gebhart/patrepeval huggingface dataset:
Position and density effects on repression by stationary and mobile DNA-binding proteins. (1989)

We have investigated the effects of two types of DNA-binding proteins on bacterial repression. First, the effects of operator positioning on repression by stationary DNA-binding proteins, the Lac repressor and the Trp repressor, were examined in vivo. Both operator number and positioning play a role in determining in vivo levels of repression. Operators located within a promoter are more efficient regulators than those positioned at the start of transcription. Second, we investigated the effects of DNA-binding protein density on repression using a mobile DNA-binding protein, Escherichia coli RNA polymerase. We employed a transcriptional interference assay using convergent transcriptional units. The strong synthetic promoter conI and its derivatives were observed to interfere with expression of the aadA gene, which confers spectinomycin resistance upon its host. Transcriptional interference by RNA polymerase occurred only in cis and had a strong dependence on polymerase density that was modulated by varying the promoter strengths. A change in the density of approximately fourfold completely abolished the observed transcriptional interference. Several models are discussed to explain the repression patterns observed for stationary and mobile DNA-binding proteins.
CARS: Context-Aware Rate Selection for vehicular networks (2008)

Traffic querying, road sensing and mobile content delivery are emerging application domains for vehicular networks whose performance depends on the throughput these networks can sustain. Rate adaptation is one of the key mechanisms at the link layer that determine this performance. Rate adaptation in vehicular networks faces the following key challenges: (1) due to the rapid variations of the link quality caused by fading and mobility at vehicular speeds, the transmission rate must adapt fast in order to be effective, (2) during infrequent and bursty transmission, the rate adaptation scheme must be able to estimate the link quality with few or no packets transmitted in the estimation window, (3) the rate adaptation scheme must distinguish losses due to environment from those due to hidden-station induced collision. Our extensive outdoor experiments show that the existing rate adaptation schemes for 802.11 wireless networks under utilize the link capacity in vehicular environments. In this paper, we design, implement and evaluate CARS, a novel context-aware rate selection algorithm that makes use of context information (e.g. vehicle speed and distance from neighbor) to systematically address the above challenges, while maximizing the link throughput. Our experimental evaluation in real outdoor vehicular environments with different mobility scenarios shows that CARS adapts to changing link conditions at high vehicular speeds faster than existing rate-adaptation algorithms. Our scheme achieves significantly higher throughput, up to 79%, in all the tested scenarios, and is robust to packet loss due to collisions, improving the throughput by up to 256% in the presence of hidden stations.
Eliminating ghosting and exposure artifacts in image mosaics (2005)

As panoramic photography becomes increasingly popular, there is a greater need for high-quality software to automatically create panoramic images. Existing algorithms either produce a rough "stitch" that cannot deal with common artifacts, or require user input. This paper presents methods for dealing with two artifacts that often occur in practice. Our first contribution is a method for dealing with objects that move between different views of a dynamic scene. If such moving objects are left in, they will appear blurry and "ghosted". Treating such regions as nodes in a graph, we use a vertex cover algorithm to selectively remove all but one instance of each object. Our second contribution is a method for continuously adjusting exposure across multiple images in order to eliminate visible shifts in brightness or hue. We compute exposure corrections on a block-by block basis, then smoothly interpolate the parameters using a spline to get spatially continuous exposure adjustment. Our enhancements, combined with previously published techniques for automatic image stitching, result in a high-quality automated stitcher that exhibits far fewer artifacts than existing software.
Toward a Light-Driven Motorized Nanocar: Synthesis and Initial Imaging of Single Molecules (2011)

A second generation motorized nanocar was designed, synthesized, and imaged. To verify structural integrity, NMR-based COSY, NOESY, DEPT, HSQC, and HMBC experiments were conducted on the intermediate motor. All signals in (1)H NMR were unambiguously assigned, and the results were consistent with the helical structure of the motor. The nanocar was deposited on a Cu(111) surface, and single intact molecules were imaged by scanning tunneling microscopy (STM) at 5.7 K, thereby paving the way for future single-molecule studies of this motorized nanocar atop planar substrates.
Human lactotransferrin: amino acid sequence and structural comparisons with other transferrins (1984)

