gebhart/patrepeval huggingface dataset:
Local application of FTY720 to the lung abrogates experimental asthma by altering dendritic cell function (2006)

Airway DCs play a crucial role in the pathogenesis of allergic asthma, and interfering with their function could constitute a novel form of therapy. The sphingosine 1-phosphate receptor agonist FTY720 is an oral immunosuppressant that retains lymphocytes in lymph nodes and spleen, thus preventing lymphocyte migration to inflammatory sites. The accompanying lymphopenia could be a serious side effect that would preclude the use of FTY720 as an antiasthmatic drug. Here we show in a murine asthma model that local application of FTY720 via inhalation prior to or during ongoing allergen challenge suppresses Th2-dependent eosinophilic airway inflammation and bronchial hyperresponsiveness without causing lymphopenia and T cell retention in the lymph nodes. Effectiveness of local treatment was achieved by inhibition of the migration of lung DCs to the mediastinal lymph nodes, which in turn inhibited the formation of allergen-specific Th2 cells in lymph nodes. Also, FTY720-treated DCs were intrinsically less potent in activating naive and effector Th2 cells due to a reduced capacity to form stable interactions with T cells and thus to form an immunological synapse. These data support the concept that targeting the function of airway DCs with locally acting drugs is a powerful new strategy in the treatment of asthma.
Peripherally-Derived BDNF Promotes Regeneration of Ascending Sensory Neurons after Spinal Cord Injury (2008)

Our data suggest that endogenous BDNF in DRG and spinal cord is required for the enhanced regeneration of ascending sensory neurons after conditioning lesion of sciatic nerve and peripherally applied BDNF may have therapeutic effects on the spinal cord injury.
The Gene Expression Program of Prostate Fibroblast Senescence Modulates Neoplastic Epithelial Cell Proliferation through Paracrine Mechanisms (2006)

Abstract The greatest risk factor for developing carcinoma of the prostate is advanced age. Potential molecular and physiologic contributors to the frequency of cancer occurrence in older individuals include the accumulation of somatic mutations through defects in genome maintenance, epigenetic gene silencing, oxidative stress, loss of immune surveillance, telomere dysfunction, chronic inflammation, and alterations in tissue microenvironment. In this context, the process of prostate carcinogenesis can be influenced through interactions between intrinsic cellular alterations and the extrinsic microenvironment and macroenvironment, both of which change substantially as a consequence of aging. In this study, we sought to characterize the molecular alterations that occur during the process of prostate fibroblast senescence to identify factors in the aged tissue microenvironment capable of promoting the proliferation and potentially the neoplastic progression of prostate epithelium. We evaluated three mechanisms leading to cell senescence: oxidative stress, DNA damage, and replicative exhaustion. We identified a consistent program of gene expression that includes a subset of paracrine factors capable of influencing adjacent prostate epithelial growth. Both direct coculture and conditioned medium from senescent prostate fibroblasts stimulated epithelial cell proliferation, 3-fold and 2-fold, respectively. The paracrine-acting proteins fibroblast growth factor 7, hepatocyte growth factor, and amphiregulin (AREG) were elevated in the extracellular environment of senescent prostate fibroblasts. Exogenous AREG alone stimulated prostate epithelial cell growth, and neutralizing antibodies and small interfering RNA targeting AREG attenuated, but did not completely abrogate the growth-promoting effects of senescent fibroblast conditioned medium. These results support the concept that aging-related changes in the prostate microenvironment may contribute to the progression of prostate neoplasia. (Cancer Res 2006; 66(2): 794-802)
The astrocytic transporter SLC7A10 (Asc-1) mediates glycinergic inhibition of spinal cord motor neurons (2016)

SLC7A10 (Asc-1) is a sodium-independent amino acid transporter known to facilitate transport of a number of amino acids including glycine, L-serine, L-alanine, and L-cysteine, as well as their D-enantiomers. It has been described as a neuronal transporter with a primary role related to modulation of excitatory glutamatergic neurotransmission. We find that SLC7A10 is substantially enriched in a subset of astrocytes of the caudal brain and spinal cord in a distribution corresponding with high densities of glycinergic inhibitory synapses. Accordingly, we find that spinal cord glycine levels are significantly reduced in Slc7a10-null mice and spontaneous glycinergic postsynaptic currents in motor neurons show substantially diminished amplitudes, demonstrating an essential role for SLC7A10 in glycinergic inhibitory function in the central nervous system. These observations establish the etiology of sustained myoclonus (sudden involuntary muscle movements) and early postnatal lethality characteristic of Slc7a10-null mice, and implicate SLC7A10 as a candidate gene and auto-antibody target in human hyperekplexia and stiff person syndrome, respectively.
An OspA-Based DNA Vaccine Protects Mice against Infection with Borrelia burgdorferi (1997)

