gebhart/patrepeval huggingface dataset:
Regulation of hepcidin transcription by interleukin-1 and interleukin-6 (2005)

Hepcidin is a peptide that regulates iron homeostasis by inhibiting iron absorption by the small intestine and release of iron from macrophages. Its production is stimulated by iron overload and by inflammation. It has been suggested that IL-6 is the only cytokine that stimulates hepcidin transcription. However, mice with targeted disruption of the gene encoding IL-6 (IL-6-/-) respond to endotoxin by increasing the expression of hepcidin transcripts in the liver. We show that incubating murine hepatocytes with IL-6, IL-1alpha, and IL-1beta strongly stimulates hepcidin transcription. IL-10 has little or no stimulatory effect, and IFN-beta inhibits transcription of hepcidin. All of the hepcidin stimulatory activity of macrophages from IL-6-/- mice can be accounted for by IL-1 that they secrete. Hepatocytes from IL-6-/- mice, hfe-/- mice, and mice with a hypomorphic transferrin receptor 2 mutation responded to IL-6 and IL-1 by up-regulating hepcidin transcription. Nitric oxide does not seem to be involved in the stimulation of hepcidin transcription by cytokines: aminoguanidine does not inhibit the stimulation of hepcidin transcription by cytokines. IL-1 may play a significant role in the anemia of inflammation by up-regulating hepcidin.
Functional Improvement of Infarcted Heart by Co-Injection of Embryonic Stem Cells with Temperature-Responsive Chitosan Hydrogel (2008)

Transplantation of embryonic stem cells (ESCs) can improve cardiac function in treatment of myocardial infarction. The low rate of cell retention and survival within the ischemic tissues makes the application of cell transplantation techniques difficult. In this study, we used a temperature-responsive chitosan hydrogel (as scaffold) combined with ESCs to maintain viable cells in the infarcted tissue. Temperature-responsive chitosan hydrogel was prepared and injected into the infarcted heart wall of rat infarction models alone or together with mouse ESCs. The result showed that the 24-h cell retention and 4 week graft size of both groups was significantly greater than with a phosphate buffered saline control. After 4 weeks of implantation, heart function, wall thickness, and microvessel densities within the infarct area improved in the chitosan + ESC, chitosan, and ESC group more than the PBS control. Of the three groups, the chitosan + ESC performed best. Results of this study indicate that temperature-responsive chitosan hydrogel is an injectable scaffold that can be used to deliver stem cells to infarcted myocardium. It can also increase cell retention and graft size. Cardiac function is well preserved, too.
The Enigmatic Escherichia coli fadE Gene Is yafH (2002)

The identity of the gene encoding acyl coenzyme A dehydrogenase is a major remaining mystery of the Escherichia coli fatty acid degradation (fad) regulon. Our prior genome array analyses showed that transcription of the yafH gene is controlled by the FadR regulatory protein. We now report direct experimental proof that yafH and fadE are the same gene.
NK1.1+ CD4+ T cells lose NK1.1 expression upon in vitro activation (1997)

NK1.1+ CD4+ T cells produce IL-4 promptly in vivo upon injection of anti-CD3 and may play a role in initiating Th2 cell-mediated immunity. To characterize their in vitro activation properties, NK1.1+ CD4+ T cells were obtained in high purity from spleens of normal C57BL/6 mice, where they represent 2 to 5% of CD4+ T cells, or from MHC-class II I-Ab gene knockout mice, where they constitute 42% of CD4+ T cells. Activation of NK1.1+ CD4+ T cells from either source with plate-bound anti-CD3 resulted in loss of expression of NK1.1 as determined both by flow cytometric analysis and by reverse transcriptase-PCR analysis. A portion of these cells also lost CD4 expression. Both the CD4+ and CD4- activated cells retained the over-representation of V beta8 and V alpha14 chains and expressed the intermediate levels of the TCR-CD3 complex that is characteristic of resting NK1.1+ CD4+ T cells. The anti-NK1.1 mAb used for cell sorting was not the cause of NK1.1 or CD4 disappearance, since the sorted cells remain both NK1.1+ and CD4+ when cultured in the absence of anti-CD3 or in the presence of anti-CD3 and cyclosporin A. Furthermore, NK1.1+ CD4+ T cells that were not treated with anti-NK1.1 Ab also lost NK1.1 expression after activation. Populations of activated CD4+ and CD4- cells (derived from NK1.1+ CD4+ T cells) produced both IL-4 and IFN-gamma upon restimulation with plate-bound anti-CD3.
Glycogen Synthase Kinase-3β Inhibitors Prevent Cellular Polyglutamine Toxicity Caused by the Huntington’s Disease Mutation (2002)

