gebhart/patrepeval huggingface dataset:
Update on the glomerular filtration barrier (2009)

We suggest viewing the GFB as a dynamic rather than as a rigid barrier, requiring three healthy layers and a hemodynamic steady state. Multiple challenges to studying the endothelium, the tubular handling of albumin, and the role of hemodynamic forces will require new tools, new hypotheses, and open minds.
Unsupervised Visual-Linguistic Reference Resolution in Instructional Videos (2017)

We propose an unsupervised method for reference resolution in instructional videos, where the goal is to temporally link an entity (e.g., dressing) to the action (e.g., mix yogurt) that produced it. The key challenge is the inevitable visual-linguistic ambiguities arising from the changes in both visual appearance and referring expression of an entity in the video. This challenge is amplified by the fact that we aim to resolve references with no supervision. We address these challenges by learning a joint visual-linguistic model, where linguistic cues can help resolve visual ambiguities and vice versa. We verify our approach by learning our model unsupervisedly using more than two thousand unstructured cooking videos from YouTube, and show that our visual-linguistic model can substantially improve upon state-of-the-art linguistic only model on reference resolution in instructional videos.
Novel polysilicon/TiN stacked-gate structure for fully-depleted SOI/CMOS (1992)

Fully-depleted SOI/CMOS transistors were fabricated using titanium-nitride (TiN) gates with near midgap work-function in order to optimize the p- and n-channel threshold voltages for operation at low supply voltage. To simplify the process as well as to minimize the strain, a novel gate structure was used in which a thick polysilicon (300 nm) was stacked on a thin TiN layer (<50 nm). Excellent symmetrical subthreshold characteristics were obtained with relatively low values of threshold voltage and low off-state leakages. The subthreshold swing, transconductance, and saturation drain current were comparable with those for conventional n/sup +//p/sup +/ polysilicon gates. In addition, hot-carrier stress results indicate no significant differences from the poly-gate cases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
THE ACTION OF HYDROXYLAMINE, ITS O-METHYL ETHER, AND THEIR HYDROCHLORIDES ON CELLULOSE TRINITRATE IN PYRIDINE (1952)

Solution of cellulose trinitrate in dry pyridine containing an excess of hydroxylamine base caused the evolution of 1 mole of nitrogen gas of 99% purity and the formation in high yield of a fibrous cellulose substituted with 1.7 nitrate and about 0.08 oxime groups per glucose unit. The replacement of the hydroxylamine by o-methylhydroxylamine suppressed the evolution of gas in the above reaction but the product was similar except for a small substitution (about 0.2) of methyloxime groups. Replacement of hydroxylamine base by the hydrochloride altered the composition of the evolved gas to nitrous oxide, about 85%, and nitrogen, about 15%. The fibrous product, isolated in high yield, had the composition of a cellulose substituted with 1.7 nitrate and about 1 oxime groups. No gas was produced in the parallel experiments with o-methylhydroxylamine hydrochloride and the product contained 1 methyloxime instead of 1 oxime unit.The above partial denitrations involved only an incidental degradation of the cellulose trinitrate, and probably only nitrate groups in the second, or third, rather than the sixth, positions of the glucose residues. All four products had a. wide solubility in organic liquids and were remarkable for their relatively great stability toward pyridine or caustic soda.
Actin dynamics in living mammalian cells (1998)

The actin cytoskeleton maintains the cellular architecture and mediates cell movements. To explore actin cytoskeletal dynamics, the enhanced green fluorescent protein (EGFP) was fused to human &bgr ;-actin. The fusion protein was incorporated into actin fibers which became depolymerized upon cytochalasin B treatment. This functional EGFP-actin construct enabled observation of the actin cytoskeleton in living cells by time lapse fluorescence microscopy. Stable expression of the construct was obtained in mammalian cell lines of different tissue origins. In stationary cells, actin rich, ring-like structured 'actin clouds' were observed in addition to stress fibers. These ruffle-like structures were found to be involved in the reorganization of the actin cytoskeleton. In migratory cells, EGFP-actin was found in the advancing lamellipodium. Immobile actin spots developed in the lamellipodium and thin actin fibers formed parallel to the leading edge. Thus EGFP-actin expressed in living cells unveiled structures involved in the dynamics of the actin cytoskeleton.
Carbohydrate Binding Specificity of the Neutrophil-activating Protein of Helicobacter pylori (1997)