The complete amino acid sequence (703 amino acid residues) of human lactotransferrin has been determined. The location of the disulfide bridges has also been investigated. Computer analysis established internal homology of the two domains (residues 1-338 and residues 339-703). Each domain contains a single iron-binding site and a single glycosylation site (asparagine residues 137 and 490) located in homologous positions. Prediction of the secondary structure of the two homologous moieties of human lactotransferrin has also been performed. The present results allowed a series of comparisons to be made with human serum transferrin and hen ovotransferrin.
Multi-CRC Polar Codes and Their Applications (2015)

Polar codes under successive cancelation list (SCL) decoding are capable of achieving almost the same or better performance than turbo codes or low density parity-check codes with the help of single cyclic redundancy check (CRC). This decoding scheme, however, suffers from very high complexity with long delay and large memory space. Motivated by this research problem, we propose a novel coding scheme called multi-CRC polar code for significant reduction of memory size and decoding delay but with negligible performance loss. Our analysis and simulation have shown that about half reduction of memory size and decoding delay can be achieved in SCL decoding. We also apply this scheme to hybrid automatic repeat request (HARQ) system to aid retransmission and show that the throughput of multi-CRC polar code is higher than that of the single-CRC one.
Autologous transplantation with peripheral blood mononuclear cells collected after administration of recombinant granulocyte stimulating factor (1993)

Peripheral blood mononuclear cells (PBMC) were collected after the administration of recombinant human granulocyte colony-stimulating factor (rhG-CSF) and used as the sole source of hematopoietic stem cells after myeloablative therapy with busulfan (Bu) and cyclophosphamide (Cy). These studies were performed in 12 patients with malignancies (4 non-Hodgkin's lymphoma, 5 breast cancer, 1 testicular carcinoma, 1 Wilm's tumor, and 1 undifferentiated carcinoma) who had bone or bone marrow disease or had low marrow cellularity. rhG-CSF (16 micrograms/kg/d) was administered for 5 to 7 days by subcutaneous injection and PBMC were collected for 2 to 5 days beginning on day 4 after initiation of rhG-CSF, using continuous-flow blood-cell separators that processed 10 to 12 L of whole blood. From a median of three collections, a mean of 24.0 x 10(8) (+/- 10.5 SD) total nucleated cells/kg containing 12.6 x 10(8) (+/- 4.5 SD) mononuclear cells/kg, 7.3 x 10(6) (+/- 4.3 SD) CD34+ cells/kg and 20.5 x 10(4) (+/- 28.1 SD) granulocyte-macrophage colony-forming units (CFU-GM)/kg were harvested and cryopreserved. After the administration of Bu 14 to 17 mg/kg and Cy 120 to 150 mg/kg, PBMC were thawed and infused. One patient received rhG-CSF after the infusion of PBMC and the remaining 11 patients did not receive postinfusion growth factors. Mean days to recovery of neutrophil levels of 0.1, 0.5, and 1.0 x 10(9)/L were 11.4 (range, 9 to 13), 12.7 (range, 10 to 15), and 13.6 (range, 11 to 16) and the mean day to platelet transfusion independence was 13.3 (range, 7 to 49). Time to recovery of neutrophils to 0.5 and 1.0 x 10(9)/L and platelets to 20 x 10(9)/L was more rapid than in historical patients treated with Bu and Cy who received marrow alone or marrow followed by the posttransplant administration of rh-G or GM-CSF. No graft failures have been observed with a follow-up of 4 to 12 months. These results indicate that PBMC collected after rhG-CSF lead to rapid hematopoietic recovery after myeloablative chemotherapy.
Predicted Regional Flux of Hydrogen Sulfide Correlates with Distribution of Nasal Olfactory Lesions in Rats (2002)

