gebhart/patrepeval huggingface dataset:
Brain-derived neurotrophic factor is an endogenous modulator of nociceptive responses in the spinal cord (1999)

The primary sensory neurons that respond to noxious stimulation and project to the spinal cord are known to fall into two distinct groups: one sensitive to nerve growth factor and the other sensitive to glial cell-line-derived neurotrophic factor. There is currently considerable interest in the ways in which these factors may regulate nociceptor properties. Recently, however, it has emerged that another trophic factor-brain-derived neurotrophic factor (BDNF)-may play an important neuromodulatory role in the dorsal horn of the spinal cord. BDNF meets many of the criteria necessary to establish it as a neurotransmitter/neuromodulator in small-diameter nociceptive neurons. It is synthesized by these neurons and packaged in dense core vesicles in nociceptor terminals in the superficial dorsal horn. It is markedly up-regulated in inflammatory conditions in a nerve growth factor-dependent fashion. Postsynaptic cells in this region express receptors for BDNF. Spinal neurons show increased excitability to nociceptive inputs after treatment with exogenous BDNF. There are both electrophysiological and behavioral data showing that antagonism of BDNF at least partially prevents some aspects of central sensitization. Together, these findings suggest that BDNF may be released from primary sensory nociceptors with activity, particularly in some persistent pain states, and may then increase the excitability of rostrally projecting second-order systems. BDNF released from nociceptive terminals may thus contribute to the sensory abnormalities associated with some pathophysiological states, notably inflammatory conditions.
BeLieving in Native Girls: Characteristics from a Baseline Assessment (2012)

BeLieving In Native Girls (BLING) is a juvenile delinquency and HIV intervention at a residential boarding school for American Indian/Alaska Native adolescent girls ages 12-20 years. In 2010, 115 participants completed baseline surveys to identify risk and protective factors. Initial findings are discussed regarding a variety of topics, including demographics and general characteristics, academic engagement, home neighborhood characteristics and safety, experience with and perceptions of gang involvement, problem-solving skills, self-esteem, depression, sexual experiences and risk-taking behaviors, substance abuse, and dating violence.
Serine racemase: A glial enzyme synthesizing d -serine to regulate glutamate- N -methyl- d -aspartate neurotransmission (1999)

Although D amino acids are prominent in bacteria, they generally are thought not to occur in mammals. Recently, high levels of D-serine have been found in mammalian brain where it activates glutamate/N-methyl-D-aspartate receptors by interacting with the "glycine site" of the receptor. Because amino acid racemases are thought to be restricted to bacteria and insects, the origin of D-serine in mammals has been puzzling. We now report cloning and expression of serine racemase, an enzyme catalyzing the formation of D-serine from L-serine. Serine racemase is a protein representing an additional family of pyridoxal-5' phosphate-dependent enzymes in eukaryotes. The enzyme is enriched in rat brain where it occurs in glial cells that possess high levels of D-serine in vivo. Occurrence of serine racemase in the brain demonstrates the conservation of D-amino acid metabolism in mammals with implications for the regulation of N-methyl-D-aspartate neurotransmission through glia-neuronal interactions.
Solution NMR studies of the integral membrane proteins OmpX and OmpA from Escherichia coli (2001)

Membrane proteins are usually solubilized in polar solvents by incorporation into micelles. Even for small membrane proteins these mixed micelles have rather large molecular masses, typically beyond 50000 Da. The NMR technique TROSY (transverse relaxation-optimized spectroscopy) has been developed for studies of structures of this size in solution. In this paper, strategies for the use of TROSY-based NMR experiments with membrane proteins are discussed and illustrated with results obtained with the Escherichia coli integral membrane proteins OmpX and OmpA in mixed micelles with the detergent dihexanoylphosphatidylcholine (DHPC). For OmpX, complete sequence-specific NMR assignments have been obtained for the polypeptide backbone. The 13C chemical shifts and nuclear Overhauser effect data then resulted in the identification of the regular secondary structure elements of OmpX/DHPC in solution, and in the collection of an input of conformational constraints for the computation of the global fold of the protein. For OmpA, the NMR assignments are so far limited to about 80% of the polypeptide chain, indicating different dynamic properties of the reconstituted OmpA beta-barrel from those of OmpX. Overall, the present data demonstrate that relaxation-optimized NMR techniques open novel avenues for studies of structure, function and dynamics of integral membrane proteins.
The P2X 7 purinergic receptor: from physiology to neurological disorders (2009)