The possible interaction of the neutrophil-activating protein of Helicobacter pylori with target cell glycoconjugates was investigated by the binding of 125I-labeled recombinant protein to glycosphingolipids from human neutrophils in solid phase assays. Thereby, a distinct binding of the neutrophil-activating protein to four bands in the acid glycosphingolipid fraction from human neutrophils was detected, whereas no binding to the non-acid glycosphingolipids or polyglycosyl ceramides from these cells was obtained. When using glycosphingolipids not present in the cell membrane of human neutrophils, it was found that the neutrophil-activating protein also bound to sulfated glycosphingolipids as sulfatide and sulfated gangliotetraosyl ceramide. Comparison of the binding preferences of the protein to reference glycosphingolipids from other sources suggested that in human granulocytes, the neutrophil-activating protein of H. pylori preferentially recognizes glycoconjugates with a terminally unsubstituted NeuAcalpha3Galbeta4GlcNAcbeta3Galbeta4GlcNAcbeta sequence.
Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China (2009)

The high incidence of lung cancer in Xuanwei County, China has been attributed to exposure to indoor smoky coal emissions that contain polycyclic aromatic hydrocarbons (PAHs). The inflammatory response induced by coal smoke components may promote lung tumor development. We studied the association between single nucleotide polymorphisms (SNPs) in genes involved in innate immunity and lung cancer risk in a population-based case-control study (122 cases and 122 controls) in Xuanwei. A total of 1,360 tag SNPs in 149 gene regions were included in the analysis. FCER2 rs7249320 was the most significant SNP (OR: 0.30; 95% CI: 0.16-0.55; P: 0.0001; false discovery rate value, 0.13) for variant carriers. The gene regions ALOX12B/ALOX15B and KLK2 were associated with increased lung cancer risk globally (false discovery rate value <0.15). In addition, there were positive interactions between KLK15 rs3745523 and smoky coal use (OR: 9.40; P-interaction = 0.07) and between FCER2 rs7249320 and KLK2 rs2739476 (OR: 10.77; P-interaction = 0.003). Our results suggest that genetic polymorphisms in innate immunity genes may play a role in the genesis of lung cancer caused by PAH-containing coal smoke. Integrin/receptor and complement pathways as well as IgE regulation are particularly noteworthy.
Development framework for firewall processors (2003)

High-performance firewalls can benefit from the increasing size, speed and flexibility of advanced reconfigurable hardware. However direct translation of conventional firewall rules in a router-based rule set often leads to inefficient hardware implementation. Moreover, such lowlevel description of firewall rules tends to be difficult to manage and to extend. We describe a framework, based on the high-level policy specification language Ponder for capturing firewall rules as authorization policies with user-definable constraints. Our framework supports optimisations to achieve efficient utilisation of hardware resources. A pipelined firewall implementation developed using this approach running at 10 MHz is capable of processing 2.5 million packets per second, which provides similar performance to a version without optimisation and is about 50 times faster than a software implementation running on a 700 MHz PIII processor.
Finite element analyses of uniform current density electrodes for radio-frequency cardiac ablation (2000)

The high current density at the edge of a metal electrode causes hot spots, which can lead to charring or blood coagulation formation during radio-frequency (RF) cardiac ablation. We used finite element analysis to predict the current density distribution created by several electrode designs for RF ablation. The numerical results demonstrated that there were hot spots at the edge of the conventional tip electrode and the insulating catheter. By modifying the shape of the edge of the 5-mm tip electrode, we could significantly reduce the high current density at the electrode-insulator interface. We also studied the current density distribution produced by a cylindrically shaped electrode. We modified the shape of a cylindrical electrode by recessing the edge and filled in a coating material so that the overall structure was still cylindrical. We analyzed the effects of depth of recess and the electrical conductivity of the added material. The results show that more uniform current density can be accomplished by recessing the electrode, adding a curvature to the electrode, and by coating the electrode with a resistive material.
Regulation of mRNA Translation and Stability by microRNAs (2010)