Hydrogen sulfide (H(2)S) is a toxic gas that is released by both natural and industrial sources. H(2)S selectively targets the olfactory system in humans and rodents. The purpose of this study was to test the hypothesis that the distribution of H(2)S-induced nasal pathology is correlated with the location of high-flux areas within the upper respiratory tract. To investigate whether the location of the olfactory lesion is dependent on regional gas uptake patterns, a comparison was made between lesion locations and regions of high H(2)S flux predicted using a 3-dimensional, anatomically accurate computational fluid dynamics (CFD) model of rat nasal passages. Rats were exposed by inhalation to 0, 10, 30, or 80 ppm H(2)S for 6 h/day for 70 days. The regional incidence of olfactory lesions and predicted H(2)S flux were determined at the mid-dorsomedial meatus and the middle portion of the ethmoid recess, and their rank correlation was evaluated. At these 2 levels, regions lined by respiratory epithelium were predicted to exhibit the highest mass flux values; however, H(2)S exposure elicited little or no response in this tissue. In contrast, regions lined by olfactory epithelium showed a close correlation between H(2)S flux and lesion incidence (p < 0.005) for both the 30 and 80-ppm exposure groups. These results indicate that airflow-driven patterns of H(2)S uptake within the inherently sensitive olfactory epithelium play an important role in the distribution of H(2)S-induced lesions and should therefore be taken into consideration when extrapolating from nasal lesions in rats to estimates of risk to human health.
Gene Therapy for Hypertension (2001)

Despite several drugs for the treatment of hypertension, there are many patients with poorly controlled high blood pressure. This is partly because all of the available drugs are short-lasting (</=24 hours), have side effects, and are not highly specific. Gene therapy offers a possibility of producing longer-lasting effects with precise specificity based on the genetic design. Preclinical studies on gene therapy for hypertension have taken 2 approaches. Chao et al have performed extensive studies on gene transfer to increase vasodilator proteins. They have transferred kallikrein, atrial natriuretic peptide, adrenomedullin, and endothelin NO synthase into different rat models. Their results show that blood pressure can be lowered for 3 to 12 weeks with the expression of these genes. The antisense approach, which we began by targeting angiotensinogen and the angiotensin type 1 (AT(1)) receptor, has now been tested independently by several different groups in multiple models of hypertension. Other genes targeted include the beta(1)-adrenoceptor, thyrotropin-releasing hormone, angiotensin gene-activating elements, carboxypeptidase Y, c-fos, and CYP4A1. There have been 2 methods of delivering antisense: one is by oligodeoxynucleotides, and the other is with full-length DNA in viral vectors. All the studies show a decrease in blood pressure lasting several days to weeks or months. Oligos are safe and nontoxic and could be delivered orally or eventually by skin patches. Systemic delivery of recombinant adeno-associated virus with DNA antisense to AT(1) receptors in adult rodents decreases hypertension for up to 6 months. We conclude that there is sufficient preclinical data to give serious consideration to phase I trials for testing some of the antisense oligodeoxynucleotides, although testing the viral vectors needs much more work.
The Styx® architecture for distributed systems (2002)

A distributed system is constructed from a set of relatively independent components that form a unified but geographically and functionally diverse entity. Examples include networked operating systems, Internet services, the national telephone switching system, and, in general, all the technology using today's diverse digital networks. Nevertheless, distributed systems remain difficult to design, build, and maintain, primarily due to the lack of a clean, perspicuous interconnection model for the components. Our experience with two distributed operating systems, Plan 9® and Inferno®, encourages us to propose such a model. These systems depend on, advocate, and generally push to the limit a fruitful idea — to present their resources as files in a hierarchical name space. The objects appearing as files may represent stored data, but they may also be devices, dynamic information sources, interfaces to services, and control points. The approach unifies and provides basic naming, structuring, and access control mechanisms for all system resources. A simple underlying network protocol, Styx®, forms the core of the architecture by presenting a common language for communication within the system. Even within nondistributed systems, the presentation of services as files advantageously extends a familiar scheme for naming, classifying, and connecting to system resources. More important, the approach provides a natural way to build distributed systems by using well-known technology for attaching remote file systems. If resources are represented as files and there are remote file systems, one has a distributed system — resources available in one place are usable from another.
QSulf1, a heparan sulfate 6- O -endosulfatase, inhibits fibroblast growth factor signaling in mesoderm induction and angiogenesis (2004)

