gebhart/patrepeval huggingface dataset:
Scanning Laser Ophthalmoscope (1981)

An instrument is described which functions as a low light level ocular fundus camera and ophthalmoscope, and which is capable of making a wide range of quantitative measurements in the eye. Light levels for ophthalmoscopy (20 μW/cm2 at the retina) are at least two orders of magnitude below those in current use. μ focused laser bearn forms a flying spot, moved physically by scanning mirrors. This allows a 20 μm or smaller resolution element, with only a 0.9 mm diameter area of the patient's pupil used for the entering beam. The remaining pupillary area forms the exit pupil-a critical inversion of the division of pupils necessary for systems using conventional imaging. It is this inversion which allows the low light level and the unique measurement capabilities. We discuss the constraints imposed by viewing the inside of a spheroid through a small hole in its wall, and our solutions-both optical and electronic-to these problems. We also describe electronic problems encountered in the video system, which arise from our special detection and display systems. Some specifics of the instrument's measurement capabilities are discussed.
Induced α Helix in the VP16 Activation Domain upon Binding to a Human TAF (1997)

Activation domains are functional modules that enable sequence-specific DNA binding proteins to stimulate transcription. The structural basis for the function of activation domains is poorly understood. A combination of nuclear magnetic resonance (NMR) and biochemical experiments revealed that the minimal acidic activation domain of the herpes simplex virus VP16 protein undergoes an induced transition from random coil to alpha helix upon binding to its target protein, hTAFII31 (a human TFIID TATA box-binding protein-associated factor). Identification of the two hydrophobic residues that make nonpolar contacts suggests a general recognition motif of acidic activation domains for hTAFII31.
Recent Advances in Carbohydrate Bioengineering (1999)

Structure and Synthesis of Carbohydrates and Carbohydrate Analogues Post-transitional Glycosylation of Proteins Biochemistry of Carbohydrate Modifying Enzymes Structure of the Catalytic Domains of Carbohydrate Modifying Enzymes Structure and Function of Non-Catalytic Modules Industrial Exploitation of Carbohydrate Modifying Enzymes Engineering Carbohydrate Modifying Enzymes Subject Index.
Variation in H-2Kk peptide motif revealed by sequencing naturally processed peptides from T-cell hybridoma class I molecules (1996)

Class I major histocompatibility complex (MHC) molecules interact with a diverse array of self and foreign peptides, displaying them on the cell surface and providing an extracellular indication of intracellular invasion. The most clearly defined role for these class I/peptide complexes is to cause effector responses upon binding to antigen-specific receptors of cytotoxic T cells. We have characterized the mouse thymoma/rat V beta 8.2+ T-cell hybridoma C14/BW12-12A1 by fluorescence-activated cell sorting analysis and have used immunoaffinity chromatography to purify class I molecules from these cells. The peptides bound to the class I molecules were fractionated by high-performance liquid chromatography and sequenced. Self-peptide mixtures eluted from the mouse H-2Kk class I allele revealed a dominant primary sequence motif, with a carboxyl-terminal residue that appeared to be invariantly valine and a secondary or auxiliary anchor residue at position 2 that could be either glutamate or proline. The majority of naturally processed peptide ligands appeared to be octamers. Although peptides eluted off H-2Kk molecules from tissue derived from a number of different inbred mouse strains also appeared to be octamers, others have reported that isoleucine is the dominant carboxyl-terminal residue. Thus, different cell types displayed distinct differences in naturally processed peptides bound by the same class I alleles. The variation in naturally processed peptides loaded onto the same class I allele most likely reflects the nature of the pool of peptides within the cell available for loading class I molecules.
Channel polarization: A method for constructing capacity-achieving codes (2008)