MicroRNAs (miRNAs) are small noncoding RNAs that extensively regulate gene expression in animals, plants, and protozoa. miRNAs function posttranscriptionally by usually base-pairing to the mRNA 3'-untranslated regions to repress protein synthesis by mechanisms that are not fully understood. In this review, we describe principles of miRNA-mRNA interactions and proteins that interact with miRNAs and function in miRNA-mediated repression. We discuss the multiple, often contradictory, mechanisms that miRNAs have been reported to use, which cause translational repression and mRNA decay. We also address the issue of cellular localization of miRNA-mediated events and a role for RNA-binding proteins in activation or relief of miRNA repression.
MAgent: A Many-Agent Reinforcement Learning Platform for Artificial Collective Intelligence (2017)

We introduce MAgent, a platform to support research and development of many-agent reinforcement learning. Unlike previous research platforms on single or multi-agent reinforcement learning, MAgent focuses on supporting the tasks and the applications that require hundreds to millions of agents. Within the interactions among a population of agents, it enables not only the study of learning algorithms for agents' optimal polices, but more importantly, the observation and understanding of individual agent's behaviors and social phenomena emerging from the AI society, including communication languages, leaderships, altruism. MAgent is highly scalable and can host up to one million agents on a single GPU server. MAgent also provides flexible configurations for AI researchers to design their customized environments and agents. In this demo, we present three environments designed on MAgent and show emerged collective intelligence by learning from scratch.
Long-Term Culture of Purified Postnatal Oligodendrocyte Precursor Cells (2000)

Oligodendrocytes myelinate axons in the vertebrate central nervous system (CNS). They develop from precursor cells (OPCs), some of which persist in the adult CNS. Adult OPCs differ in many of their properties from OPCs in the developing CNS. In this study we have purified OPCs from postnatal rat optic nerve and cultured them in serum-free medium containing platelet-derived growth factor (PDGF), the main mitogen for OPCs, but in the absence of thyroid hormone in order to inhibit their differentiation into oligodendrocytes. We find that many of the cells continue to proliferate for more than a year and progressively acquire a number of the characteristics of OPCs isolated from adult optic nerve. These findings suggest that OPCs have an intrinsic maturation program that progressively changes the cell's phenotype over many months. When we culture the postnatal OPCs in the same conditions but with the addition of basic fibroblast growth factor (bFGF), the cells acquire these mature characteristics much more slowly, suggesting that the combination of bFGF and PDGF, previously shown to inhibit OPC differentiation, also inhibits OPC maturation. The challenge now is to determine the molecular basis of such a protracted maturation program and how the program is restrained by bFGF.
Publishing flow cytometry data (2009)

Cellular measurements by flow cytometric analysis constitute an important step toward understanding individual attributes within a population of cells. Assessing individual cells within a population by protein expression using fluorescently labeled antibodies and other fluorescent probes can identify cellular patterns. The technology for accurately identifying subtle changes in protein expression within a population of cells using a vast array of technology has resulted in controversy and questions regarding reproducibility, which can be explained at least in part by the absence of standard methods to facilitate comparison of flow cytometric data. The complexity of technological advancements and the need for improvements in biological resolution results in the generation of complex data that demands the use of minimum standards for their publication. Herein we present a summarized view for the inclusion of consistent flow cytometric experimental information as supplemental data. Four major points, experimental and sample information, data acquisition, analysis, and presentation are emphasized. Together, these guidelines will facilitate the review and publication of flow cytometry data that provide an accurate foundation for ongoing studies with this evolving technology.
Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation (2007)

