gebhart/patrepeval huggingface dataset:
Transcriptional repression in Saccharomyces cerevisiae by a SIN3-LexA fusion protein. (1993)

The yeast SIN3 gene (also known as SDI1, UME4, RPD1, and GAM2) has been identified as a transcriptional regulator. Previous work has led to the suggestion that SIN3 regulates transcription via interactions with DNA-binding proteins. Although the SIN3 protein is located in the nucleus, it does not bind directly to DNA in vitro. We have expressed a LexA-SIN3 fusion protein in Saccharomyces cerevisiae and show that this fusion protein represses transcription from heterologous promoters that contain lexA operators. The predicted amino acid sequence of the SIN3 protein contains four copies of a paired amphipathic helix (PAH) motif, similar to motifs found in HLH (helix-loop-helix) and TPR (tetratricopeptide repeat) proteins, and these motifs are proposed to be involved in protein-protein interactions. We have conducted a deletion analysis of the SIN3 gene and show that the PAH motifs are required for SIN3 activity. Additionally, the C-terminal region of the SIN3 protein is sufficient for repression activity in a LexA-SIN3 fusion, and deletion of a PAH motif in this region inactivates this repression activity. A model is presented in which SIN3 recognizes specific DNA-binding proteins in vivo in order to repress transcription.
Infliximab Dose Reduction Sustains the Clinical Treatment Effect in Active HLAB27 Positive Ankylosing Spondylitis: A Two-Year Pilot Study (2013)

The rationale of the study was to evaluate the efficacy of infliximab (IFX) treatment in patients with ankylosing spondylitis (AS) and to determine whether IFX dose reduction and interval extension sustains the treatment effect. Nineteen patients were included and treated with IFX 5 mg/kg every 6 weeks for 56 weeks. All patients concomitantly received MTX with median dose 7.5 mg/weekly. During the second year, the IFX dose was reduced to 3 mg/kg every 8 weeks. Eighteen patients completed the 1-year and 15 patients the 2-year trial. The ≥50% improvement at week 16 from baseline of BASDAI was achieved in 16/19 (84%) patients. Significant reductions in BASDAI, BASFI, and BASMI scores, decrease in ESR and CRP, and improvement in SF-36 were observed at weeks 16 and 56. The MRI-defined inflammatory changes in the sacroiliac joints disappeared in 10/15 patients (67%) already at 16 weeks. IFX treatment effect was sustained throughout the second year after IFX dose reduction and interval extension. We conclude that IFX treatment is effective in well-established active AS and a dose reduction sustains the treatment effect. These observations are of clinical importance and open the opportunity to reduce the drug costs.
Opioid peptides derived from food proteins. The exorphins (1979)

Peptides with opioid activity are found in pepsin hydrolysates of wheat gluten and alpha-casein. The opioid activity of these peptides was demonstrated by use of the following bioassays: 1) naloxone-reversible inhibition of adenylate cyclase in homogenates of neuroblastoma X-glioma hybrid cells; 2) naloxone-reversible inhibition of electrically stimulated contractions of the mouse vas deferens; 3) displacement of [3H]dihydromorphine and [3H-Tyr, dAla2]met-enkephalin amide from rat brain membranes. Substances which stimulate adenylate cyclase and increase the contractions of the mouse vas deferens but do not bind to opiate receptors are also isolated from gluten hydrolysates. It is suggested that peptides derived from some food proteins may be of physiological importance.
Automatic dragon fruit counting using adaptive thresholds for image segmentation and shape analysis (2017)

In recent years there have been many proposals for automated applications in vegetable harvesting. There are two major challenges: estimation of yield and harvesting of fruit trees. This research proposes a new algorithm that allows accurate counting of the number of fruits on a tree to accurately estimate the output of a dragon fruit. The algorithm consists of the following main steps: image segmentation, boundary determination, shape analysis, and overlap analysis to count the number of dragon fruits per tree. Experimental results show that the algorithm can solve the problem of counting the correct number of fruits per tree to accurately estimate the yield of dragon fruit in the farm.
Interaction between UV-damaged DNA Binding Activity Proteins and the c-Abl Tyrosine Kinase (2002)