Purine nucleotides are well established as extracellular signaling molecules. P2X receptors are ATP-gated cation channels that mediate fast excitatory transmission in diverse regions of the brain and spinal cord. Several P2X receptor subtypes, including P2X(7), have the unusual property of changing their ion selectivity during prolonged exposure to ATP, which results in progressive dilation of the channel pore and the development of permeability to molecules as large as 900 Da. The P2X(7) receptor was originally described in cells of hematopoietic origin, including macrophages, microglia, and certain lymphocytes, and mediates the influx of Ca(2+) and Na(+) ions, as well as the release of proinflammatory cytokines. P2X(7) receptors may affect neuronal cell death through their ability to regulate the processing and release of interleukin-1beta, a key mediator in neurodegeneration, chronic inflammation, and chronic pain. Activation of P2X(7) receptors provides an inflammatory stimulus, and P2X(7) receptor-deficient mice have substantially attenuated inflammatory responses, including models of neuropathic and chronic inflammatory pain. Moreover, P2X(7) receptor activity, by regulating the release of proinflammatory cytokines, may be involved in the pathophysiology of depression. The P2X(7) receptor may thus represent a critical communication link between the nervous and immune systems, while providing a target for therapeutic exploitation. This review discusses the current biology and cellular signaling pathways of P2X(7) receptor function, as well as insights into the role for this receptor in neurological/psychiatric diseases, outstanding questions, and the therapeutic potential of P2X(7) receptor antagonism.
Response to Wang et al. (2005)

establish the incidence of the 21-bp MEF2A deletion and pointing out the possibility of incomplete penetrance. But without proper phenotyping work and experimental biological assessment, it is a misleading report that unfortunately suggests a negative bias and premature dismissal of an important biologic underpinning of CAD.
Development of a Multi-Channel Dielectric Resonator Oscillator for Space Communication Applications (2005)

A novel multi-channel dielectric resonator oscillator (DRO) for Advanced Trans-ponder use is developed for deep-space communication applications. The Advanced Transponder receives a 7.2-GHz (X-band) uplink signal and generates an 8.4-GHz (X-band) coherent or non-coherent downlink signal. The Advanced Transponder ar-chitecture incorporates two miniature DROs. These DROs are used in receiver and exciter frequency synthesis phase-locked loops (PLLs) in the Advanced Transpon-der. The DRO is capable of tuning over 27 Deep Space Network (DSN) X-band uplink channels (30 MHz). The DROs are designed with custom monolithic mi-crowave integrated-circuit (MMIC) negative-resistance voltage-controlled oscillator chips. The receiver DRO design demonstrated a free-running single-sideband phase noise of −107 dBc/Hz at 100 kHz off the carrier frequency, a tuning linearity of ±3 percent over the channel locking range, and output power of +10 dBm ± 1 dB. Advantages of the multi-channel DRO include in-flight selection of transponder channel frequency, the enabling of novel mission operations techniques, frequency agility, and a single transponder design that will serve many missions and simplify hardware sparing strategies. I.
MHC Class I Antigen Processing Pathways (1997)

The multistep process that culminates in major histocompatibility complex (MHC) class I presentation of foreign of self-peptides begins in the last phases of protein catabolism. Although the individual roles of many key molecules-such as proteasomes, the transporter associated with antigen processing, and various endoplasmic reticulum chaperones-have recently been elucidated, there still remain many questions regarding processing of proteins into MHC class I bound peptides. This review summarizes the recent developments in antigen processing for MHC class I molecules, with a focus on how proteins are believed to be sampled and selected for degradation.
Microorganisms in Reclamation of Metals (1986)

Revue concernant les donnees actuelles sur la lixiviation bacterienne des metaux a partir des minerais et la description des technologies microbiennes en developpement pour leur recuperation
Just in Time-Selection: A Rapid Semiautomated SELEX of DNA Aptamers Using Magnetic Separation and BEAMing (2014)

