gebhart/patrepeval huggingface dataset:
Defining a novelciselement in the 3′-untranslated region of mammalian ribonucleotide reductase component R2 mRNA: role in transforming growth factor-β1induced mRNA stabilization (1995)

Ribonucleotide reductase R2 gene expression is elevated in BALB/c 3T3 fibroblasts treated with transforming growth factor beta 1. We investigated the possibility that the 3'-UTR of ribonucleotide reductase R2 mRNA contains regulatory information for TGF-beta 1 induced message stability. Using end-labeled RNA fragments in gel shift assays and UV cross-linking analyses, we detected in the 3'-UTR a novel 9 nucleotide (nt) cis element, 5'-GAGUUUGAG-3' site, which interacted specifically with a cytosolic protease sensitive factor to form a 75 kDa complex. The cis element protein binding activity was inducible and markedly up-regulated cross-link 4 h after TGF-beta 1 treatment of mouse BALB/c 3T3 cells. Other 3'-UTRs [IRE, GM-CSF, c-myc and homopolymer (U)] were poor competitors to the cis element with regard to forming the TGF-beta 1 dependent RNA-protein complex. However, the cis element effectively competed out the formation of the R2 3'-UTR protein complex. Cytosolic extracts from a variety of mammalian cell lines (monkey Cos7, several mouse fibrosarcomas and human HeLa S3) demonstrated similar TGF-beta 1 dependent RNA-protein band shifts as cell extract from BALB/c 3T3 mouse fibroblasts. Binding was completely prevented by several different mutations within the cis element, and by substitution mutagenesis, we were able to predict the consensus sequences, 5'-GAGUUUNNN-3' and 5'-NNNUUUGAG-3' for optimal protein binding. These results support a model in which the 9 nt region functions in cis to destabilize R2 mRNA in cells; and upon activation, a TGF-beta 1 responsive protein is induced and interacts with the 9 nt cis element in a mechanism that leads to stabilization of the mRNA. This appears to be the first example of a mRNA binding site that is involved in TGF-beta 1-mediated effects.
Autonomie feedback with brain entrainment (2013)

The study focused on the autonomous feedback with brain entrainment, specifically involving an user-friendly interface to control brainwave entrainment by variation in cardiac autonomie function. In combination with generation of brainwave entrainment, the device would be capable of delivering relief from pressure for user. The platform included several key technologies, such that the device could use measured cardiac rhythmic variation to control a multi-channel oscillators to bring the brain to a specific entrainment state. The excitatory state of autonomie activity, which was reflected by the cardiac rhythmic variation, including the overall potential level of autonomie activity, the potential from the sympathetic branch, and the parasympathetic activity, could be used as biofeedback of body status and an evidence of interaction for more personalized adaptation. This platform could be embedded in beds, chairs, or even the floors to provide a realistic interactive experience.
DAIDALUS: Detect and Avoid Alerting Logic for Unmanned Systems (2015)

This paper presents DAIDALUS (Detect and Avoid Alerting Logic for Unmanned Systems), a reference implementation of a detect and avoid concept intended to support the integration of Unmanned Aircraft Systems into civil airspace. DAIDALUS consists of self-separation and alerting algorithms that provide situational awareness to UAS remote pilots. These algorithms have been formally specified in a mathematical notation and verified for correctness in an interactive theorem prover. The software implementation has been verified against the formal models and validated against multiple stressing cases jointly developed by the US Air Force Research Laboratory, MIT Lincoln Laboratory, and NASA. The DAIDALUS reference implementation is currently under consideration for inclusion in the appendices to the Minimum Operational Performance Standards for Unmanned Aircraft Systems presently being developed by RTCA Special Committee 228.
Kallikrein-related peptidase genes as promising biomarkers for prognosis and monitoring of human malignancies (2010)

Tissue kallikrein (KLK1) and the kallikrein-related peptidase (KLK2-15) genes encode for a subgroup of 15 homologous secreted serine proteases possessing numerous physiological roles, such as the regulation of blood pressure, hormone processing and tissue remodeling. The expression of KLKs is detected in a broad spectrum of human tissues where it has been found to be regulated mainly by steroids hormones. The aberrant expression of KLKs, presented in many human malignancies, highlights the significance of this gene family for early diagnosis, prognosis and monitoring of cancer patients, as it is strongly emphasized by the routine use of PSA (KLK3) for prostate cancer management. Here, we review the presently known data regarding the role of KLKs as cancer biomarkers, giving emphasis on novel information about the subject.
The role of Fcγreceptor polymorphisms and C3 in the immune defence againstNeisseria meningitidisin complement-deficient individuals (2000)