The c-Abl tyrosine kinase is activated by some forms of DNA damage, including ionizing radiation, but not UV radiation. The functions of this activation in the damage response pathways remain obscure. To identify potential targets of c-Abl kinase, we utilized the yeast two-hybrid system to screen a murine cDNA library. One c-Abl binding protein of particular interest was the large subunit (DDB1) of the heterodimeric complex with UV-damaged DNA binding activity (UV-DDB). This complex binds with high specificity to DNA damaged by UV, is absent in a subset of xeroderma pigmentosum group E cells, and is required for global genomic repair of UV-induced damage. The association of c-Abl with DDB1 required the kinase domain of c-Abl and preserved the interaction between DDB1 and the small subunit (DDB2) of the UV-DDB complex. Significantly, overexpression of c-Abl increased tyrosine phosphorylation of DDB2 and suppressed UV-DDB activity. Conversely, a dominant negative, kinase-deficient allele of c-Abl decreased tyrosine phosphorylation of DDB2 and dramatically stimulated UV-DDB activity. These results suggest that one role of c-Abl may be to negatively regulate UV-DDB activity by phosphorylation of DDB2.
Role of HZSM-5 Aluminosilicates on Asphaltenes Deposition by High-Throughput in Situ Characterizations of a Microreservoir (2017)

Hydrocarbon reservoirs are complex in their mineralogy and chemistry. Microfluidics offers an effective platform for rapid, in situ characterizations at experimental conditions that intend to simulate sandstone reservoirs (near wellbore, in production time scale). We have begun to examine the influence of the Al2O3/SiO2 ratio (an important characteristic of reservoir mineralogy) on asphaltenes precipitated in quartz packed-bed microreactors using in situ Raman spectroscopy (2D to 3D mapping), UV–vis spectroscopy, and pressure sensors. The reservoir matrix was created by injecting 707 nm·aggregate–1 HZSM-5 zeolite fine particles (a model aluminosilicate available with Al2O3/SiO2 ratios of 1/91 and 1/26) on a quartz bed. The methodologies were developed to identify the effect of the chemical interactions, giving insights about asphaltenes’ sheet size (nm) and bed occupancy variations. Our results show that, in the precipitation process, an Al2O3/SiO2 ratio of 1/26 leads to 13% higher asphaltenes’ sheet size and >10% higher bed occupancy compared to a bed with no Al2O3 particles. When increasing the ratio, the number of pore volumes required to plug the pore throats increases, leading to greater deposit thickness. Our findings support that the Al2O3 content delays asphaltenes’ nanoaggregation and has higher selectivity toward bigger molecules.
DCT based error concealment for RTSP video over a modem Internet connection (2002)

Data lost in the form of dropped packets is a major obstacle to actualizing real time Internet video via modem connection with frame rates as high as 30 frames per second. Error concealment (EC) techniques must restore the lost data. Due to rigid system specifications of this application, only the computationally simplest error concealment methods are plausible. Replication, which is the simplest temporal error concealment (TEC) method, fits well in this situation. There are however circumstances when replication is inadequate and linear interpolation, the simplest spatial EC, is used in its place. In this work, we consider an alternative spatial EC to linear interpolation, i.e. the DCT-coefficient based EC algorithm, with comparable computational cost and consistently better image quality in real-time Internet video applications.
Cloning and expression of the potato alternative oxidase gene (1990)

Mitochondria from 24-hour-aged potato slices possess an alternative path capacity and a 36kD protein not present in fresh potato mitochondria. This 36kD protein was identified by a monoclonal antibody against the Sauromatum guttatum alternative oxidase. These results suggest de novo synthesis of the 36kD protein during the aging process. To investigate this phenomenon, a clone containing a potato alternative oxidase gene was isolated from a cDNA library using the S. guttatum gene as a probe. This clone shows areas of high homology to the S. guttatum gene. Norther blots of RNA from fresh and 24-hour-aged potato slices are being probed with the potato gene to examine its expression in relation to the appearance of the 36kD protein.
Skin-Surface Warming (1990)