Huntington's disease is one of nine known neurodegenerative disorders caused by an expanded polyglutamine (poly(Q)) tract in the disease protein. These diseases are associated with intraneuronal protein aggregates. Heat-inducible chaperones like HSP70 and HSP27 suppress poly(Q) aggregation and/or toxicity/cell death. Heat shock transcription factors, including HSF-1, regulate HSP70 and HSP27 expression. HSF-1 activity is reduced by glycogen synthase kinase-3 (GSK-3) and enhanced by GSK-3 inhibitors, like lithium. Thus, we hypothesized that lithium treatment may partially rescue death in Huntington's disease cell models. LiCl reduced poly(Q) toxicity in neuronal and nonneuronal cell lines, but this was not associated with elevation of HSP70 or HSP27. The protective effect of lithium involved GSK-3beta inhibition, since poly(Q) toxicity was also reduced by SB216763, a GSK-3beta inhibitor, and by overexpression of a dominant-negative GSK-3beta mutant. LiCl and SB216763 increased beta-catenin-dependent T-cell factor-mediated transcription. Since beta-catenin overexpression protected cells from poly(Q) toxicity, we tested whether this pathway was impaired by a poly(Q) expansion mutation. Cells expressing expanded repeats had reduced beta-catenin levels associated with a parallel decrease in T-cell factor-mediated transcription, compared with cells expressing wild type constructs. Since LiCl can protect against polyglutamine toxicity in cell lines, it is an excellent candidate for further in vivo therapeutic trials.
Constructive feedforward ART clustering networks. I (2002)

For pt.I see ibid., p.645-61 (2002). Part I of this paper defines the class of constructive unsupervised on-line learning simplified adaptive resonance theory (SART) clustering networks. Proposed instances of class SART are the symmetric fuzzy ART (S-Fuzzy ART) and the Gaussian ART (GART) network. In Part II of our work, a third network belonging to class SART, termed fully self-organizing SART (FOSART), is presented and discussed. FOSART is a constructive, soft-to-hard competitive, topology-preserving, minimum-distance-to-means clustering algorithm capable of: 1) generating processing units and lateral connections on an example-driven basis and 2) removing processing units and lateral connections on a minibatch basis. FOSART is compared with Fuzzy ART, S-Fuzzy ART, GART and other well-known clustering techniques (e.g., neural gas and self-organizing map) in several unsupervised learning tasks, such as vector quantization, perceptual grouping and 3-D surface reconstruction. These experiments prove that when compared with other unsupervised learning networks, FOSART provides an interesting balance between easy user interaction, performance accuracy, efficiency, robustness, and flexibility.
Intracellular nitric oxide delivery from stable NO-polymeric nanoparticle carriers (2012)

The encapsulation of S-nitrosoglutathione into polymeric nanoparticles substantially improves NO stability in aqueous media without affecting the efficacy of intracellular delivery. The combination of nano-NO delivery and chemotherapy has been found to enhance antitumour activity of chemotherapeutics, as demonstrated using preliminary in vitro experiments with neuroblastoma cells.
Mobility Anisotropy of Electrons in Inversion Layers on Oxidized Silicon Surfaces (1971)

Measurements of the field-effect mobility of electrons in $n$-type inversion layers of Si as functions of the crystalline orientation of the surface and of the azimuthal direction of the current path within the layers are reported. Significant mobility anisotropy observed over a range of strong electric fields perpendicular to the surface at temperatures from 77 to 320 \ifmmode^\circ\else\textdegree\fi{}K contrasts substantially with that in the case of $p$-type inversion layers reported previously. The anisotropy at room temperature can be successfully interpreted in terms of the effective-mass anisotropy calculated on the basis of Stern and Howard's formula for the two-dimensional carriers. For a full understanding of the experimental results, particularly at low temperatures, theoretical investigations including the anisotropy of the relaxation time are required, but have not been explored enough. Extensive data on the dependences of the mobility on the electric field and temperature as well as bulk-acceptor concentration are presented and discussed in the light of existing scattering theories. Some hole-mobility data are included for comparison.
Single-layer fanout routing and routability analysis for Ball Grid Arrays (1995)