Individuals with either a late (C5-9) complement component deficiency (LCCD) or properdin deficiency are at increased risk to develop meningococcal disease, often due to serogroups W135 and Y. Anti-meningococcal defence in both LCCD persons and properdin-deficient individuals without bactericidal antibodies depends mainly on phagocytosis. Three types of opsonin receptors are involved in phagocytosis by polymorphonuclear cells (PMN). These represent the polymorphic FcgammaRIIa (CD32) and FcgammaRIIIb (CD16b) receptors, and the C3 receptor CR3 (CD11b/CD18). When the distribution of FcgammaRIIa and FcgammaRIIIb allotypes was assessed in 15 LCCD and in 15 properdin-deficient patients with/without previous meningococcal disease, we found the combination of FcgammaRIIa-R/R131 with FcgammaRIIIb-NA2/NA2 allotypes to be associated with previous meningococcal disease (odds ratio 13.9, Fisher's test P = 0.036). No such relation was observed in the properdin-deficient patients. The importance of FcgammaRIIa allotypes was also demonstrated using in vitro phagocytosis assays. PMN from FcgammaRIIa-R/R131 homozygous donors internalized IgG2 opsonized meningococci W135 significantly (P < 0.05) less than PMN from FcgammaRIIa-H/H131 donors. When properdin-deficient serum was tested, it was observed that reconstitution with properdin resulted in enhanced PMN phagocytosis of the W135 meningococci (P = 0.001). This enhanced phagocytosis was parallelled by an increase in C3 deposition onto the opsonized meningococci W135 (r = 0.6568, P = 0. 01). We conclude that the occurrence of meningococcal disease in LCCD patients is associated with certain FcgammaR allotypes. Properdin-deficient individuals are susceptible to meningococcal disease because of an insufficient C3 deposition on the surface of meningococci, resulting in insufficient phagocytosis.
Block of LTP in rat hippocampus in vivo by β-amyloid precursor protein fragments (1997)

The effects of beta-amyloid precursor protein (beta-APP) fragments on plasticity of glutamtatergic synaptic transmission were examined in the hippocampus of urethane anaesthetized rats. I.c.v. injection of beta-amyloid (A beta) 1-40 and 1-42 and the C-terminal fragment CT105 greatly shortened the duration of high frequency stimulation-induced long-term potentiation (LTP) of field excitatory postsynaptic potentials in the CA1 area. Whereas in vehicle injected animals LTP was stable over a 5 h recording period, doses of these peptides (A beta 1-40, 0.4 and 3.5 nmol; A beta1-42, 0.01 nmol; CT105, 0.05 nmol) which did not affect baseline synaptic transmission abolished LTP within 3-5 h. The reduced duration of this form of synaptic plasticity may contribute to the cognitive deficits in Alzheimer's disease.
Novel Agonist Monoclonal Antibodies Activate TrkB Receptors and Demonstrate Potent Neurotrophic Activities (2006)

Tyrosine kinase receptor B (TrkB) mediates neurotrophic effects of brain-derived neurotrophic factor (BDNF) to increase neuronal survival, differentiation, synaptic plasticity, and neurogenesis. The therapeutic potential of TrkB activation using BDNF has been demonstrated well in several preclinical models of CNS diseases, validating TrkB as a promising drug target. Therefore, we aimed to develop TrkB-specific receptor agonists by using a monoclonal antibody approach. After generation of hybridoma clones and assessment of their binding and functional activity, we identified five mouse monoclonal antibodies that show highly selective binding to TrkB and that induce robust activation of TrkB signaling. Epitope mapping studies using competition analysis showed that each of the monoclonal antibodies recognizes a unique binding site on TrkB, some of which are distinct from BDNF docking sites. These antibodies behave as true agonists based on their ability to both activate proximal and secondary signaling molecules downstream of TrkB receptors and promote neuronal survival and neurite outgrowth. The binding affinities and the functional efficacy of these antibodies are comparable to those of BDNF, whereas they do not bind to the p75 low-affinity neurotrophin receptor at all. Therefore, they could represent novel reagents to explore the pathophysiological roles of TrkB and its potential therapeutic utility in treating CNS disorders.
Polymeric Prodrugs: Novel Polymers with Bioactive Components (1998)