A method is proposed, called channel polarization, to construct code sequences that achieve the symmetric capacity I(W) of any given binary-input discrete memoryless channel (B-DMC) W. The symmetric capacity I(W) is the highest rate achievable subject to using the input letters of the channel equiprobably and equals the capacity C(W) if the channel has certain symmetry properties. Channel polarization refers to the fact that it is possible to synthesize, out of N independent copies of a given B-DMC W, a different set of N binary-input channels such that the capacities of the latter set, except for a negligible fraction of them, are either near 1 or near 0. This second set of N channels are well-conditioned for channel coding: one need only send data at full rate through channels with capacity near 1 and at 0 rate through the others. The main coding theorem about polar coding states that, given any B-DMC W with I(W) > 0 and any fixed 0 < delta < I(W), there exist finite constants n <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> (W, delta) and c(W, delta) such that for all ngesn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> , there exist polar codes with block length N = 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> rate R > I(W)-delta, and probability of block decoding error P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> les cN <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1/4</sup> . The codes with this performance can be encoded and decoded within complexity O(N log N).
Optimization of Electroporation-Enhanced Intradermal Delivery of DNA Vaccine Using a Minimally Invasive Surface Device (2012)

In vivo electroporation (EP) is an efficient nonviral method for enhancing DNA vaccine delivery and immunogenicity in animals and humans. Intradermal delivery of DNA vaccines is an attractive strategy because of the immunocompetence of skin tissue. We have previously reported a minimally invasive surface intradermal EP (SEP) device for delivery of prophylactic DNA vaccines. Robust antibody responses were induced after vaccine delivery via surface EP in several tested animal models. Here we further investigated the optimal EP parameters for efficient delivery of DNA vaccines, with a specific emphasis on eliciting cellular immunity in addition to robust humoral responses. In a mouse model, using applied voltages of 10-100 V, transgene expression of green fluorescent protein and luciferase reporter genes increased significantly when voltages as low as 10 V were used as compared with DNA injection only. Tissue damage to skin was undetectable when voltages of 20 V and less were applied. However, inflammation and bruising became apparent at voltages above 40 V. Delivery of DNA vaccines encoding influenza virus H5 hemagglutinin (H5HA) and nucleoprotein (NP) of influenza H1N1 at applied voltages of 10-100 V elicited robust and sustained antibody responses. In addition, low-voltage (less than 20 V) EP elicited higher and more sustained cellular immune responses when compared with the higher voltage (above 20 V) EP groups after two immunizations. The data confirm that low-voltage EP, using the SEP device, is capable of efficient delivery of DNA vaccines into the skin, and establishes that these parameters are sufficient to elicit both robust and sustainable humoral as well as cellular immune responses without tissue damage. The SEP device, functioning within these parameters, may have important clinical applications for delivery of prophylactic DNA vaccines against diseases such as HIV infection, malaria, and tuberculosis that require both cellular and humoral immune responses for protection.
Aging of mice is associated with p16(Ink4a)- and β-galactosidase-positive macrophage accumulation that can be induced in young mice by senescent cells (2016)

Senescent cells (SCs) have been considered a source of age-related chronic sterile systemic inflammation and a target for anti-aging therapies. To understand mechanisms controlling the amount of SCs, we analyzed the phenomenon of rapid clearance of human senescent fibroblasts implanted into SCID mice, which can be overcome when SCs were embedded into alginate beads preventing them from immunocyte attack. To identify putative SC killers, we analyzed the content of cell populations in lavage and capsules formed around the SC-containing beads. One of the major cell types attracted by secretory factors of SCs was a subpopulation of macrophages characterized by p16(Ink4a) gene expression and β-galactosidase activity at pH6.0 (β-gal(pH6)), thus resembling SCs. Consistently, mice with p16(Ink4a) promoter-driven luciferase, developed bright luminescence of their peritoneal cavity within two weeks following implantation of SCs embedded in alginate beads. p16(Ink4a)/β-gal(pH6)-expressing cells had surface biomarkers of macrophages F4/80 and were sensitive to liposomal clodronate used for the selective killing of cells capable of phagocytosis. At the same time, clodronate failed to kill bona fide SCs generated in vitro by genotoxic stress. Old mice with elevated proportion of p16(Ink4a)/β-gal(pH6)-positive cells in their tissues demonstrated reduction of both following systemic clodronate treatment, indicating that a significant proportion of cells previously considered to be SCs are actually a subclass of macrophages. These observations point at a significant role of p16(Ink4a)/β-gal(pH6)-positive macrophages in aging, which previously was attributed solely to SCs. They require re-interpretation of the mechanisms underlying rejuvenating effects following eradication of p16(Ink4a)/β-gal(pH6)-positive cells and reconsideration of potential cellular target for anti-aging treatment.
Myocardin related transcription factors are required for coordinated cell cycle progression (2013)