A semiautomated two-step method for in vitro selection of DNA aptamers using magnetic separation and solid-phase emulsion polymerase chain reaction has been developed. The application of a magnetic separator allows the simultaneous processing of up to 12 SELEXs (systematic evolution of ligands by exponential enrichment) with different targets or buffer conditions. Using a magnetic separator and covalent target immobilization on magnetic beads, the selection process was simplified and the substeps of aptamer/target incubation, washing, and elution of the aptamers were merged into one automated procedure called "FISHing". Without further processing the resulting FISHing eluates are suitable for BEAMing (beads, emulsion, amplification, and magnetics), which includes the amplification by emPCR (emulsion polymerase chain reaction) and strand separation by the implementation of covalently immobilized reverse primers on magnetic beads. The novel selection process has been proved and validated by selecting and characterization of aptamers to the wine fining agent lysozyme.
The MAPK signaling cascade (1995)

The transmission of extracellular signals into their intracellular targets is mediated by a network of interacting proteins that regulate a large number of cellular processes. Cumulative efforts from many laboratories over the past decade have allowed the elucidation of one such signaling mechanism, which involves activations of several membranal signaling molecules followed by a sequential stimulation of several cytoplasmic protein kinases collectively known as mitogen‐activated protein kinase (MAPK) signaling cascade. Up to six tiers in this cascade contribute to the amplification and specificity of the transmitted signals that eventually activate several regulatory molecules in the cytoplasm and in the nucleus to initiate cellular processes such as proliferation, differentiation, and development. Moreover, because many oncogenes have been shown to encode proteins that transmit autogenic signals upstream of this cascade, the MAPK pathway provides a simple unifying explanation for the mechanism of action of most, if not all, nonnuclear oncogenes. The pattern of MAPK cascade is not restricted to growth factor signaling and it is now known that signaling pathways initiated by phorbol esters, iono‐phors, heat shock, and liganda for seven transmembrane receptors use distinct MAPK cascades with little or no cross‐reactivity between them. In this review we emphasize primarily the first MAPK cascade to be discovered that uses the MEK and ERK isoforms and describe their involvement in different cellular processes.—Seger, R., Krebs, E. G. The MAPK signaling cascade. FASEB J. 9, 726‐735 (1995)
Extension of Cell Life-Span and Telomere Length in Animals Cloned from Senescent Somatic Cells (2000)

The potential of cloning depends in part on whether the procedure can reverse cellular aging and restore somatic cells to a phenotypically youthful state. Here, we report the birth of six healthy cloned calves derived from populations of senescent donor somatic cells. Nuclear transfer extended the replicative life-span of senescent cells (zero to four population doublings remaining) to greater than 90 population doublings. Early population doubling level complementary DNA-1 (EPC-1, an age-dependent gene) expression in cells from the cloned animals was 3.5- to 5-fold higher than that in cells from age-matched (5 to 10 months old) controls. Southern blot and flow cytometric analyses indicated that the telomeres were also extended beyond those of newborn (<2 weeks old) and age-matched control animals. The ability to regenerate animals and cells may have important implications for medicine and the study of mammalian aging.
To C or not to C: these are the questions (1995)

C LONING OF THE HEPATITIS C virus (HCV) in the absence of an observed particle, a tissue-culture system, an established genomic sequence, or a serologic assay was a remarkable accomplishment that has illuminated the perplexing entity long known as non-A, non-B (NANB) hepatitis.',* However, despite this illumination, the discovery of HCV has raised innumerable questions, only some of which were contemplated in the dark ages of NANB hepatitis research. This review will focus on the questions and the biologic and clinical issues they engender.
Summary of the Scientific Conference on the Efficacy of Hypocholesterolemic Dietary Interventions (1996)

HomeCirculationVol. 94, No. 12Summary of the Scientific Conference on the Efficacy of Hypocholesterolemic Dietary Interventions
Relationship of vaccine efficacy to the kinetics of DC and T-cell responses induced by PLG-based cancer vaccines (2011)

