addition of IL-10, and macrophages cultured in M-CSF + IL-10 were more elongated compared to macrophages cultured with M-CSF alone. Binding of 125I-M-CSF to monocytes incubated with M-CSF + IL-10 was about 1.7-fold higher than that to monocytes incubated with M-CSF alone. In accordance with the binding study, Northern blot analysis showed that the levels of the expression of c-fms, M-CSF receptor, mRNA in macrophages cultured in M-CSF + IL-10 were higher than that in macrophages cultured in M-CSF alone. Macrophages cultured in M-CSF + IL-10 expressed higher level of FcγRI, II, III, and showed augmented Fcγ receptor mediated phagocytosis. The former also produced higher level of H2O2 and O−2 , when stimulated with zymosan, and of IL-6 when stimulated with lipopolysaccharide compared to the latter. These results taken together suggest that IL-10 augments the growth and differentiation of human monocytes cultured in M-CSF.
Grafting of Zwitterion from Cellulose Membranes via ATRP for Improving Blood Compatibility (2009)

A p-vinylbenzyl sulfobetaine was grafted from cellulose membrane (CM) using surface-initiated atom transfer radical polymerization for blood compatibility improvement. Surface structure, wettability, morphology, and thermal stability of the CM substrates before and after modification were characterized by attenuated total reflectance Fourier transform infrared spectra, X-ray photoelectron spectroscopy measurement, water contact angle measurement, atomic force microscopy, and thermogravimetric analysis, respectively. The results showed that zwitterionic brushes were successfully fabricated on the CM surfaces, and the content of the grafted layer increased gradually with the polymerization time. The blood compatibility of the CM substrates was evaluated by protein adsorption tests and platelet adhesion tests in vitro. It was found that all the CMs functionalized with zwitterionic brush showed improved resistance to nonspecific protein adsorption and platelet adhesion, even though the grafting polymerization was conducted for several minutes.
Trans-inactivation of the Drosophila brown gene: evidence for transcriptional repression and somatic pairing dependence. (1989)

Position-effect variegation in Drosophila is the variable inactivation of a gene that occurs when it is juxtaposed to heterochromatic regions of chromosomes. The brown gene, required for pteridine pigment in the eye, is unusual in that expression of the unrearranged homolog also is affected. This dominant effect can be very strong, as inactivation is detectable when as many as three trans copies of the gene are present. We show that pteridine reductions coincide with similar reductions in the accumulation of brown mRNA. The dominant effect is suppressed by certain altered structural configurations of the brown region, suggesting that somatic pairing is involved in the phenomenon. We propose that direct transmission of the altered chromatin structure characteristic of position-effect variegation (heterochromatinization) occurs between paired homologs in the region of the brown locus.
Transgene-Free Disease-Specific Induced Pluripotent Stem Cells from Patients with Type 1 and Type 2 Diabetes (2012)

The induced pluripotent stem cell (iPSC) technology enables derivation of patient-specific pluripotent stem cells from adult somatic cells without using an embryonic cell source. Redifferentiation of iPSCs from diabetic patients into pancreatic islets will allow patient-specific disease modeling and autologous cell replacement therapy for failing islets. To date, diabetes-specific iPSCs have been generated from patients with type 1 diabetes using integrating retroviral vectors. However, vector integration into the host genome could compromise the biosafety and differentiation propensities of derived iPSCs. Although various integration-free reprogramming systems have been described, their utility to reprogram somatic cells from patients remains largely undetermined. Here, we used nonintegrating Sendai viral vectors to reprogram cells from patients with type 1 and type 2 diabetes (T2D). Sendai vector infection led to reproducible generation of genomic modification-free iPSCs (SV-iPSCs) from patients with diabetes, including an 85-year-old individual with T2D. SV-iPSCs lost the Sendai viral genome and antigens within 8-12 passages while maintaining pluripotency. Genome-wide transcriptome analysis of SV-iPSCs revealed induction of endogenous pluripotency genes and downregulation of genes involved in the oxidative stress response and the INK4/ARF pathways, including p16(INK4a), p15(INK4b), and p21(CIP1). SV-iPSCs and iPSCs made with integrating lentiviral vectors demonstrated remarkable similarities in global gene expression profiles. Thus, the Sendai vector system facilitates reliable reprogramming of patient cells into transgene-free iPSCs, providing a pluripotent platform for personalized diagnostic and therapeutic approaches for diabetes and diabetes-associated complications.
Reinforcing Epoxy Polymer Composites Through Covalent Integration of Functionalized Nanotubes (2004)