Myocardin related transcription factors A and B (MRTFs) activate serum response factor-driven transcription in response to Rho signaling and changes in actin dynamics. Myocardin and MRTFs have been implicated in anti-proliferative effects on a range of cell types. The precise mechanisms, however, remained elusive. We employed double knockdown of MRTF-A and MRTF-B in NIH 3T3 fibroblasts to evaluate its effects on cell cycle progression and proliferation. We show that transient depletion of MRTFs conveys a modest anti-proliferative effect and impinges on normal cell cycle progression, resulting in significantly shortened G 1 phase and slightly extended S and G 2 phase under normal growth conditions. Under serum-starved conditions we observed aberrant entry into the S and G 2 phases without subsequent cell division. This was accompanied by downregulation of cyclin-CDK inhibitors p27Kip1, p18Ink4c and 19Ink4d as well as upregulation of p21Waf1 and cyclin D1. Extended knockdown led to increased formation of micronuclei, while cells stably depleted of MRTFs tend to become aneuploid and polyploid. Thus, MRTFs are required for accurate cell cycle progression and maintenance of genomic stability in fibroblast cells.
Effect of Human Macrophage Colony‐stimulating Factor on Granulopoiesis and Survival in Bone‐marrow‐transplanted Mice (1990)

Human macrophage colony-stimulating factor (hM-CSF) has been isolated from normal human urine and purified to a homogeneous protein. The effect of hM-CSF on granulopoiesis was investigated in BALB/c mice transplanted with a suboptimal number of bone marrow cells. Lethally irradiated (7.8 Gy) mice were transplanted with 1 x 10(6) syngeneic mouse bone marrow cells and treated with a daily intraperitoneal dose of 64 micrograms/kg of hM-CSF for 5 days following the transplant. The hM-CSF injection resulted in stimulation of the recovery of blood neutrophils as well as an increase in the number of granulocyte-macrophage progenitor cells (CFU-GM) in the femur and spleen. The survival of lethally irradiated mice was dependent on the cell number transplanted; most mice transplanted with 2 x 10(4) cells died within 2 weeks. The recovery of hematopoiesis in mice transplanted with 2 x 10(4) cells was modestly but significantly stimulated by hM-CSF administration initiated from 5 days before or 1 day after transplantation for a 5-day period. Furthermore, the hM-CSF administrations markedly reduced the mortality in these mice during the early period after the transplantation. Since anaerobic bacteria were frequently detected in arterial blood immediately before the deaths but were not found in the surviving mice, it is speculated that early deaths occurring within 2 weeks after the transplant may be caused by opportunistic infections, and hM-CSF injection may prevent these mortal infections through its stimulating effect on monocyte-macrophage functions that are responsible for the production of hematopoietic regulators.
Obesity is a risk factor for transformed migraine but not chronic tension-type headache (2006)

Chronic daily headache and obesity are associated. Obesity is a stronger risk factor for transformed migraine than for chronic tension-type headache.
Thermal resistance of VCSELs bonded to integrated circuits (1999)

The thermal resistance of vertical-cavity surface-emitting lasers (VCSELs) flip chip bonded to GaAs substrates and CMOS integrated circuits has been measured. The measurements on GaAs show that if the bonding is done properly, the bonding does not add significantly to the thermal resistance. However, the SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> under the CMOS bonding pad can double the thermal resistance unless measures are taken to improve the thermal conductance of these layers. Finite element simulations indicate that the thermal resistance of bonded VCSELs increases rapidly as the solder bond size and the aperture size decrease below /spl sim/10 μm.
0.8bit/s/Hz of Information Spectral Density by Vestigial Sideband Filtering of 42.66 Gb/s NRZ (2002)

Vestigial sideband filtering(VSB) technique is demonstrated at 42.66 Gbit/s NRZ data to achieve a high information density (ISD) of 0.8 bit/s/Hz with 50 GHz channel spacing without PDM (polarization division demultiplexing).
Purification and characterization of PTP2C, a widely distributed protein tyrosine phosphatase containing two SH2 domains. (1994)