The authors determined the efficacy of four postoperative warming devices by measuring cutaneous and tympanic membrane temperatures, and heat loss/gain using 11 thermocouples and ten thermal flux transducers in five healthy, unanesthetized volunteers. Overall thermal comfort was evaluated at 5-10 min intervals using a 10-cm visual analog scale. The warming devices were: 1) a pair of 250-W infrared heating lamps mounted 71 cm above the abdomen; 2) the Thermal Ceiling MTC XI UL (500 W) set on "high" and mounted 56 cm above the volunteer; 3) a 54-by-145-cm circulating-water blanket set to 40 degrees C placed over the volunteer; and 4) the Bair Hugger forced air warmer with an adult-sized cover set on "low" (approximately 33 degrees C), "medium" (approximately 38 degrees C), and "high" (approximately 43 degrees C). Following a 10-min control period, each device was placed over the volunteer and activated for a 30-min period. All devices were started "cold" and warmed up during the study period. The Bair Hugger set on "medium" decreased heat loss more than each radiant warming device and as much as the circulating-water blanket. All methods reached maximum efficacy within 20 min. Set on "high," the Bair Hugger increased skin-surface temperature more than the circulating-water blanket. The Bair Hugger (all settings) and the water blanket raised skin temperature more than the radiant heaters. The circulating-water blanket was the most effective device for heating an optimally placed transducer on the chest (directly under and parallel to the radiant heat sources, and touching the water and Bair Hugger blankets).(ABSTRACT TRUNCATED AT 250 WORDS)
Securing Mobile Ad Hoc Networks with Certificateless Public Keys (2006)

This paper studies key management, a fundamental problem in securing mobile ad hoc networks (MANETs). We present IKM, an ID-based key management scheme as a novel combination of ID-based and threshold cryptography. IKM is a certificateless solution in that public keys of mobile nodes are directly derivable from their known IDs plus some common information. It thus eliminates the need for certificate-based authenticated public-key distribution indispensable in conventional public-key management schemes. IKM features a novel construction method of ID-based public/private keys, which not only ensures high-level tolerance to node compromise, but also enables efficient network-wide key update via a single broadcast message. We also provide general guidelines about how to choose the secret-sharing parameters used with threshold cryptography to meet desirable levels of security and robustness. The advantages of IKM over conventional certificate-based solutions are justified through extensive simulations. Since most MANET security mechanisms thus far involve the heavy use of certificates, we believe that our findings open a new avenue towards more effective and efficient security design for MANETs
Survival of Autologous Fat Grafts in Humans and in Mice (1981)

Autologous fat grafts have been used in a number of surgical procedures, yet properties of fat as a transplant material have remained unclear. This study was designed to compare experimental observations of subcutaneous fat grafts in mice with clinical observations of autologous fat grafts placed over the dura following laminectomy in humans. Subcutaneous fat grafts were observed daily in 75 CFl mice with the use of modified Algire back chambers. Grafts were examined histologically and histochemically at intervals up to 60 days after transplantation. Gross and microscopic observations suggest that fat grafts went through a period of initial breakdown of fat cells which was followed by revascularization. This resulted in normal appearing fat, although a smaller volume than the original graft. Three samples of autologous fat grafts from humans were removed during reoperation in the lumbar region up to 22 months after the original procedure. Histological examination revealed revascularized grafts reduced in size: the fat was normal and never replaced by scar tissue.
Robust design of a dynamically controlled low-power level-up shifter operating up to 300V (2004)

A new low-power level-up shifter circuit is presented. This circuit produces a digital output signal in the 0-300 V range from a digital input signal in the 0-5 V range. The proposed circuit reduces power through two key features: dynamic charge control reduces the power dissipated in the level-up stage, and a "break before make" logic reduces the short-circuit power of the output stage. Detailed design methodology and optimized circuits for different voltage ranges are described in this paper. This circuit is designed under DALSA semiconductor's 0.8 /spl mu/m 5 V/HV CMOS/DMOS technology. Simulation results validate its operation and performance.
Cellular transfer of macromolecules across the developing choroid plexus of <i>Monodelphis domestica</i> (2009)