The signaling activities of multiple developmental ligands require sulfated heparan sulfate (HS) proteoglycans as coreceptors. QSulf1 and its mammalian orthologs are cell surface HS 6-O-endosulfatases that are expressed in embryonic mesodermal and neural progenitors and promote Wnt signal transduction. In this study, we have investigated the function of QSulf1 in fibroblast growth factor (FGF) signaling, which requires 6-O-sulfated HS for FGF receptor (FGFR) dimerization and tyrosine kinase activation. Here, we report that QSulf1 inhibits FGF2- and FGF4-induced mesoderm formation in the Xenopus embryo and FGF-dependent angiogenesis in the chicken embryo through 6-O-desulfation of cell surface HS. QSulf1 regulates FGF signaling through inhibition of HS-mediated FGFR1 activation by interfering with FGF-HS-FGFR1 ternary complex formation. Furthermore, QSulf1 can produce enzymatically modified soluble heparin that acts as a potent inhibitor of FGF2-induced angiogenesis in the chicken embryo. QSulf1, therefore, has dual regulatory functions as a negative regulator of FGF signaling and a positive regulator of Wnt signaling. Therefore, QSulf1 provides another reagent to produce enzymatically modified heparin compounds, in vivo and in vitro, to modulate cellular signaling in stem cell-based therapies to promote tissue regeneration and in cancer therapies to control cell growth and block angiogenesis.
Cholecystokinin CCK2receptors mediate the peptide's inhibitory actions on the contractile activity of human distal colon via the nitric oxide pathway (2007)

CCK(2) receptors mediate inhibitory actions of cholecystokinin on motor activity of human distal colon. It is suggested that CCK(2) receptors exert their modulating actions through a nitric oxide pathway, independent of the activity of the neuronal nitric oxide synthase isoform.
Tissue factor residues 157-167 are required for efficient proteolytic activation of factor X and factor VII. (1992)

The cell surface receptor tissue factor (TF) initiates coagulation by supporting the proteolytic activation of factors X and IX as well as VII to active serine proteases. Architectural similarity of TF to the cytokine receptor family suggests a strand-loop-strand structure for TF residues 151-174. Site-directed Ala exchanges in the predicted surface loop demonstrated that residues Tyr157, Lys159, Ser163, Gly164, Lys165, and Lys166 are important for function. Addition of side chain atoms at the Ser162 position decreased function, whereas the Ala exchange was tolerated. The dysfunctional mutants bound VII with high affinity and fully supported the catalysis of small peptidyl substrates by the mutant TF.VIIa complex. Lys159-->Ala substitution was compatible with efficient activation of factor X, whereas the Try157-->Ala exchange and mutations in the carboxyl aspect of the predicted loop resulted in diminished activation of factor X. The specific plasma procoagulant activity of all functionally deficient mutants increased 7- to 200-fold upon the supplementation of VIIa suggesting that TF residues 157-167 also provide important interactions that accelerate the activation of VII to VIIa. These data are consistent with assignment of the TF 157-167 region as contributing to protein substrate recognition and cleavage by the TF.VIIa complex.
Selective two-photon microscopy with shaped femtosecond pulses (2003)

Selective two-photon excitation of fluorescent probe molecules using phase-only modulated ultrashort 15-fs laser pulses is demonstrated. The spectral phase required to achieve the maximum contrast in the excitation of different probe molecules or identical probe molecules in different micro-chemical environments is designed according to the principles of multiphoton intrapulse interference (MII). The MII method modulates the probabilities with which specific spectral components in the excitation pulse contribute to the two-photon absorption process due to the dependence of the absorption on the power spectrum of E2(t) [1-3]. Images obtained from a number of samples using the multiphoton microscope are presented.
Selection of Therapeutic Agents for Intraocular Proliferative Disease (1984)

A variety of antimetabolites, steroids, and nonsteroidal anti-inflammatory agents were tested for their ability to inhibit rabbit dermal and conjunctival fibroblast proliferation in cell culture. Doxorubicin hydrochloride and fluorouracil produced notable inhibition in concentrations of less than 1 mg/L. Meclofenamate sodium and indomethacin produced notable inhibition at concentrations of 11 and 40 mg/L, respectively. Dexamethasone sodium phosphate and triamcinolone acetonide produced inhibition at 200 and 150 mg/L, respectively, but paradoxically increased proliferation almost two-fold at concentrations ranging from 1 to 30 mg/L under identical culture conditions. Methotrexate sodium demonstrated only limited effectiveness. This assay system may be a useful approach to drug selection in the treatment of a variety of ocular proliferative disorders. Fluorouracil may prove to be of significant value in the treatment of intraocular proliferative disorders.
The use of a novel intense pulsed light and heat source and ALA-PDT in the treatment of moderate to severe inflammatory acne vulgaris. (2005)