PTP2C, a widely distributed protein tyrosine phosphatase (PTP) containing two SH2 domains, was expressed as a recombinant enzyme in Escherichia coli and purified to near homogeneity. The purified enzyme and a truncated form lacking the SH2 domains (delta SH2-PTP2C) have been characterized with four commonly used substrates. Both forms showed pH optima of around neutrality for protein substrates but below 5.5 for a peptide substrate and para-nitrophenylphosphate. The dependence of the enzymes on ionic strength varied with the nature of the substrates involved. Like its analog PTP1C, PTP2C displayed a specific activity of less than 0.1% of that observed with other known PTPs toward protein substrates. Deletion of the SH2 domains increased its activity by 12-45-fold, depending on the substrates used. Limited trypsinolysis which cleaved about 4 kDa from the carboxyl terminus resulted in a 2-5-fold activation of the full-length enzyme but was essentially without effect on the truncated enzyme. Both forms showed similar responses to effectors including activators (e.g. anionic phospholipids) or inhibitors (e.g. vanadate, molybdate, or Zn2+). PTP2C and delta SH2-PTP2C were phosphorylated in vitro by mitogen-activated protein kinase, protein kinase C, and various protein tyrosine kinases; in the latter case, they underwent autodephosphorylation. No significant effect of the phosphorylation reactions on enzyme activity could be observed in vitro.
Antibody Coated Bacteria in Otitis Media with Effusions (1980)

The significance of bacterial isolates of coagulase negative Staphylococcus epidermidis and Corynebacterium species in middle ear fluids remains controversial. This study was undertaken to evaluate the possible role of these organisms in different effusions. Cultures were obtained from the external cartilaginous ear, bony canal, tympanic membrane, middle ear fluids, tonsils and nasopharynx of 93 patients at the time of myringotomy for otitis media with effusion. Isolates of coagulase negative staphylococci from the middle ear, external ear and posterior aural skin were evaluated in regard to antibiotic sensitivity, biochemical tests and phage typing. Furthermore, in another series of patients in whom these organisms were isolated, specific antibody activity in both middle ear washings and corresponding sera were measured, using the technique of indirect immunofluorescence. The results suggest that the isolates from the middle ear and ear canal are not always identical. There is some evidence that specific IgM and IgG as well as IgA responses to these organisms are present in middle ear washings and not in corresponding serum. These results suggest that coagulase negative Staphylococcus and Corynebacterium species in middle ear effusions may not be contaminants from the external canal and that a local immune response may be produced by these organisms. Whether or not these organisms represent etiologic agents responsible for otitis media with effusion cannot be ascertained from this data. One very interesting point is the presence of IgF coating of organisms in some effusions.
Hypoxia in Static and Dynamic 3D Culture Systems for Tissue Engineering of Bone (2008)

Tissue engineering of sizeable cell-scaffold constructs is limited by gradients in tissue quality from the periphery toward the center. Because homogenous delivery of oxygen to three-dimensional (3D) cell cultures remains an unsolved challenge, we hypothesized that uneven oxygen supply may impede uniform cellular growth on scaffolds. In this study we challenged static and dynamic 3D culture systems designed for bone tissue engineering applications with a well-growing subclone of MC3T3-E1 preosteoblasts and continuously measured the oxygen concentrations in the center of cell-seeded scaffolds and in the surrounding medium. After as little as 5 days in static culture, central oxygen concentrations dropped to 0%. Subsequently, cells died in central regions of the scaffold but not in its periphery, where oxygen levels were approximately 4%. The use of perfusion bioreactors successfully prevented cell death, yet central oxygen concentrations did not rise above 4%. We conclude that 3D culture in vitro is associated with relevant oxygen gradients, which can be the cause of inhomogeneous tissue quality. Perfusion bioreactors prevent cell death but they do not entirely eliminate 3D culture-associated oxygen gradients. Therefore, we advise continuous oxygen monitoring of 3D culture systems to ensure tissue quality throughout engineered constructs.
Activation of nuclear factor κB in hepatitis C virus infection: Implications for pathogenesis and hepatocarcinogenesis (2000)