Choroid plexus epithelial cells secrete cerebrospinal fluid (CSF) and transfer molecules from blood into CSF. Tight junctions between choroidal epithelial cells are functionally effective from early in development: the route of transfer is suggested to be transcellular. Routes of transfer for endogenous and exogenous plasma proteins and dextrans were studied in Monodelphis domestica (opossum). Pups at postnatal (P) days 1-65 and young adults were injected with biotinylated dextrans (3-70 kDa) and/or foetal protein fetuin. CSF, plasma and brain samples were collected from terminally anaesthetized animals. Choroid plexus cells containing plasma proteins were detected immunocytochemically. Numbers of plasma protein-positive epithelial cells increased to adult levels by P28, but their percentage of plexus cells declined. Numbers of cells positive for biotinylated probes increased with age, while their percentage remained constant. Colocalization studies showed specificity for individual proteins in some epithelial cells. Biotinylated probes and endogenous proteins colocalized in about 10% of cells in younger animals, increasing towards 100% by adulthood. Injections of markers into the ventricles demonstrated that protein is transferred only from blood into CSF, whereas dextrans pass in both directions. These results indicate that protein and lipid-insoluble markers are transferred by separate mechanisms present in choroid plexuses from the earliest stage of brain development, and transfer of proteins from plasma across choroid plexus epithelial cells contributes to the high protein concentration in CSF in the immature brain.
Induction of Cytokine Gene Expression in Human Thyroid Epithelial Cells Irradiated with HZE Particles (Iron Ions) (2009)

Gene expression profiles were examined using cDNA microarray technology in human thyroid epithelial (Htori-3) cells exposed to a low, non-toxic dose (10 cGy) of radiation from HZE particles in the form of iron ions in the absence or presence of selenomethionine (SeM). A total of 215 genes were differentially regulated 2 h after exposure to a 10-cGy dose of iron-ion radiation. In the microarray analysis, SeM had profound effects on the radiation-induced expression of several specific genes, which includes PLAU, IGFBP3, FOLR1, B4GALT1 and COL1A1. Of particular interest to us was a gene cluster, "secreted proteins", that was up-regulated after radiation exposure. Seven up-regulated genes of this gene cluster fall within the chemokine/cytokine gene cluster, namely, CXCL1, CXCL2, IL6, IL11, IL8, IL24 and TGFbeta2. In microarray studies, the radiation-induced up-regulated expression of some these genes encoding cytokine/chemokine proteins was significantly decreased by SeM treatment. For IL8, TGFbeta2, CXCL1 and CXCL2, these observations were validated by qPCR techniques. It is concluded that SeM can regulate ionizing radiation-induced gene expression and may serve as an effective countermeasure for some of the acute inflammatory/immune responses induced by low-dose HZE-particle radiation.
Voice Communication in Integrated Digital Voice and Data Networks (1980)

Voice communication networks have traditionally been designed to provide either analog signal paths or fixed-rate synchronous digital connections between individual subscribers. These designs were aimed at accommodating the "streamlike" character of speech, which has traditionally been considered to flow from source to destination at a more or less constant rate. By way of contrast, interactive and computer-to-computer data transactions tend to be "bursty" in nature, and this has given rise to the development of packet-switching methods for data communications. The dichotomous nature of these two major traffic classes and the apparent conflict between the types of network services they require has resulted in the deployment of separate military communications facilities for voice and data. A challenge in the design of future systems is to achieve overall economy and flexibility in the allocation of resources via the efficient integration of both traffic types in common network facilities. This paper summarizes a number of advanced concepts for switching and flow control of combined voice and data traffic in integrated environments. Performance characteristics are described based on analysis results and computer simulation studies for both multilink terrestrial and broadcast satellite network topologies.
LexOnto: A Model for Ontology Lexicons for Ontology-based NLP (2007)