AU-rich elements (AREs) and microRNA target sites are conserved sequences in messenger RNA (mRNA) 3' untranslated regions (3'UTRs) that control gene expression posttranscriptionally. Upon cell cycle arrest, the ARE in tumor necrosis factor-alpha (TNFalpha) mRNA is transformed into a translation activation signal, recruiting Argonaute (AGO) and fragile X mental retardation-related protein 1 (FXR1), factors associated with micro-ribonucleoproteins (microRNPs). We show that human microRNA miR369-3 directs association of these proteins with the AREs to activate translation. Furthermore, we document that two well-studied microRNAs-Let-7 and the synthetic microRNA miRcxcr4-likewise induce translation up-regulation of target mRNAs on cell cycle arrest, yet they repress translation in proliferating cells. Thus, activation is a common function of microRNPs on cell cycle arrest. We propose that translation regulation by microRNPs oscillates between repression and activation during the cell cycle.
Ricin: structure, mode of action, and some current applications (1994)

Ricin is an abundant protein component of Ricinus communis seeds (castor beans) that is exquisitely toxic to mammalian cells. It consists of an enzymic polypeptide that catalyzes the N-glycosidic cleavage of a specific adenine residue from 28S ribosomal RNA, joined by a single disulfide bond to a galactose (cell)-binding lectin. The enzymatic activity renders ribosomes containing depurinated 28S RNA incapable of protein synthesis. The bipartite molecular structure of ricin allows it to bind to the mammalian cell surface, enter via endocytic uptake, and deliver the catalytically active polypeptide into the cell cytosol where it irreversibly inhibits protein synthesis causing cell death. Because of its cytotoxic potency, modified ricin is being used for the selective killing of unwanted cells and for the toxigenic ablation of cell lineages in transgenic organisms.
The use of botulinum toxin type A in spastic diplegia due to cerebral palsy (1999)

Spastic diplegia is a severely disabling condition and many current treatment options offer the patient no real therapeutic benefit. Intramuscular injection of botulinum toxin type A (BTX‐A) has demonstrated the ability to decrease spasticity, improve mobility and delay the need for surgery in patients with spastic diplegia. The study described here was a pilot to a larger study and it aimed to identify the most suitable and sensitive outcome measures to detect the benefits of BTX‐A injection. Five adolescents with hip spasticity due to cerebral palsy were injected with BTX‐A into the psoas major muscle (for thigh adduction problems) or the soleus muscle (to correct ‘toe clawing’). Assessments of gait and mobility were carried out every month for the 4‐month study period. Following injection with BTX‐A, improvement in patient mobility was most evident in subjects with thigh adduction problems. A reduction in 10‐m walking time and an increase in stride length was also more pronounced in patients injected in the psoas. Three of the five patients treated demonstrated an improved Modified Ashworth Scale score at the end of the 4‐month observation period. The results conclude that spastic diplegics with problems related to the hip, may benefit from BTX‐A. Patients who experience ‘toe clawing’ present different problems and the measures used did not pick up on the benefits gained by the patients.
<title>Flexible automated assembly of micro-optical elements (optical SMD)</title> (1996)

An automated assembly technique for small optical components has been developed. It concerns components such as, e.g., laser diodes and LEDs, fibers, lenses beamsplitters, polarizers, mirrors, crystals, prisms, diffractive elements or photodiodes. It is based on the flexible 2-dimensional arrangement of a universal tripod holder (10 by 10 by 4 mm) on a planar mounting plate. Its particular mechanical structure allows to align the optical elements on-line and to attach them to the mounting plate in a one step procedure. The different elements are aligned with an accuracy of plus or minus 1 micrometer and attached one after the other. Very good position stability (plus or minus 0.7 micrometer, plus or minus 0.2 mrad) during the attachment procedure has been achieved by laser point welding. They are optically interconnected by free-space propagation of a light beam with diameter of up to 8 millimeters. Mass production has been shown with a collimator as test vehicle. The collimator is composed of two elements (laser diode and collimating lens) and is mounted entirely automatically by two co-working robots. Easy prototyping has been shown with the realization of the optical position sensing system featuring a high precision linear magnetic bearing. Flexibility, simple handling, high packaging density and low cost make this new assembly technique satiable to both mass production and prototyping of small opto electronical devices.
Discrete sequential boundaries for clinical trials (1983)