Abstract Strong interfacial bonding and homogenous dispersion have been found to be necessary conditions to take full advantage of the extraordinary properties of nanotubes for reinforcement of composites. We have developed a fully integrated nanotube composite material through the use of functionalized single‐walled carbon nanotubes (SWNTs). The functionalization was performed via the reaction of terminal diamines with alkylcarboxyl groups attached to the SWNTs in the course of a dicarboxylic acid acyl peroxide treatment. Nanotube‐reinforced epoxy polymer composites were prepared by dissolving the functionalized SWNTs in organic solvent followed by mixing with epoxy resin and curing agent. In this hybrid material system, nanotubes are covalently integrated into the epoxy matrix and become part of the crosslinked structure rather than just a separate component. Results demonstrated dramatic enhancement in the mechanical properties of an epoxy polymer material, for example, 30–70 % increase in ultimate strength and modulus with the addition of only small quantities (1–4 wt.‐%) of functionalized SWNTs. The nanotube‐reinforced epoxy composites also exhibited an increased strain to failure, which suggests higher toughness.
Regulation of the Human Enkephalin Promoter by Two Isoforms of the Catalytic Subunit of Cyclic Adenosine 3′,5′-Monophosphate-Dependent Protein Kinase (1991)

Cyclic AMP regulates a variety of cellular responses through activation of the catalytic subunit of cAMP-dependent protein kinase. The cDNAs for two protein isoforms of the catalytic subunit, C alpha and C beta, were placed into expression vectors, and their ability to stimulate cAMP-dependent transcription of the human enkephalin promoter was examined in transiently transfected CV-1 cells. Expression vectors for C alpha and C beta that were directed by the human cytomegalovirus promoter produced up to 350- and 200-fold increases in chloramphenicol acetyltransferase activity, respectively, when cotransfected with the ENKAT-12 reporter plasmid. Transcriptional activation was shown to be dependent upon functional kinase activity by point mutations in catalytic subunit vectors which eliminated activation. Transcriptional activation by C alpha and C beta was eliminated when the cAMP response elements (CREs) were deleted from the native enkephalin promoter, but activation was recovered when this region was replaced with an oligonucleotide containing two copies of the somatostatin CRE consensus TGACGTCA. C alpha expression vectors were found to produce 2-fold greater transcriptional activation than C beta expression vectors. These results were most likely due to the cellular kinase activity produced by the catalytic subunit expression vectors and did not appear to be dependent on CRE motif or substrate specificity. In vitro mutagenesis indicates that neither C alpha nor C beta requires N-terminal myristylation for transcriptional activation, but threonine-197 is critical to subunit function.
Discovery of Novel Inhibitors Targeting the Menin-Mixed Lineage Leukemia Interface Using Pharmacophore- and Docking-Based Virtual Screening (2016)

Disrupting the interaction between mixed lineage leukemia (MLL) fusion protein and menin provides a therapeutic approach for MLL-mediated leukemia. Here, we aim to discover novel inhibitors targeting the menin-MLL interface with virtual screening. Both structure-based molecular docking and ligand-based pharmacophore models were established, and the models used for compound screening show a remarkable ability to retrieve known active ligands from decoy molecules. Verified by a fluorescence polarization assay, five hits with novel scaffolds were identified. Among them, DCZ_M123 exhibited potent inhibitory activity with an IC50 of 4.71 ± 0.12 μM and a KD of 14.70 ± 2.13 μM, and it can effectively inhibit the human MLL-rearranged leukemia cells MV4;11 and KOPN8 with GI50 values of 0.84 μM and 0.54 μM, respectively.
Convergence-provable statistical timing analysis with level-sensitive latches and feedback loops (2006)