Fanout routing for Ball Grid Array (BGA) packages becomes non-trivial when the I/O pin count increases. When the number of I/Os gets larger and larger, the number of I/Os we can put on a package may not be limited by the available area but sometimes by the ability to fan them out on the next level of interconnect-the PCB or MCM substrate. This paper presents an efficient algorithm (EVENFANOUT) which generates the optimal uniform distribution of wires. We have found the three cuts that is decisive on the routability of the package using EVENFANOUT. These decisive cuts form the base for design optimization of the package.
The Tyrosine Phosphatase PTP1C Associates with Vav, Grb2, and mSos1 in Hematopoietic Cells (1996)

The association of the murine motheaten phenotype of severe hemopoietic dysregulation with loss of PTP1C tyrosine phosphatase activity indicates a critical role for this SH2 domain-containing phosphotyrosine phosphatase in the regulation of hemopoietic cell growth and differentiation. To explore the molecular basis for PTP1C effects on hematopoiesis, we have investigated the possibility that this enzyme interacts with the product of the Vav proto-oncogene, a putative guanine nucleotide exchange factor expressed exclusively in hemopoietic cells. Our data indicate that PTP1C physically associates with Vav in murine spleen cells and in EL4 T lymphoma and P815 mastocytoma cells, and that this interaction is increased following mitogenic stimulation and the induction of both PTP1C and Vav tyrosine phosphorylation. The results also reveal tyrosine phosphatase activity to be present in Vav immunoprecipitates from stimulated splenic and P815 cells and suggest that a major portion of total cellular PTP1C catalytic activity is associated with Vav. As Vav-associated tyrosine phosphatase activity was not detected in PTP1C-deficient motheaten splenic cells, it appears that PTP1C accounts for most, if not all, Vav-coprecipitable tyrosine phosphatase activity in normal cells. The data also demonstrate the capacity of the Vav SH2 domain alone to bind to PTP1C in activated P815 cells, but suggest a role for the two Vav SH3 domains in enhancing this interaction. In addition, the results reveal PTP1C association with two other molecules implicated in Ras activation, the Grb2 adaptor protein and mSos1, a GTP/GDP exchanger for Ras. PTP1C therefore has the capacity to bind and potentially modulate various signaling effectors involved in activation of Ras or Ras-related proteins, and, accordingly, regulation of Ras activation represents a possible mechanism whereby PTP1C influences hemopoietic cellular responses.
Surface States in the Photoionization of High-Quality CdSe Core/Shell Nanocrystals (2009)

We use electric force microscopy (EFM) to study single nanocrystal photoionization in two classes of high-quality nanocrystals whose exciton luminescence quantum yields approach unity in solution. The CdSe/CdS/ZnS core/shell nanocrystals do not photoionize, while the CdSe/CdS nanocrystals do show substantial photoionization. This verifies the theoretical prediction that the ZnS shell confines the excited electron within the nanocrystal. Despite the high luminescence quantum yield, photoionization varies substantially among the CdSe/CdS nanocrystals. We have studied the nanocrystal photoionization with both UV (396 nm) and green (532 nm) light, and we have found that the magnitude of the charge due to photoionization per absorbed photon is greater for UV excitation than for green excitation. A fraction of the photoionization occurs directly via a "hot electron" process, using trap states that are either on the particle surface, within the ligand sphere, or within the silicon oxide layer. This must occur without relaxation to the thermalized, lowest-energy, emitting exciton. We discuss the occurrence of hot carrier processes that are common to photoionization, luminescence blinking, and the fast transient optical absorption that is associated with multiple exciton generation MEG studies.
Lift Enhancement for Low-Aspect-Ratio Wings with Periodic Excitation (2010)

In an effort to enhance lift on low-aspect-ratio rectangular flat-plate wings in low-Reynolds-number&#13;\npost-stall flows, periodic injection of momentum is considered along the trailing edge in this numerical&#13;\nstudy. The purpose of actuation is not to reattach the flow but to change the dynamics of the wake&#13;\nvortices such that the resulting lift force is increased. Periodic forcing is observed to be effective&#13;\nin increasing lift for various aspect ratios and angles of attack, achieving a similar lift enhancement&#13;\nattained by steady forcing with less momentum input. Through the investigation on the influence of&#13;\nthe actuation frequency, it is also found that there exists a frequency at which the flow locks on to a&#13;\ntime-periodic high-lift state.
Phase I trial of BCL-2 antisense oligonucleotide (G3139) administered by continuous intravenous infusion in patients with advanced cancer. (2002)