Immunization with recombinant OspA protein of Borrelia burgdorferi protects against experimental Lyme disease. In the present study, mice were injected intramuscularly with plasmid DNA (VR2210) encoding strain B31 OspA. In this vector, the ospA-coding sequence was under transcriptional control of the cytomegalovirus immediate early promoter. For negative and positive controls, mice were immunized with either the plasmid vector without an osp-coding sequence or recombinant OspA protein, respectively. Mice immunized with VR2210 DNA produced OspA-specific antibodies that bound to B. burgdorferi in a whole cell ELISA and inhibited the growth of a homologous strain of B. burgdorferi. Immunization with VR2210 protected mice against challenge with 2 infectious strains of B. burgdorferi, Sh-2-82 and N40. These results indicate that vaccination with plasmid DNA expressing OspA is an efficacious method for providing a protective response against B. burgdorferi infection.
Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd. (1975)

The primary structure of a strong RNA polymerase binding site in the replicative form DNA of phage fd has been determined by direct DNA sequencing. It is: (see article). The molecule contains regions with 2-fold symmetry and sequence homologies to promoter regions from other DNAs. The startpoint of transcription is located in the center of the binding site.
Single-Inductor Multi-Output (SIMO) DC-DC Converters With High Light-Load Efficiency and Minimized Cross-Regulation for Portable Devices (2009)

A load-dependant peak-current control single-inductor multiple-output (SIMO) DC-DC converter with hysteresis mode is proposed. It includes multiple buck and boost output voltages. Owing to the adaptive adjustment of the load-dependant peak-current control technique and the hysteresis mode, the cross-regulation can be minimized. Furthermore, a new delta-voltage generator can automatically switch the operating mode from pulse width modulation (PWM) mode to hysteresis mode, thereby avoiding inductor current accumulation when the total power of the buck output terminals is larger than that of the boost output terminals. The proposed SIMO DC-DC converter was fabricated in TSMC 0.25 mum 2P5M technology. The experimental results show high conversion efficiency at light loads and small cross-regulation within 0.35%. The power conversion efficiency varies from 80% at light loads to 93% at heavy loads.
Inhibition of oncogene product enzyme activity as an approach to cancer chemoprevention. Tyrosine-specific protein kinase inhibition by purpurogallin fromQuercus sp. Nutgall (1999)

Inhibitors of oncogene product enzyme activity were sought as a prescreen for potential cancer chemopreventive agents. Purpurogallin, a polyphenol from Quercus sp. nutgall, was found to inhibit the tyrosine-specific protein kinase of the human erb-b oncogene product (epidermal growth factor receptor) for both autophosphorylation (IC50 = 27.5 microM) and phosphorylation of an exogenous substrate (IC50 = 45.3 microM). An examination of enzyme kinetics indicated that purpurogallin is a competitive inhibitor of both ATP (Ki = 54.9 microM for autophosphorylation, Ki = 33.9 microM for phosphorylation of exogenous substrate) and the tyrosine-containing acceptor substrate poly(glutamate, alanine, tyrosine) 6:3:1 (Ki = 83.7 microM).
Learning to Understand: Incorporating Local Contexts with Global Attention for Sentiment Classification (2017)

Recurrent neural networks have shown their ability to construct sentence or paragraph representations. Variants such as LSTM overcome the problem of vanishing gradients to some degree, thus being able to model long-time dependency. Still, these recurrent based models lack the ability of capturing complex semantic compositions. To address this problem, we propose a model which can incorporate local contexts with the guide of global context attention. Both the local and global contexts are obtained through LSTM networks. The working procedure of this model is just like how we human beings read a text and then answer a related question. Empirical studies show that the proposed model can achieve state of the art on some benchmark datasets. Attention visualization also verifies our intuition. Meanwhile, this model does not need pretrained embeddings to get good results.
Site of phrenic nerve stimulation-induced upper airway collapse: influence of expiratory time (2002)