Statistical timing analysis has been widely applied to predict the timing yield of VLSI circuits when process variations become significant. Existing statistical latch timing methods are either having exponential complexity or unable to treat the random variable's self-dependence caused by the coexistence of level-sensitive latches and feedback loops.In this paper, an efficient iterative statistical timing algorithm with provable convergence is proposed for latch-based circuits with feedback loops. Based on a new notion of iteration mean, we prove that the algorithm converges unconditionally. Moreover, we show that the converged value of iteration mean can be used to predict the circuit yield during design time. Tested by ISCAS'89 benchmark circuits, the proposed algorithm shows an error of 1.1% and speedup of 303 x on average when compared with the Monte Carlo simulation.
Tea Catechin Supplementation Increases Antioxidant Capacity and Prevents Phospholipid Hydroperoxidation in Plasma of Humans (1999)

The effect of green tea catechin supplementation on antioxidant capacity of human plasma was investigated. Eighteen healthy male volunteers who orally ingested green tea extract (254 mg of total catechins/subject) showed 267 pmol of epigallocatechin-3-gallate (EGCg) per milliliter of plasma at 60 min after administration. The plasma phosphatidylcholine hydroperoxide (PCOOH) levels attenuated from 73.7 pmol/mL in the control to 44.6 pmol/mL in catechin-treated subjects, being correlated inversely with the increase in plasma EGCg level. The results suggested that drinking green tea contributes to prevent cardiovascular disease by increasing plasma antioxidant capacity in humans.
RNA-Guided RNA modification: functional organization of the archaeal H/ACA RNP (2005)

In eukaryotes and archaea, uridines in various RNAs are converted to pseudouridines by RNA-guided RNA modification complexes termed H/ACA RNPs. Guide RNAs within the complexes base-pair with target RNAs to direct modification of specific ribonucleotides. Cbf5, a protein component of the complex, likely catalyzes the modification. However, little is known about the organization of H/ACA RNPs and the roles of the multiple proteins thought to comprise the complexes. We have reconstituted functional archaeal H/ACA RNPs from recombinant components, defined the components necessary and sufficient for function, and determined the direct RNA-protein and protein-protein interactions that occur between the components. The results provide substantial insight into the functional organization of this RNP. The functional complex requires a guide RNA and each of four proteins: Cbf5, Gar1, L7Ae, and Nop10. Two proteins interact directly with the guide RNA: L7Ae and Cbf5. L7Ae does not interact with other H/ACA RNP proteins in the absence of the RNA. We have defined two novel functions for Cbf5. Cbf5 is the protein that specifically recognizes and binds H/ACA guide RNAs. In addition, Cbf5 recruits the two other essential proteins, Gar1 and Nop10, to the pseudouridylation guide complex.
Acetylation of lysine 40 in alpha-tubulin is not essential in Tetrahymena thermophila. (1995)

In Tetrahymena, at least 17 distinct microtubule structures are assembled from a single primary sequence type of alpha- and beta-tubulin heterodimer, precluding distinctions among microtubular systems based on tubulin primary sequence isotypes. Tetrahymena tubulins also are modified by several types of posttranslational reactions including acetylation of alpha-tubulin at lysine 40, a modification found in most eukaryotes. In Tetrahymena, axonemal alpha-tubulin and numerous other microtubules are acetylated. We completely replaced the single type of alpha-tubulin gene in the macronucleus with a version encoding arginine instead of lysine 40 and therefore cannot be acetylated at this position. No acetylated tubulin was detectable in these transformants using a monoclonal antibody specific for acetylated lysine 40. Surprisingly, mutants lacking detectable acetylated tubulin are indistinguishable from wild-type cells. Thus, acetylation of alpha-tubulin at lysine 40 is non-essential in Tetrahymena. In addition, isoelectric focusing gel analysis of axonemal tubulin from cells unable to acetylate alpha-tubulin leads us to conclude that: (a) most or all ciliary alpha-tubulin is acetylated, (b) other lysines cannot be acetylated to compensate for loss of acetylation at lysine 40, and (c) acetylated alpha-tubulin molecules in wild-type cells contain one or more additional charge-altering modifications.
Differential effect of interferon on the expression of tumor-associated antigens and histocompatibility antigens on human melanoma cells: relationship to susceptibility to immune lysis mediated by monoclonal antibodies. (1981)