BCL-2 antisense therapy is well tolerated. Relative to other dose-finding studies of G3139, fatigue was somewhat more prominent in this study, possibly because of the protracted i.v. infusion schedule of the antisense oligonucleotide. Current randomized trials are using the highest daily dose established in this study given by shorter infusion periods (i.e., 7 mg/kg/day for 5-7 days) to enhance the antitumor activity of standard cytotoxic drugs.
Language and Auditory-verbal Short-term Memory Impairments: Evidence for Common Underlying Processes (1997)

We report an investigation of the short-term memory STM impairments of 15 aphasic subjects whose language profiles varied with respect to the relative involvement of lexical-semantic and phonological processes. On the hypothesis that STM is dependent on capacities intrinsic to language processing, repetition span should vary in conjunction with lexical-semantic and phonological impairment: Specifically, when lexical-semantic processing is impaired, phonological abilities provide primary support to span performance; when phonological processing is impaired, there should be increased reliance on lexical-semantic information. Support for this hypothesis was provided by correlating measures of semantic and phonological abilities with effects of imageability and frequency on repetition performance, and with serial position effects in retrieval of phonemes within a word and words within a string. The data are discussed within the framework of an interactive activation model of language processing.
Rescue of severely affected dystrophin/utrophin-deficient mice through scAAV-U7snRNA-mediated exon skipping (2012)

Duchenne muscular dystrophy (DMD) is a severe neuromuscular disorder caused by mutations in the dystrophin gene that result in the absence of functional protein. Antisense-mediated exon skipping is one of the most promising approaches for the treatment of DMD and recent clinical trials have demonstrated encouraging results. However, antisense oligonucleotide-mediated exon skipping for DMD still faces major hurdles such as extremely low efficacy in the cardiac muscle, poor cellular uptake and relatively rapid clearance from circulation, which means that repeated administrations are required to achieve some therapeutic efficacy. To overcome these limitations, we previously proposed the use of small nuclear RNAs (snRNAs), especially U7snRNA to shuttle the antisense sequences after vectorization into adeno-associated virus (AAV) vectors. In this study, we report for the first time the efficiency of the AAV-mediated exon skipping approach in the utrophin/dystrophin double-knockout (dKO) mouse which is a very severe and progressive mouse model of DMD. Following a single intravenous injection of scAAV9-U7ex23 in dKO mice, near-normal levels of dystrophin expression were restored in all muscles examined, including the heart. This resulted in a considerable improvement of their muscle function and dystrophic pathology as well as a remarkable extension of the dKO mice lifespan. These findings suggest great potential for AAV-U7 in systemic treatment of the DMD phenotype.
Epitope Tag Mapping of the Extracellular and Cytoplasmic Domains of the Rat Parathyroid Hormone (PTH)/PTH-Related Peptide Receptor (1998)

The PTH/PTH-related peptide (PTHrP) receptor is predicted to span the plasma membrane seven times with an amino-terminal extracellular extension and a cytoplasmic carboxyl-terminal tail. To assess this prediction, we inserted 10- or 9-amino acid epitope tags from c-myc or hemophilus influenza hemaglutinin (HA), which are recognized by the monoclonal antibodies 9E10 and 12Ca5, respectively, in different extracellular and cytoplasmic regions of the receptor and examined the immunoreactivity of the epitopes in intact and permeabilized cells. The data show that the epitopes were well tolerated when introduced into the E2 region of the extracellular amino-terminus (E2-myc and E2-HA), in the first extracellular loop (EL1), in the second and third cytoplasmic loops (CL2c and CL3), or in the carboxyl-terminal tail (T-myc). Receptors tagged at these locations were well expressed, bound PTH with high affinity, and increased cAMP accumulation with a good efficiency. Receptors tagged in the second and third extracellular loops (EL2c and EL3c) or the first cytoplasmic loop (CL1c) bound the PTH radioligand with a low affinity, stimulated cAMP accumulation with a low efficiency, and had low expression levels. The receptors tagged on presumed extracellular regions, E2-myc, E2-HA, EL1, EL2c, and EL3c, were readily detected on the surface of intact cells with the monoclonal antibody against the epitope tag. In contrast, receptors tagged with the c-myc epitope in the cytoplasmic loops (CL1c, CL2c, and CL3) or in the carboxyl-terminal tail (T-myc) did not show any 9E10 binding in intact cells. These receptors, however, were well expressed on the cell surface, as detected by the binding of the monoclonal antibody, 12Ca5, to the HA tag that was introduced into the E2 region of these constructs. The c-myc epitopes, however, became accessible after permeabilization of the cell membrane. In conclusion, these data provide experimental evidence for the sidedness of the extracellular and cytoplasmic domains of the PTH/PTHrP receptor.
Upregulating CD4+CD25+FOXP3+ Regulatory T Cells in Pancreatic Lymph Nodes in Diabetic NOD Mice by Adjuvant Immunotherapy (2009)