Electrical phrenic nerve stimulation (EPNS) applied at end expiration during exclusive nasal breathing can be used to characterize upper airway (UA) dynamics during wakefulness by dissociating phasic activation of UA and respiratory muscles. The UA level responsible for the EPNS-induced increase in UA resistance is unknown. The influence of the twitch expiratory timing (200 ms and 2 s) on UA resistance was studied in nine normal awake subjects by looking at instantaneous flow, esophageal and pharyngeal pressures, and genioglossal electromyogram (EMG) activity during EPNS at baseline and at -10 cmH(2)O. The majority of twitches had a flow-limited pattern. Twitches realized at 200 ms and 2 s did not differ in their maximum inspiratory flows, but esophageal pressure measured at maximum inspiratory flow was significantly less negative with late twitches (-6.6 +/- 2.7 and -5.0 +/- 3.0 cmH(2)O respectively, P = 0.04). Pharyngeal resistance was higher when twitches were realized at 2 s than at 200 ms (6.4 +/- 2.4 and 2.7 +/- 1.1 cmH(2)O x l(-1). s, respectively). EMG activity significant rose at peak esophageal pressure with a greater increase for late twitches. We conclude that twitch-induced UA collapse predominantly occurs at the pharyngeal level and that UA stability assessed by EPNS depends on the expiratory time at which twitches are performed.
Glycoengineering Approach to Half-Life Extension of Recombinant Biotherapeutics (2012)

The potential for protein-engineered biotherapeutics is enormous, but pharmacokinetic modulation is a major challenge. Manipulating pharmacokinetics, biodistribution, and bioavailability of small peptide/protein units such as antibody fragments is a major pharmaceutical ambition, illustrated by the many chemical conjugation and recombinant fusion approaches being developed. We describe a recombinant approach that leads to successful incorporation of polysialic acid, PSA for the first time, onto a therapeutically valuable protein. This was achieved by protein engineering of the PSA carrier domain of NCAM onto single-chain Fv antibody fragments (one directed against noninternalizing carcinoembryonic antigen-CEA and one against internalizing human epidermal growth factor receptor-2-HER2). This created novel polysialylated antibody fragments with desired pharmacokinetics. Production was achieved in human embryonic kidney cells engineered to express human polysialyltransferase, and the recombinant, glycosylated product was successfully fractionated by ion-exchange chromatography. Polysialylation was verified by glycosidase digestion and mass spectrometry, which showed the correct glycan structures and PSA chain length similar to that of native NCAM. Binding was demonstrated by ELISA and surface plasmon resonance and on live cells by flow cytometry and confocal immunofluorescence. Unexpectedly, polysialylation inhibited receptor-mediated endocytosis of the anti-HER2 scFv. Recombinant polysialylation led to an estimated 3-fold increase in hydrodynamic radius, comparable to PEGylation, leading to an almost 30-fold increase in blood half-life and a similar increase in blood exposure. This increase in bioavailability led to a 12-fold increase in tumor uptake by 24 h. In summary, recombinant polysialylation of antibody fragments in our system is a novel and feasible approach applicable for pharmacokinetic modulation, and may have wider applications.
Reduced c-Met expression by an adenovirus expressing a c-Met ribozyme inhibits tumorigenic growth and lymph node metastases of PC3-LN4 prostate tumor cells in an orthotopic nude mouse model. (2003)

Reduction in c-Met expression substantially inhibits both tumor growth and lymph node metastasis of PC3-LN4 cells in orthotopic nude mouse models. Therefore, targeting the c-Met signaling pathways may be important in controlling tumor growth and metastasis in human prostate cancers.
Encapsulated Cellular Implants for Recombinant Protein Delivery and Therapeutic Modulation of the Immune System (2015)

Ex vivo gene therapy using retrievable encapsulated cellular implants is an effective strategy for the local and/or chronic delivery of therapeutic proteins. In particular, it is considered an innovative approach to modulate the activity of the immune system. Two recently proposed therapeutic schemes using genetically engineered encapsulated cells are discussed here: the chronic administration of monoclonal antibodies for passive immunization against neurodegenerative diseases and the local delivery of a cytokine as an adjuvant for anti-cancer vaccines.
Production and Expression of Inflammatory Mediators in Leukocytes of Sickle Cell Anaemia Patients and Effects of Hydroxyurea Therapy on This Production (2008)