Pocock (1977), O'Brien & Fleming (1979) and Slud & Wei (1982) have proposed different methods to construct discrete sequential boundaries for clinical trials. These methods require that the total number of decision times be specified in advance. In the present paper, we propose a more flexible way to construct discrete sequential boundaries. The method is based on the choice of a function, α*(t), which characterizes the rate at which the error level α is spent. The boundary at a decision time is determined by α*(t), and by past and current decision times, but does not depend on the future decision times or the total number of decision times.
Relationship of Structure and Biological Activity of Monosaccharide Lipid A Analogues to Induction of Nitric Oxide Production by Murine Macrophage RAW264.7 Cells (1998)

Lipid A is the active center of bacterial lipopolysaccharide (LPS), which exhibits diverse biological activities via the production of various mediators. We investigated the production of nitric oxide (NO), one of the mediators, by a murine macrophage cell line, RAW264. 7, upon stimulation with a series of monosaccharide lipid A analogues to elucidate the relationship of structure and activity in NO production. The production of other representative mediators, such as tumor necrosis factor alpha (TNF-alpha) and interleukin-6 (IL-6), was also investigated to compare the structural requirements for the production of these cytokines with those for the production of NO. Structure-activity relationships in NO production correlated well with those in the production of TNF-alpha and IL-6. Among the lipid A analogues possessing different numbers of acyl groups on a 4-O-phosphono-D-glucosamine backbone, compounds like GLA-60 that possess three tetradecanoyl (C14) groups exhibited stronger activities in the production of the mediators than compounds possessing four or two C14 groups. Time course study of the production of these mediators showed that production of NO started and peaked later than those of TNF-alpha and IL-6. Neither neutralization of TNF-alpha activity by antibody nor suppression of TNF-alpha production by pentoxifylline showed a significant suppressive effect on production of NO and IL-6 upon stimulation with LPS or lipid A analogues. Neutralization of IL-6 activity by antibody showed no significant suppressive effect on production of NO and TNF-alpha. A monosaccharide lipid A analogue (GLA-58) which exhibited no detectable agonistic activity showed a suppressive effect on the production of all three mediators upon stimulation with LPS or lipid A analogues. These results indicate that signals for NO production by LPS agonists in murine macrophages are transduced in good correlation with those for production of TNF-alpha and IL-6, although they are not transduced via production of those cytokines.
Differential role of distinct determinants of intercellular adhesion molecule-1 in immunologic phenomena. (1989)

This study analyzed 1) the relationship between the molecules recognized by anti-intercellular adhesion molecule-1 (ICAM-1) mAb RR 1/1 and by anti-96K melanoma-associated Ag mAb CL203.4 in lymphoid cells, 2) the induction of ICAM-1 on activated PBMC, and 3) the functional activity of distinct and spatially distant determinants recognized by mAb CL203.4 and RR1/1. Sequential immunoprecipitation experiments showed that the determinant recognized by mAb CL203.4 is expressed on a slightly broader population of ICAM-1 molecules than that defined by mAb RR1/1. Serologic and immunochemical assays have shown that ICAM-1 is induced on lymphocytes activated with Con A, PHA-M, IL-2, allogeneic HLA mismatched lymphocytes and autologous PHA-M-activated T cells. However, ICAM-1 was not detected on lymphocytes incubated with IFN-gamma. Incubation of monocytes with LPS induced ICAM-1 in the subpopulation which lacks it and increased its density on the cells which express it. Induction of ICAM-1 is an early event in the activation process and precedes the appearance of IL-2 and transferrin receptors. Comparison of the functional activity of the anti-ICAM-1 mAb CL203.4 and RR1/1 showed that both of them inhibit to a similar extent proliferation of lymphocytes stimulated with PHA-M and with allogeneic lymphocytes, but that only mAb RR1/1 inhibits PMA-induced aggregation of cultured B lymphoid cells JY, of promonocytic cells U-937 and of PHA-blasts as well as LAK cell-mediated cytotoxicity of target cells. mAb CL203.4 represents the first example of anti-ICAM-1 mAb without inhibitory effect on the aggregation of lymphoid cells. The differential functional activity of mAb CL203.4 and RR1/1 does not reflect differences in their affinity, because they display a similar affinity constant to lymphoid cells. These results suggest that distinct determinants of ICAM-1 play a different role in immunologic phenomena.