Our results demonstrated that CFA treatment ameliorates autoimmunity in diabetic NOD mice by up-regulating CD4=CD25+Foxp3+ regulatory T cells and increasing TGF-beta1 production. Exendin-4 enhanced the effect of CFA on reversing diabetes in NOD mice by stimulating beta-cell replication.
A double-edged sword in B-cell-targeted therapy for inflammatory diseases (2009)

Cells of the immune system, including B cells, perform inflammatory functions against microbial invasion, accompanied by anti-inflammatory responses to avoid host damage. B-cell-depletion therapy using anti-CD20 monoclonal antibodies against inflammatory diseases has beneficial or adverse effects depending on the timing and/or microenvironment in which they are used. To achieve effective B-cell-targeted therapy, it is necessary to identify and understand the modes of action of pathogenic and regulatory B cells, which include antibody production, formation of immune complexes, cytokine and chemokine production, cytotoxic killing, lymphoid neogenesis and antigen presentation. B cells interact with multiple cells, including dendritic cells, T cells and natural killer T cells, creating a complex regulatory network. Specific targeting of B-cell subsets and/or their interaction partners might lead to clinical benefits with minimal host damage.
Analise estrutural da regeneração natural em floresta tropical densa na região do Tapajos no estado do Para (2013)

A estrutura da regeneracao natural e analisada em 35 hectares de floresta tropical umida, nao explorada, na Floresta Nacional do Tapajos. A importância do trabalho esta relacionada aos futuros planejamentos de manejo para a floresta alta de terra firme, sem ocorrencia de babacu, no Baixo Tapajos. Todas as plantas existentes no intervalo entre 10 cm de altura e 15 cm de DAP foram medidas e distribuidas em sete classes sociologicas. Determinou-se a composicao floristica, a abundância, e frequencia, a posicao sociologica e o grau de agregacao das especies. Com base na discussao dos resultados concluiu-se que: a composicao floristica e formada por 106 especies pertencentes a 36 familias; exite uma media de dez plantas por especie na populacao; as plantas de 21 especies tem ocorrencia agrupada e de 29 ocorrem distribuidas aleatoriamente na area; as especies mais abundantes na regeneracao natural sao em numero de 20, apresentando uma abundância relativa de 80,17%, sao 19 as especies que ocorrem em todas as parcelas; o numero de plantas e de especie mais importantes na estrutura da regeneracao natural sao aquelas que se apresentam mais abundantes, mais frequentes e de mais alta posicao sociologica relativa.
PointSIFT: A SIFT-like Network Module for 3D Point Cloud Semantic Segmentation (2018)

Recently, 3D understanding research sheds light on extracting features from point cloud directly, which requires effective shape pattern description of point clouds. Inspired by the outstanding 2D shape descriptor SIFT, we design a module called PointSIFT that encodes information of different orientations and is adaptive to scale of shape. Specifically, an orientation-encoding unit is designed to describe eight crucial orientations, and multi-scale representation is achieved by stacking several orientation-encoding units. PointSIFT module can be integrated into various PointNet-based architecture to improve the representation ability. Extensive experiments show our PointSIFT-based framework outperforms state-of-the-art method on standard benchmark datasets. The code and trained model will be published accompanied by this paper.
Empirical Evaluation of Entry and Selection Methods: For Specifying Dates (1988)

Experienced and inexperienced computer users used seven different interaction methods to specify dates of events. Key results were that the three entry methods were faster, more accurate, and preferred over the four selection methods—by both experienced and inexperienced computer users. The rank order of performance with these methods was about the same for both groups. Number of keystrokes required by each method was a good predictor of performance time. For selection tasks, decomposing them into separate fields is advisable.