Abstract Leukocytosis is frequently observed in sickle cell disease (SCD) in the absence of bacterial infection. An elevated baseline leukocyte count is associated with an increased risk of early death and leukocytes play a significant role in the initiation of vaso-occlusive events. Inflammation, cell adhesion to vascular endothelium, and subsequent endothelial injury appear to contribute to sickle cell anemia (SCA) vaso-occlusion. Furthermore, blood levels of inflammatory and anti-inflammatory cytokines are reported to be elevated (TNF-α, IL-6, IL-10, GM-CSF), both in steady state and during crisis, but reports have been conflicting and a conclusive role for these molecules in the disease remains to be established. Furthermore, the effect of hydroxyurea therapy (HU) on the release of inflammatory mediators is not understood. The aim of this study was to determine plasma levels and leukocyte gene expressions of inflammatory mediators in healthy controls (n=30), steady-state SCA patients (n=45) and SCA patients on HU therapy (n=24). qRT-PCR analysis was use to examine gene expression and ELISA protein production. TNF-α, IL-8 and PGE2 plasma levels were significantly higher in the plasma of steady-state SCA individuals, when compared to control individuals (2.95 ± 0.4 pg/ml; 16.5 ± 2.5 pg/ml; 5.7 ± 0.6 pg/ml; 128.3 ± 12.2 pg/ml vs 1.43 ± 0.2 pg/ml, 88.5 ± 5.9 pg/ml, P=0.006; P&amp;lt;0.0001; P=0.012, respectively). HU therapy significantly reversed augmented TNF-α (1.6 ± 0.2 pg/ml, P=0.006) and, interestingly, increased plasma anti-inflammatory IL-10 (P&amp;lt;0.05). IL-10, IFN-γ, COX-2 and iNOS gene expressions were unaltered in SCA mononuclear cells (MC), however gene expressions of TNF-α, IL-8 and the protective enzyme, heme oxygenase-1 (HO-1), were significantly higher compared to healthy controls (0.46 ± 0.01; 0.08 ± 0.02; 0.21 ± 0.05 vs 0.18 ± 0.04; 0.02 ± 0.005; 0.035 ± 0.008; respectively, P&amp;lt;0.02). HU therapy was not associated with significantly altered SCA MC inflammatory gene expression, although COX-2 mRNA expression was decreased (0.11 ± 0.05; 0.37 ± 0.12, SCAHU and SCA, respectively; P&amp;lt;0.05). In SCA neutrophils, gene expressions of IL-8, IFN-γ, iNOS and HO-1 were significantly higher compared to those of control subjects (0.32 ± 0.07; 0.69 ± 0.19; 0.19 ± 0.06; 0.33 ± 0.09, P=0.02, P=0.025, P&amp;lt;0.05; P=0.027, respectively). Patients on HU therapy demonstrated lower iNOS and higher IL-10 neutrophil gene expressions compared to SCA not on HU therapy (0.038 ± 0.03; 0.72 ± 0.13, P&amp;lt;0.05; P&amp;lt;0.05, respectively). Taken together, data suggest that alterations in the gene expressions and productions of a number of pro-and anti-inflammatory mediators are present in SCA and knowledge of these pathways may be important for identifying novel drug targets for the disease.
Immunotherapy of cancer by systemic administration of lymphoid cells plus interleukin-2. (1984)

The adoptive transfer of specifically immune lymphocytes is capable of mediating the regression of a variety of established experimental tumors. We have studied the factors responsible for successful adoptive immunotherapy. Following injection of FBL-3 lymphoma into the footpad of syngeneic mice, this tumor forms a local nodule and is disseminated throughout the mouse within 5 days. Systemic administration of fresh immune lymphocytes on day 5, or of in vitro boosted immune splenocytes, or immune lymphoid cells expanded in interleukin-2 (IL-2), is capable of mediating total regression of both local and disseminated tumor. The efficacy of this immunotherapy can be enhanced by the simultaneous administration of IL-2. Because specifically immune cells can be difficult to obtain in many murine and human tumor systems, we have investigated the use of nonspecifically sensitized cells for use in adoptive immunotherapy. Lymphokine-activated killer cells (LAK) can easily be generated by incubating fresh murine or human lymphocytes in IL-2. Systemic injection of LAK cells can reduce the growth of established pulmonary metastases in murine tumor models when the LAK cells are administered in conjunction with IL-2. A variety of methods for activating human lymphoid cells to become lytic for fresh human tumors have been developed, including activation by IL-2, activation by lectins such as phytohemagglutinin and concanavalin A, and by allosensitization with pooled stimulator cells. The characteristics of these different activated killer cells have been defined. In a series of Phase I studies, we have demonstrated that activated killer cells can be safely administered to humans with advanced cancer. Studies are actively proceeding to develop an effective and practical method for the adoptive immunotherapy of cancer in humans, using both specifically activated and nonspecifically activated lymphoid cells.
Mutations in the Zinc Fingers of ADR1 That Change the Specificity of DNA Binding and Transactivation (1992)