The hepatitis C virus (HCV) core protein is a multifunctional protein. It may bind to the death domain of tumor necrosis factor receptor 1 (TNFR1) and to the cytoplasmic tail of lymphotoxin-beta receptor, implying that it may be involved in the apoptosis and anti-apoptosis signaling pathways. In vitro studies have been inconclusive regarding its ability to inhibit or enhance TNF-alpha-induced apoptosis. To address this issue, electrophoretic mobility shift assay (EMSA) and immunohistochemical studies were used to show the activation of nuclear factor kappaB (NF-kappaB) in HCV-infected liver tissues and in HCV core-transfected cells. The activation of NF-kappaB was correlated with the apoptosis assays. The results showed that NF-kappaB activation could be shown in HCV-infected livers and HCV core-transfected cells. The data of EMSA correlated with those of immunohistochemical studies, which revealed a higher frequency of NF-kappaB nuclear staining in HCV-infected than in normal livers. NF-kappaB activation conferred resistance to TNF-alpha-induced apoptosis in HCV core-transfected cells. Inhibition of NF-kappaB activation by pyrrolidine dithiocarbamate sensitized them to TNF-alpha-induced apoptosis. These findings suggest that HCV infection may cause anti-apoptosis by activation of NF-kappaB and implicate a mechanism by which HCV may evade the host's immune surveillance leading to viral persistence and possibly to hepatocarcinogenesis.
Effects of Calmodulin on Aromatase Activity in the Preoptic Area (2005)

Oestrogens derived from the neural aromatisation of testosterone play a key role in the activation of male sexual behaviour in many vertebrates. Besides their slow action on gene transcription mediated by the binding to nuclear receptors, oestrogens have now been recognised to have more rapid membrane-based effects on brain function. Rapid changes in aromatase activity, and hence in local oestrogen concentrations, could thus rapidly modulate behavioural responses. We previously demonstrated that calcium-dependent kinases are able to down-regulate aromatase activity after incubations of 10-15 min in phosphorylating conditions. In the present study, in quail hypothalamic homogenates, we show that Ca2+ or calmodulin alone can very rapidly change aromatase activity. Preincubation with 1 mM EGTA or with a monoclonal antibody raised against calmodulin immediately increased aromatase activity. The presence of calmodulin on aromatase purified by immunoprecipitation and electrophoresis was previously identified by western blot and two consensus binding sites for Ca2+-calmodulin are identified here on the deduced amino acid sequence of the quail brain aromatase. The rapid control of brain aromatase activity thus appears to include two mechanisms: (i) an immediate regulatory process that involves the Ca2+-calmodulin binding site and (ii) a somewhat slower phosphorylation by several protein kinases (PKC, PKA but also possibly Ca2+-calmodulin kinases) of the aromatase molecule.
ASC amino-acid transporter 2 (ASCT2) as a novel prognostic marker in non-small cell lung cancer (2014)

ASC amino-acid transporter 2 expression has a crucial role in the metastasis of pulmonary AC, and is a potential molecular marker for predicting poor prognosis after surgery.
Cellular functions of immunophilins (1996)

Immunophilins are members of a highly conserved family of proteins all of which are cis-trans peptidyl-prolyl isomerases. The prototypic members of the immunophilin family, cyclophilin A and FKPB12, were discovered on the basis of their ability to bind and mediate the immunosuppressive effects of the drugs cyclosporin, FK506, and rapamycin. However, the prolyl isomerase activity of these proteins is not involved in any of the immunosuppressive effects. Indeed, despite the fact that all members of the family are prolyl isomerases, the cellular role of this enzymatic function has not been clearly defined. In many cases, immunophilins are widely expressed and are present at high levels in some tissues. Moreover, while the number of proteins that belong to the immunophilin family continues to grow, the natural cellular functions of all but a few remain obscure. An example where immunophilins do appear to have a defined cellular role, in the absence of immunosuppressive ligands, is the modulation of intracellular calcium release channel function by FKBP12 and FKBP12.6. In this case, FKBPs are integral parts of three types of calcium release channel complexes, skeletal and cardiac ryanodine receptors and the inositol 1,4,5-trisphosphate receptor. In each case, FKBPs modulate channel function possibly by enhancing the cooperativity between subunits.