Our goal is to synthesize a polymer that will act as a controlled delivery device in targeting specific areas, such as the colon, over an extended period of time. The polymers we are synthesizing, poly(anhydride-esters), are composed of alkyl chains linked by ester bonds to aromatic moieties, specifically salicylic acid -- the active component of aspirin. With the medicinal properties attributed to salicylic acid and the ease of metabolism, the incorporation of this compound into a polymer backbone yields a polymeric prodrug that may have potential in a variety of applications, in particular, inflammatory bowel disease. For these reasons, we designed a synthetic scheme that yields the desired poly(anhydride-esters). Interest in these polymers arises from the fact that the polymer degradation products may reduce symptoms associated with inflammatory bowel disease.
First light performance of a near-UV spatial heterodyne spectrometer for interstellar emission line studies (2004)

This paper describes the characteristics and performance of a novel spatial heterodyne spectrometer designed to measure the extremely faint [OII] 372.6 nm (&lambda;3726 &angst;) and 372.9 nm (&lambda;3729 &angst;) emission lines from the warm (10,000 K) ionized component of our Galaxy's interstellar medium. These [OII] lines are a principal coolant for this wide spread, photoionized gas and are a potential tracer of variations in the gas temperature resulting from unidentified interstellar heating processes that appear to be acting within the Galaxy. In the basic SHS system, Fizeau fringes of wavenumber-dependent spatial frequency are produced by a Michelson interferometer modified by replacing the return mirrors with diffraction gratings; these fringes are recorded on a position sensitive detector and Fourier transformed to recover the spectrum over a limited spectral range centered at the Littrow wavenumber of the gratings. The system combines interferometric and field-widening gains in tandem to achieve 10,000-fold sensitivity gains compared to conventional grating instruments of similar size and resolving power. SHS systems also have relaxed flatness tolerances (20-50 times compared to Fabry-Perots) and do not require precision imaging to achieve diffraction-limited spectroscopic performance. Defects can largely be removed in data processing. Early results from our [OII] SHS system confirm the superb performance of the SHS technique for measurements of spatially extended faint emissions, including the first detection of [OII] emission lines extending out to 20 degrees from the Galactic equator ([OII] intensities ranged from tens of rayleighs near the Galactic plane to less than one rayleigh at high latitudes; the [OII] line profiles show structure indicating emission along the lines of sight from both the local interstellar gas and more distant gas in the Perseus spiral arm).
Carbon nanotube arrays and their composites for electrochemical capacitors and lithium-ion batteries (2009)

One of the greatest challenges for our society is to provide powerful electrochemical energy conversion and storage devices. Electrochemical capacitors and lithium-ion batteries are among the most promising candidates in terms of power- and energy-densities. The choice of electrode material is key to improving the performance of these energy conversion devices. Carbon nanotube arrays (CNTAs) and their composites show good capacity, excellent rate performance, and long cycle life when used as electrode materials because they present superior electronic conductivity, high surface area, developed porous structure, and robust properties. This review deals with recent progress in the fabrication, microstructure, and energy storage performance of different CNTA electrodes and their composites in electrochemical capacitors and lithium-ion batteries. In particular, representative examples of our CNTA-based electrodes are highlighted.
Exact Design of Band-Stop Microwave Filters (1964)

An exact method for the design of band-stop filters which adapts synthesis techniques due to Ozaki and Ishii is discussed. This method places no theoretical limit on the width of the stop-band, although, for practical reasons, different (but equivalent) circuit configurations are used for stop-bands of different widths.These configurations include a form having open-circuited shunt stubs separated by lengths of line; a second form using resonators which are separate from the main line but parallel to it, so that coupling takes place by way of fringing fields; and a third form in which the resonators are attached directly to the main line, but are folded parallel to it so that coupling is both by direct connection and by fringing fields. Easy to use formulas are given for the exact design of band-stop filters from low-pass prototype filters and equations are given for converting from one form of filter structure to any of the other equivalent forms. The experimental results of trial designs are presented.
A Body-mounted Camera System for Capturing User-view Images without Head-mounted Camera (2005)