The use of lasers and noncoherent light sources is becoming more commonplace in the treatment of inflammatory acne vulgaris. Topical 5-aminolevulinic acid (ALA) is finding its niche as an enhancer to these laser and light sources. Twenty patients with moderate to severe inflammatory acne vulgaris were enrolled in a clinical trial to evaluate the efficacy of ALA-PDT with activation by a SkinStation LHE (Radiancy, Inc., Orangeburg, NY), a novel intense pulsed light (IPL) and heat source that emits 430-nm to 1100-nm radiation at 3 to 9 J/cm2 fluences. Patients were given topical ALA (Levulan Kerastick, Dusa Pharmaceuticals, Inc., Wilmington, MA) photosensitizing agent that remained in contact with skin for one hour before irradiation. Fifteen patients completed the trial and 12 responded to the treatment. Among respondents, reduction in active inflammatory acne lesions was, on average, 50.1% at the end of the 4-week treatment period, 68.5% 4 weeks after the final treatment, and 71.8% 12 weeks after the final treatment. ALA-PDT with IPL activation was well-tolerated by all patients. No treated lesion recurred at the end of the follow-up period. ALA-PDT with IPL activation is a treatment option for patients with moderate to severe inflammatory acne vulgaris.
Purification, Cloning, and Properties of an Acyltransferase Controlling Shikimate and Quinate Ester Intermediates in Phenylpropanoid Metabolism (2002)

A protein hydrolyzing hydroxycinnamoyl-CoA esters has been purified from tobacco stem extracts by a series of high pressure liquid chromatography steps. The determination of its N-terminal amino acid sequence allowed design of primers permitting the corresponding cDNA to be cloned by PCR. Sequence analysis revealed that the tobacco gene belongs to a plant acyltransferase gene family, the members of which have various functions. The tobacco cDNA was expressed in bacterial cells as a recombinant protein fused to glutathione S-transferase. The fusion protein was affinity-purified and cleaved to yield the recombinant enzyme for use in the study of catalytic properties. The enzyme catalyzed the synthesis of shikimate and quinate esters shown recently to be substrates of the cytochrome P450 3-hydroxylase involved in phenylpropanoid biosynthesis. The enzyme has been named hydroxycinnamoyl-CoA: shikimate/quinate hydroxycinnamoyltransferase. We show that p-coumaroyl-CoA and caffeoyl-CoA are the best acyl group donors and that the acyl group is transferred more efficiently to shikimate than to quinate. The enzyme also catalyzed the reverse reaction, i.e. the formation of caffeoyl-CoA from chlorogenate (5-O-caffeoyl quinate ester). Thus, hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase appears to control the biosynthesis and turnover of major plant phenolic compounds such as lignin and chlorogenic acid.
Structure-Based Engineering of Internal Cavities in Coiled-Coil Peptides, (2005)

Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial catalysts and receptors. Even so, structural characterizations of designed cavities are rare. To address this issue, we performed a systematic study of the structural effects of single-amino acid substitutions within the hydrophobic cores of tetrameric coiled-coil peptides. Peptides containing single glycine, serine, alanine, or threonine amino acid substitutions at the buried L9, L16, L23, and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-phase and crystallographic techniques. All peptides adopt the expected tetrameric state and contain tunnels or internal cavities ranging in size from 80 to 370 A(3). Two closely related sequences containing an L16G substitution, one of which adopts an antiparallel configuration and one of which adopts a parallel configuration, illustrate that cavities of different volumes and shapes can be engineered from identical core substitutions. Finally, we demonstrate that two of the peptides (L9G and L9A) bind the small molecule iodobenzene when present during crystallization, leaving the general peptide quaternary structure intact but altering the local peptide conformation and certain superhelical parameters. These high-resolution descriptions of varied molecular surfaces within solvent-occluded internal cavities illustrate the breadth of design space available in even closely related peptides and offer valuable models for the engineering of de novo helical proteins.