Current vaccine methods produce short-lived bioactivity, and cancer vaccines have failed to reproducibly cause the regression of solid tumors. 3] More recently, material-based particulate systems have been developed to control antigen localization in tissue or to target host DCs specifically via antibody or ligand conjugation. Although current biomaterial-based vaccines can enhance antigen loading to DCs, leading to antigen-specific T-cell activation, they lack concurrent regulation of effector T-cell activity. Therapeutic vaccination against an established disease, including solid tumors, requires methods that stimulate not only innate immunity and DCs, but also persistent cytotoxic T lymphocyte (CTL) responses, which kill tumor cells until the disease has cleared. Therefore, the natural kinetics of innate and adaptive cancer vaccines are typically formulated for bolus injection and often produce short-lived immunostimulation resulting in poor temporal control over immune cell activation and weak oncolytic activity. One means of overcoming these limitations utilizes immunologically active biomaterial constructs. We previously reported that antigen-laden, macroporous pLG scaffolds induce potent dendritic cell (Dc) and cytotoxic T-lymphocyte (cTL) responses via the controlled signaling of inflammatory cytokines, antigen and toll-like receptor agonists. In this study, we describe the kinetics of these responses and illustrate their fundamental relationship to potent tumor rejection when implanted subcutaneously in a mouse B16 model of melanoma. By explanting scaffolds from mice at times ranging from 1-7 d, a seamless relationship was observed between the production of controlled cTL responses, tumor growth and long-term survival in both prophylactic and therapeutic models. Scaffolds must be implanted for > 7 d to augment cTL responses via the prolonged presentation of tumor antigen, and the benefits included a notable regression of established tumors. host Dc infiltration into the porous material persisted for 12 days (peaking at day 5 ~1.4 x 10 6 cells), and a sharp attenuation in Dc numbers coincided with peak cD8 + cTL infiltration at day 12 (~8 x 10 5 cells). Importantly, these pLG systems enhanced Dc numbers in the draining lymph node, resulting in increased cD8(+) cTL subsets at days 10-16 of vaccination. These results indicate that material systems can finely control innate and adaptive immune cell responses to kill typically untreatable melanoma tumors and provide critical kinetic data for the design of vaccine carriers.
Cytokine Molecular Adjuvants Modulate Immune Responses Induced by DNA Vaccine Constructs for HIV-1 and SIV (1999)

DNA or nucleic acid immunization has been shown to induce both antigen-specific cellular and humoral immune responses in vivo. Moreover, immune responses induced by DNA immunization can be enhanced and modulated by the use of molecular adjuvants. To further engineer the immune response in vivo, we investigated the induction and regulation of immune responses from the codelivery of Thl cytokines (interleukin-2 [IL-2] and IL-12), Th2 cytokines (IL-4 and IL-10), and granulocyte-macrophage colony-stimulating factor (GM-CSF) genes along with a DNA vaccine construct encoding for simian immunodeficiency virus (SIV) gag/pol proteins. We observed that coinjection with IL-2, IL-4, IL-10, and GM-CSF resulted in increased levels of antigen-specific antibodies. In addition, we found that coinjection with cytokine genes drove the immune responses toward a more Thl or Th2 phenotype. We also observed that coadministration of IL-2, IL-12, and GM-CSF genes resulted in a dramatic enhancement of Th proliferation responses. Moreover, coimmunization with IL-12 genes resulted in a dramatic enhancement of antigen-specific cytotoxic T lymphocyte (CTL) responses. These results support the potential utility of molecular adjuvants in DNA vaccine regimens.
A many-core hardware acceleration platform for short read mapping problem using distributed memory interface with 3D-stacked architecture (2014)

Next Generation Sequencing technologies produce huge amounts of short reads consisting randomly fragmented DNA base pair strings, while assembling poses a challenge on the mapping of short reads to a reference genome in terms of both sensitivity and execution time. In this paper, we propose a many-core hardware acceleration platform for short read mapping based on hash-index method, which benefit from a distributed memory interface with 3D-stacked architecture for local memory access. Our design provides an amazingly 45012 times speedup over software approach for single end short reads and 21102 times for paired end reads, while also beats similar single FPGA solution for 1466 times in case of single end reads.
Self-aligned, gated field emitter arrays with integrated high-aspect-ratio current limiters (2013)

We report the fabrication of arrays of silicon field emitters with 1-micron pitch with integrated, self-aligned extractor gates and 10-micron tall high-aspect-ratio silicon vertical current limiters.
Activation of Caspase-3 in the Retina of Transgenic Rats with the Rhodopsin Mutation S334ter during Photoreceptor Degeneration (1999)