ADR1 is a yeast transcription factor that contains two zinc fingers of the Cys-2-His-2 (C2H2) class. Mutations that change the specificity of DNA binding of ADR1 to its target site, upstream activation sequence 1 (UAS1), have been identified at three positions in the first zinc finger. Mutations Arg-115 to Gln, His-118 to Thr, and Arg-121 to Asn led to new specificities of DNA binding at adjacent positions 10, 9, and 8 (3'-GAG-5') in UAS1. Arg-115 is at the finger tip, and His-118 and Arg-121 are at positions 3 and 6, respectively, in the alpha helix of finger 1. One double mutant displayed the binding specificity expected from the properties of its constituent new-specificity mutations. Mutations in the second finger that allowed its binding site to be identified through loss-of-contact phenotypes were made. These mutations imply a tail-to-tail orientation of the two ADR1 monomers on their adjacent binding sites. Finger 1 is aligned on UAS1 in an amino-to-carboxyl-terminal orientation along the guanine-rich strand in a 3'-to-5' direction. One of the ADR1 mutants was functional in vivo with both its cognate binding site and wild-type UAS1, but the other two mutants were defective in transactivation despite their ability to bind with high affinity to their cognate binding sites.
RAIDR: Retention-aware intelligent DRAM refresh (2012)

Dynamic random-access memory (DRAM) is the building block of modern main memory systems. DRAM cells must be periodically refreshed to prevent loss of data. These refresh operations waste energy and degrade system performance by interfering with memory accesses. The negative effects of DRAM refresh increase as DRAM device capacity increases. Existing DRAM devices refresh all cells at a rate determined by the leakiest cell in the device. However, most DRAM cells can retain data for significantly longer. Therefore, many of these refreshes are unnecessary. In this paper, we propose RAIDR (Retention-Aware Intelligent DRAM Refresh), a low-cost mechanism that can identify and skip unnecessary refreshes using knowledge of cell retention times. Our key idea is to group DRAM rows into retention time bins and apply a different refresh rate to each bin. As a result, rows containing leaky cells are refreshed as frequently as normal, while most rows are refreshed less frequently. RAIDR uses Bloom filters to efficiently implement retention time bins. RAIDR requires no modification to DRAM and minimal modification to the memory controller. In an 8-core system with 32 GB DRAM, RAIDR achieves a 74.6% refresh reduction, an average DRAM power reduction of 16.1%, and an average system performance improvement of 8.6% over existing systems, at a modest storage overhead of 1.25 KB in the memory controller. RAIDR's benefits are robust to variation in DRAM system configuration, and increase as memory capacity increases.
Aberrant Luteinizing Hormone-Releasing Hormone-Stimulated Adrenocorticotropic Hormone Secretion in a Patient with Pituitary Hyperplasia due to Primary Hypothyroidism. (2000)

We report a patient with primary hypothyroidism associated with an aberrant ACTH response to the LH-RH test. A 40-year-old woman was admitted to our hospital displaying headache, nausea, and numbness on the left side of her face, upper limbs, and tips of her toes. Computed tomography and magnetic resonance imaging revealed a mass-like lesion in the pituitary. A high serum TSH concentration with concomitant low thyroid hormone concentrations resulted in a diagnosis of primary hypothyroidism. To exclude the possibility of a coexisting pituitary tumor including a TSH-secreting tumor, we performed dynamic TSH secretion tests. TRH testing showed an excessive, delayed TSH response, typical of primary hypothyroidism. Serum TSH decreased not only after administration of CRH, octreotide, or L-DOPA, but also after administration of LH-RH. In this case, LH-RH testing induced ACTH secretion. To determine if aberrant ACTH secretion in response to LH-RH loading is a common phenomenon in severe primary hypothyroidism, we performed the LH-RH test on 4 additional patients with pituitary enlargement due to primary hypothyroidism. Two patients demonstrated aberrant ACTH secretion in response to LH-RH loading, but the others did not. To our knowledge, this is the first report of aberrant LH-RH-stimulated ACTH secretion in primary hypothyroidism.