Incubation of cultured human melanoma cells with human leukocyte interferon did not change the expression of melanoma-associated antigens (MAA) recognized by monoclonal antibodies and of Ia-like antigens but significantly increased the expression of HLA-A,B antigens and of beta 2-microglobulin (beta 2-mu). The effect is dependent on the dose of interferon and on the incubation time. Interferon-treated melanoma cells showed an increased susceptibility to lysis mediated by monoclonal antibodies to HLA-A,B antigens and to human beta 2-mu; on the other hand, interferon-treated melanoma cells did not change in their susceptibility to murine natural killer (NK) cell lysis and to immune lysis mediated by monoclonal antibodies to MAA and to Ia-like antigens, and they displayed a reduced susceptibility to human NK cell lysis. Therefore, the increased susceptibility of interferon-treated melanoma cells to lysis mediated by anti HLA-A,B and anti beta 2-mu monoclonal antibodies is likely to reflect the increase in cell surface expression of the corresponding antigens.
Effect of externally applied skin surface forces on tissue vasculature. (1986)

The effect of surface forces on the morphologic pattern of skin capillaries was examined on the anterior surface of the forearm of healthy volunteers. A rig was designed to permit the application of uniaxial forces between two pads attached to the skin surface. A grid was printed onto the skin surface, and mechanical data are presented in terms of force intensity versus strain. During force application the skin capillaries were monitored using vital capillary microscopy. Mean values of force intensity and strain of 1.33N/mm and 10%, respectively, were sufficient to produce virtual obliteration of the blood flow to the capillaries. A simplified finite element model of the tissue was also employed to illustrate the effect of surface forces at different depths within the tissue. This study emphasizes the potentially damaging effects of surface forces on the integrity of the skin vasculature. If these forces are maintained or repeated, cell necrosis and eventual tissue damage would result.
Menadione is a metabolite of oral vitamin K (2006)

Phylloquinone is converted into menaquinone-4 and accumulates in extrahepatic tissues. Neither the route nor the function of the conversion is known. One possible metabolic route might be the release of menadione from phylloquinone by catabolic activity. In the present study we explored the presence of menadione in urine and the effect of vitamin K intake on its excretion. Menadione in urine was analysed by HPLC assay with fluorescence detection. Urine from healthy male volunteers was collected before and after administration of a single dose of K vitamins. Basal menadione excretion in non-supplemented subjects (n 6) was 5.4 (sd 3.2) microg/d. Urinary menadione excretion increased greatly after oral intake of the K vitamins, phylloquinone and menaquinone-4 and -7. This effect was apparent within 1-2 h and peaked at about 3 h after intake. Amounts of menadione excreted in 24 h after vitamin K intake ranged, on a molar basis, from 1 to 5 % of the administered dose, indicating that about 5-25 % of the ingested K vitamins had been catabolized to menadione. Menadione excretion was not enhanced by phylloquinone administered subcutaneously or by 2',3'-dihydrophylloquinone administered orally. In archived samples from a depletion/repletion study (Booth et al. (2001) Am J Clin Nutr 74, 783-790), urinary menadione excretion mirrored dietary phylloquinone intake. The present study shows that menadione is a catabolic product of K vitamins formed after oral intake. The rapid appearance in urine after oral but not subcutaneous administration suggests that catabolism occurs during intestinal absorption. The observations make it likely that part of the menaquinone-4 in tissues results from uptake and prenylation of circulating menadione.
CU Partition Mode Decision for HEVC Hardwired Intra Encoder Using Convolution Neural Network (2016)