The role of caspase-3 in photoreceptor degeneration was examined in a line of transgenic rats that carry a rhodopsin mutation S334ter. Photoreceptor degeneration in these animals is rapid. It is detected as early as postnatal day (PD) 8, and by PD 20, only one of the original 12 rows of nuclei remain in the outer nuclear layer. At PD 11 and 12, the number of photoreceptors dying per day reaches a peak of approximately 30% of the total photoreceptors in the retina. Coincident with this rapid degeneration is an increase in caspase-3-like activity as assessed by the cleavage of a fluorescent substrate N-acetyl-Asp-Glu-Val-Asp-aminomethylcoumarin and an increase in activated caspase-3 as determined by Western blot analysis for its 12 kDa subunit. Intraocular injection of an irreversible caspase-3 inhibitor N-benzyloxycarbonal-Asp(OMe)-Glu(OMe)-Val-Asp(Ome)-fluoromethyk etone partially protected photoreceptors from degeneration. These findings indicate that a caspase-3-dependent mechanism is operative in photoreceptor death in the transgenic rats under investigation.
Sequence analysis of the agrA gene encoding beta-agarase from Pseudomonas atlantica (1989)

The nucleotide sequence of the agrA gene encoding an extracellular beta-agarase of Pseudomonas atlantica was determined. An open reading frame of 1,515 nucleotides which corresponded to agrA was found. The nucleotide sequence predicts a primary translation product of 504 amino acids and Mr 57,486. Comparison of the deduced amino acid sequences of beta-agarase from P. atlantica and the extracellular beta-agarase from Streptomyces coelicolor A3(2) suggests that these proteins share several domains in common.
The early experience with branchless banking (2008)

Branchless banking has great potential to extend the distribution of financial services to poor people who are not reached by traditional bank branch networks; it lowers the cost of delivery, including costs both to banks of building and maintaining a delivery channel and to customers of accessing services. This paper reviews seven key observations, Consultative Group to Assist the Poorest (CGAP) has drawn from its advisory work and research on branchless banking and, particularly, from its support of branchless banking projects around the world over the past year. Each element and player in the branchless banking delivery chain, including customers, financial service providers, agents, products, and technology platforms, is addressed. Most of the observations apply equally to the use of mobile phones to handle remote transactions (or mobile banking) and card based branchless banking networks. However, lessons from mobile banking are emphasized because of its newness relative to card-based networks.
Preferential Expression Of The Large Hepatitis B Virus Surface Antigen Gene by an Adenovirus-hepatitis B Virus Recombinant (1991)

Using an adenovirus-hepatitis B virus (HBV) recombinant, expression of the HBV surface antigen (HBsAg) genes was examined in various cell lines using S1 nuclease mapping and radioimmunoassay. The steady-state level of the 2.4 kb RNA encoding the large HBsAg was much greater than, or the same as, that of the 2.0 kb RNA, encoding the middle and major HBsAgs, in primate cells, but was negligible in non-primate cells, as is the case in most expression systems. According to the amount of 2.4 kb RNA expressed, cells were classified into three groups: those in which (1) the amount of 2.4 kb RNA was much greater than that of 2.0 kb RNA (HepG2 and JHH-4), (2) the amount of 2.4 kb RNA was the same as that of 2.0 kb (Hul-1, HeLa and other non-hepatic primate cells), and (3) the amount of 2.4 kb RNA was less than one-tenth of that of 2.0 kb RNA (rodent cells). Radioimmunoassay revealed that most HBsAg is located intracellularly in primate cells, but is secreted into the culture medium of rodent cells. The expression of 2.4 kb RNA was unaffected by an inhibitor of DNA synthesis in HepG2 cells, which are of human liver origin, whereas it was strongly inhibited in human non-hepatic HeLa cells.
Hyperthermia‐treated mesenchymal stem cells exert antitumor effects on human carcinoma cell line (2008)

This study showed that the conditioned medium of the HS-MSCs exerted a suppressive effect on tumor progression and malignancy, suggesting that hyperthermia enables tumor stromal cells to provide a sensitizing environment for tumor cells to undergo cell death.