In this paper, we propose a body-mounted system to capture the user's experience as multiple-sensor information. The proposed system consists of three cameras (stereo cameras and one wide-angle camera) and other sensors (a microphone, a GPS (global positioning system), a digital compass, and an acceleration sensor). The stereo cameras are used for capturing the user's head motions, while the wide-angle color camera is used for capturing the user's frontal view images. An image region approximately corresponding to the user's view is then synthesized from the wide-angle image based on the estimated human head motions. Other sensors record audio, global position and pose information. These data contain significant information for recording/analyzing human activities and can be used in wider application domains such as a digital diary or interaction analysis. In addition, this system can overcome the disadvantages of head-mounted cameras in terms of the ease of putting on/taking off the device and its less obtrusive visual impact on other persons. Experimental results demonstrate the effectiveness of the proposed system.
The integrin αvβ8 mediates epithelial homeostasis through MT1-MMP–dependent activation of TGF-β1 (2002)

Integrins, matrix metalloproteases (MMPs), and the cytokine TGF-beta have each been implicated in homeostatic cell behaviors such as cell growth and matrix remodeling. TGF-beta exists mainly in a latent state, and a major point of homeostatic control is the activation of TGF-beta. Because the latent domain of TGF-beta1 possesses an integrin binding motif (RGD), integrins have the potential to sequester latent TGF-beta (SLC) to the cell surface where TGF-beta activation could be locally controlled. Here, we show that SLC binds to alpha(v)beta8, an integrin expressed by normal epithelial and neuronal cells in vivo. This binding results in the membrane type 1 (MT1)-MMP-dependent release of active TGF-beta, which leads to autocrine and paracrine effects on cell growth and matrix production. These data elucidate a novel mechanism of cellular homeostasis achieved through the coordination of the activities of members of three major gene families involved in cell-matrix interactions.
Mode-locked erbium-doped fiber laser with soliton pulse shaping (1989)

We have generated pulses as short as 4 psec at 1530 nm from a mode-locked erbium-doped fiber laser. The mode locker is a wide-bandwidth, lithium niobate guided-wave modulator, and the fiber laser is completely integrated. We present evidence that soliton pulse shaping is playing a key role in the formation of the pulses.
Delayed Hypersensitivity to Fungal Antigens in Mice. II. Molecular Classes in Immunogenic RNA Extracts that Transfer Delayed Hypersensitivity (1976)

The transfer of delayed hypersensitivity to Coccidioides immitis and Candida albicans antigens with immunogenic RNA extracts was studied in a mouse model. Sensitivity was measured by skin tests and footpad swelling responses. Immunogenic RNA converted normal spleen cells in vitro so that they produced antigenspecific delayed hypersensitivity in mice that were given injections of the cells. RNase reduced the rate of, but did not abolish, in vitro interaction of immunogenic RNA extracts with lymphocytes. Immunogenic RNA transferred sensitivity on direct intraperitoneal inoculation into mice. The transfer ability was resistant to RNase preparations active against both single- and double-stranded RNA. Sedimentation gradient fractions of the immunogenic RNA were assayed by intraperitoneal injection, and converting activity was found in two fractions, >33S and 6S–13S. After treatment with RNase, all activity was shifted to the <6S fraction. Two fractions of the immunogenic RNA in its native state (>33S and 6S–13S) were also able to convert spleen cells. The data indicate that the transfer of delayed hypersensitivity by immunogenic RNA preparations is associated with RNA but may not require the intact RNA molecule.
Positional cues specify and maintain aleurone cell fate in maize endosperm development (2000)