The intensive computation of High Efficiency Video Coding (HEVC) engenders challenges for the hardwired encoder in terms of the hardware overhead and the power dissipation. On the other hand, the constrains in hardwired encoder design seriously degrade the efficiency of software oriented fast coding unit (CU) partition mode decision algorithms. A fast algorithm is attributed as VLSI friendly, when it possesses the following properties. First, the maximum complexity of encoding a coding tree unit (CTU) could be reduced. Second, the parallelism of the hardwired encoder should not be deteriorated. Third, the process engine of the fast algorithm must be of low hardware- and power-overhead. In this paper, we devise the convolution neural network based fast algorithm to decrease no less than two CU partition modes in each CTU for full rate-distortion optimization (RDO) processing, thereby reducing the encoder's hardware complexity. As our algorithm does not depend on the correlations among CU depths or spatially nearby CUs, it is friendly to the parallel processing and does not deteriorate the rhythm of RDO pipelining. Experiments illustrated that, an averaged 61.1% intraencoding time was saved, whereas the Bjøntegaard-Delta bit-rate augment is 2.67%. Capitalizing on the optimal arithmetic representation, we developed the high-speed [714 MHz in the worst conditions (125 °C, 0.9 V)] and low-cost (42.5k gate) accelerator for our fast algorithm by using TSMC 65-nm CMOS technology. One accelerator could support HD1080p at 55 frames/s real-time encoding. The corresponding power dissipation was 16.2 mW at 714 MHz. Finally, our accelerator is provided with good scalability. Four accelerators fulfill the throughput requirements of UltraHD-4K at 55 frames/s.
Intranasal Drug Delivery (1993)

The intranasal administration of drugs is a promising alternative to parenteral administration. The nasal route represents an interesting alternative for drugs which have low oral bioavailability because of degradation in GI tract or extensive mucosal or first-pass metabolism. Enzymatic deactivation is a major problem for drugs of polypeptide nature. Thus, the nasal route with low enzymatic activity and highly vascular tissue with good blood flow may be an effective alternative to the injection of these drugs. Small molecules are almost completely absorbed through the nasal membrane. The absorption of larger size molecules may be achieved by increasing the amount of drug delivered, by reducing mucociliary clearance and/or by coadministration of selected non-toxic permeation enhancers. Due to its accessibilty and excellent patient acceptability, as well as being familiar to population at large, the nasal route seems to be especially interesting for the delivery of peptides and those drugs that must demonstrate immediate therapeutic activity.
Optical tweezers applied to a microfluidic system (2004)

We will demonstrate how optical tweezers can be combined with a microfluidic system to create a versatile microlaboratory. Cells are moved between reservoirs filled with different media by means of optical tweezers. We show that the cells, on a timescale of a few seconds, can be moved from one reservoir to another without the media being dragged along with them. The system is demonstrated with an experiment where we expose E. coli bacteria to different fluorescent markers. We will also discuss how the system can be used as an advanced cell sorter. It can favorably be used to sort out a small fraction of cells from a large population, in particular when advanced microscopic techniques are required to distinguish various cells. Patterns of channels and reservoirs were generated in a computer and transferred to a mask using either a sophisticated electron beam technique or a standard laser printer. Lithographic methods were applied to create microchannels in rubber silicon (PDMS). Media were transported in the channels using electroosmotic flow. The optical system consisted of a combined confocal and epi-fluorescence microscope, dual optical tweezers and a laser scalpel.
FREAK: Fast Retina Keypoint (2012)

A large number of vision applications rely on matching keypoints across images. The last decade featured an arms-race towards faster and more robust keypoints and association algorithms: Scale Invariant Feature Transform (SIFT)[17], Speed-up Robust Feature (SURF)[4], and more recently Binary Robust Invariant Scalable Keypoints (BRISK)[I6] to name a few. These days, the deployment of vision algorithms on smart phones and embedded devices with low memory and computation complexity has even upped the ante: the goal is to make descriptors faster to compute, more compact while remaining robust to scale, rotation and noise. To best address the current requirements, we propose a novel keypoint descriptor inspired by the human visual system and more precisely the retina, coined Fast Retina Keypoint (FREAK). A cascade of binary strings is computed by efficiently comparing image intensities over a retinal sampling pattern. Our experiments show that FREAKs are in general faster to compute with lower memory load and also more robust than SIFT, SURF or BRISK. They are thus competitive alternatives to existing keypoints in particular for embedded applications.