Abstract. In this paper we present a model and a corresponding ontology for associating lexical information to entities of a given domain ontology. In particular, we focus on representing subcategorization frames as well as their mapping to ontological structures. The lexicon model and ontology can thus be used to specify the syntax-semantic interface for ontology-based NLP systems which are expected to produce output compliant with a specific domain ontology. Our lexicon ontology itself is formalized in the OWL language, thus allowing the lexica to be published together with the domain ontologies. We also discuss different ways how the creation of appropriate lexica can be supported. 1
Quantum-well charge-coupled devices for charge-coupled device-addressed multiple-quantum-well spatial light modulators (1986)

We have demonstrated a new type of GaAs/AlGaAs charge-coupled device (CCD) in which the charge is confined to a quantum-well channel. The MBE-grown quantum-well CCD (designated QWCCD) has a channel consisting of a 140 Å GaAs layer clad on both sides by AlGaAs layers. This structure was grown on a multiple-quantum-well (MQW) structure consisting of 60 periods of GaAs and AlGaAs layers of about 100 Å thickness each. Large optical modulation effects involving quantum-confined excitons were observed in the MQW structure when a bias was applied perpendicular to the plane of the layers. The combination of QWCCD and MQW structures has promise as a high-speed spatial light modulator for applications in optical signal processing.
Hyperpolarized butyrate: A metabolic probe of short chain fatty acid metabolism in the heart (2013)

In this study, butyrate has been demonstrated to be a suitable hyperpolarized substrate capable of revealing multi-step metabolism in dynamic nuclear polarization experiments and providing information on the metabolism of fatty acids not currently achievable with other hyperpolarized substrates.
Molecules of Parasites as Immunomodulatory Drugs (2004)

Parasite molecules offer unique advantages for the treatment of immunologicical disorders, and several candidate molecules have been shown to be effective. In our studies, it was shown that a factor inducing immunoglobulin E from filarial nematode parasites was suppressive in animal models of immunological disorders such as allergy and insulin dependent diabetes mellitus (IDDM). The Th1/Th2 paradigm of CD4+ T helper cell subsets can provide the basis for the development of new types of drugs and of novel strategies for the treatment of allergic and autoimmune disorders by parasite molecules. In our experimental system, parasite molecules from a filarial nematode parasite led to the down-regulation of the allergic reaction in animal models. In the majority of hosts, infection with helminths is associated with markedly reduced cellular immune reactions and polarization of T cell responses to Th2 and Th3 types. Some studies have suggested that the stimulation of host immunoregulatory networks with parasite molecules leading to the synthesis of anti-inflammatory cytokines (interleukin10, transforming growth factor-beta (TGF-beta and others) can provide new therapy for immunological disorders. It is known that parasites produce some types of molecule that mimic host molecules such as CD40 ligand, TGF-beta and macrophage migration inhibitory factor. These molecules are also candidates for medicinal agents. This review describes many of the latest possibilities in this field and shows how they can be best put to use for the development of medicinal agents, molecular target identification, and for prioritization.
Fabrication and mechanical behavior of dye-doped polymer optical fiber (2002)

The purpose of this article is to study the materials physics behind dye-doped polymethyl metharcylate (PMMA) that is important for the optical fiber drawing process. We report effects of the fabrication process on the mechanical properties of the final fiber. The qualitative degree of polymer chain alignment is found to increase with the drawing force, which in turn decreases with the drawing temperature and increases with the drawing ratio. The chain alignment relaxes when the fibers are annealed at 95 °C with a commensurate decrease in fiber length and increase in diameter. The annealed fiber has higher ductility but lower strength than the unannealed fiber. Both the yield and tensile strengths are dependent on the strain rate. The relationship between tensile strength, σb, and fiber diameter, d, is found empirically to be σb∝d−0.5. The yield strength appears to be less sensitive to the fiber diameter than the tensile strength. For PMMA doped with disperse red 1 azo dye, the yield strength, tensile strength, and Young’s modulus peak at a dye concentration of 0.0094 wt %. These results are useful for designing polymer optical fibers with well-defined mechanical properties.