A genetic analysis of maize aleurone development was conducted. Cell lineage was examined by simultaneously marking cells with C1 for anthocyanin pigmentation in the aleurone and wx1 for amylose synthesis in the starchy endosperm. The aleurone and starchy endosperm share a common lineage throughout development indicating that positional cues specify aleurone fate. Mutants in dek1 block aleurone formation at an early stage and cause peripheral endosperm cells to develop as starchy endosperm. Revertant sectors of a transposon-induced dek1 allele showed that peripheral endosperm cells remain competent to differentiate as aleurone cells until late in development. Ds-induced chromosome breakage was used to generate Dek1 loss-of-function sectors. Events occurring until late development caused aleurone cells to switch fate to starchy endosperm indicating that cell fate is not fixed. Thus, positional cues are required to specify and maintain aleurone fate and Dek1 function is required to respond to these cues. An analysis of additional mutants that disrupt aleurone differentiation suggests a hierarchy of gene functions to specify aleurone cell fate and then control aleurone differentiation. These mutants disrupt aleurone differentiation in reproducible patterns suggesting a relationship to endosperm pattern formation.
Bismuth-212-labeled anti-Tac monoclonal antibody: alpha-particle-emitting radionuclides as modalities for radioimmunotherapy. (1986)

Anti-Tac, a monoclonal antibody directed to the human interleukin 2 (IL-2) receptor, has been successfully conjugated to the alpha-particle-emitting radionuclide bismuth-212 by use of a bifunctional ligand, the isobutylcarboxycarbonic anhydride of diethylenetriaminepentaacetic acid. The physical properties of 212Bi are appropriate for radioimmunotherapy in that it has a short half-life, deposits its high energy over a short distance, and can be obtained in large quantities from a radium generator. Antibody specific activities of 1-40 microCi/microgram (1 Ci = 37 GBq) were achieved. Specificity of the 212Bi-labeled anti-Tac was demonstrated for the IL-2 receptor-positive adult T-cell leukemia line HUT-102B2 by protein synthesis inhibition and clonogenic assays. Activity levels of 0.5 microCi or the equivalent of 12 rad/ml of alpha radiation targeted by anti-Tac eliminated greater than 98% the proliferative capabilities of HUT-102B2 cells with more modest effects on IL-2 receptor-negative cell lines. Specific cytotoxicity was blocked by excess unlabeled anti-Tac but not by human IgG. In addition, an irrelevant control monoclonal antibody of the same isotype labeled with 212Bi was unable to target alpha radiation to cell lines. Therefore, 212Bi-labeled anti-Tac is a potentially effective and specific immunocytotoxic reagent for the elimination of IL-2 receptor-positive cells. These experiments thus provide the scientific basis for use of alpha-particle-emitting radionuclides in immunotherapy.
Preliminary Assessment of the Occurrence and Possible Sources of MTBE in Groundwater in the United States, 1993−1994 (1996)

The 1990 Clean Air Act Amendments require fuel oxygenates to be added to gasoline used in some metropolitan areas to reduce atmospheric concentrations of carbon monoxide or ozone. Methyl tert-butyl ether (MTBE) is the most commonly used fuel oxygenate and is a relatively new gasoline additive. Nevertheless, out of 60 volatile organic chemicals analyzed, MTBE was the second most frequently detected chemical in samples of shallow ambient groundwater from urban areas that were collected during 1993−1994 as part of the U.S. Geological Survey's National Water-Quality Assessment program. Samples were collected from five drinking water wells, 12 springs, and 193 monitoring wells in urban areas. No MTBE was detected in drinking water wells. At a reporting level of 0.2 μg/L, MTBE was detected most frequently in shallow groundwater from urban areas (27% of 210 wells and springs sampled in eight areas) as compared to shallow groundwater from agricultural areas (1.3% of 549 wells sampled in 21 areas) or deeper groundwater from major aquifers (1.0% of 412 wells sampled in nine areas). Only 3% of the shallow wells sampled in urban areas had concentrations of MTBE that exceed 20 μg/L, which is the estimated lower limit of the United States Environmental Protection Agency draft drinking water health advisory. Because MTBE is persistent and mobile in groundwater, it can move from shallow to deeper aquifers with time. In shallow urban groundwater, MTBE generally was not found with benzene, toluene, ethylbenzene, or xylene (BTEX) compounds, which commonly are associated with gasoline spills. This disassociation causes uncertainty as to the source of MTBE. Possible sources of MTBE in groundwater include point sources, such as leaking storage tanks, and non-point sources, such as recharge of precipitation and stormwater runoff.