gebhart/patrepeval huggingface dataset:
Rationally Designed Anti-HIV Peptides Containing Multifunctional Domains as Molecule Probes for Studying the Mechanisms of Action of the First and Second Generation HIV Fusion Inhibitors (2008)

We have previously shown that the first generation human immunodeficiency virus (HIV) fusion inhibitor T20 (Fuzeon) contains a critical lipid-binding domain (LBD), whereas C34, another anti-HIV peptide derived from the gp41 C-terminal heptad repeat, consists of an important pocket-binding domain (PBD), and both share a common 4-3 heptad repeat (HR) sequence (Liu, S., Jing, W., Cheung, B., Lu, H., Sun, J., Yan, X., Niu, J., Farmar, J., Wu, S., and Jiang, S. (2007) J. Biol. Chem. 282, 9612-9620). T1249, the second generation HIV fusion inhibitor, has both LBD and PBD but a different HR sequence, suggesting that these three anti-HIV peptides may have distinct mechanisms of action. Here we rationally designed a set of peptides that contain multiple copies of a predicted HR sequence (5HR) or the HR sequence plus either LBD (4HR-LBD) or PBD (PBD-4HR) or both (PBD-3HR-LBD), and we compared their anti-HIV-1 activity and biophysical properties. We found that the peptide 5HR exhibited low-to-moderate inhibitory activity on HIV-1-mediated cell-cell fusion, whereas addition of LBD and/or PBD to the HR sequence resulted in a significant increase of the anti-HIV-1 activity. The peptides containing PBD, including PBD-4HR and PBD-3HR-LBD, could form a stable six-helix bundle with the N-peptide N46 and effectively blocked the gp41 core formation, whereas the peptides containing LBD, e.g. 4HR-LBD and PBD-3HR-LBD, could interact with the lipid vehicles. These results suggest that the HR sequence in these anti-HIV peptides acts as a structure domain and is responsible for its interaction with the HR sequence in N-terminal heptad repeat, whereas PBD and LBD are critical for interactions with their corresponding targets. T20, C34, and T1249 may function like 4HR-LBD, PBD-4HR, and PBD-3HR-LBD, respectively, to interact with different target sites for inhibiting HIV fusion and entry. Therefore, this study provides important information for understanding the mechanisms of action of the peptic HIV-1 fusion inhibitors and for rational design of novel antiviral peptides against HIV and other viruses with class I fusion proteins.
Peripheral Chemoreceptor Hypersensitivity (2001)

Hypersensitivity of the peripheral chemoreceptors independently predicts adverse prognosis in ambulatory patients with CHF. This hyperactive excitatory reflex, through its inhibitory effect on the baroreflex, may be the reason for the previously observed prognostic association of the latter.
Evidence for different modes of action of cyclin-dependent kinase inhibitors: p15 and p16 bind to kinases, p21 and p27 bind to cyclins. (1995)

A number of low molecular weight proteins have recently been identified that specifically inhibit the function of cyclin-dependent protein kinases in mammalian cells. These fall into two distinct families based on primary sequence comparisons and probable modes of action. Using a simple in vitro binding assay, we show that p21CDKN1 and the related p27KIP1 can efficiently interact with cyclins D1, D2, D3, E and A, and to a lesser extent with cyclin B. By generating a deleted form of cyclin D1 that binds to p21 and p27 but not to Cdks, we confirm that these interaction do not depend on stoichiometric amounts of the relevant kinase subunit. Moreover, p21 and p27 do not detectably associated with kinase subunits unless a cyclin is present. This is in sharp contrast to the properties of p16CDKN2 and p15MTS2/INK4b which bind to Cdk4 and Cdk6 in the absence of any cyclin. These data suggest that p21 and p27 act as broad spectrum regulators of cyclin dependent kinase function by participating in ternary complexes whereas the p16 family specifically interfere with the formation of cyclin D-dependent kinase complexes.
SiGe-On-Insulator (SGOI): substrate preparation and MOSFET fabrication for electron mobility evaluation (2002)

Relaxed Si/sub 1-x/Ge/sub x/-on-insulator (SGOI) is a very promising technology, as it combines the benefits of two advanced technologies: the conventional SOI technology and the SiGe technology. SiGe-based devices have shown advantageous DC and RF performance using, the enhanced electronic properties associated with strain engineering and heterojunction energy barriers. SGOI is a versatile substrate that can be used to integrate various device structures, such as strained-Si and strained-SiGe FETs, and III-V optoelectronics. In this work, we have fabricated SGOI substrates via two different approaches. We also demonstrate strained-Si nMOSFET fabrication on SGOI and electron mobility enhancement is evaluated.
Spectral domain optical coherence tomography imaging with an integrated optics spectrometer (2011)

We designed and fabricated an arrayed-waveguide grating (AWG) in silicon oxynitride as a spectrometer for spectral domain optical coherence tomography (SD-OCT). The AWG has a footprint of only 3.0 cm × 2.5 cm, operates at a center wavelength of 1300 nm, and has 78 nm free spectral range. OCT measurements are performed that demonstrate imaging up to a maximum depth of 1 mm with an axial resolution of 19 μm, both in agreement with the AWG design parameters. Using the AWG spectrometer combined with a fiber-based SD-OCT system, we demonstrate cross-sectional OCT imaging of a multilayered scattering phantom.
Performance evaluation of disinfectant formulations using poloxamer-hydrogel biofilm-constructs (1998)

Poloxamer F127 is a di-block co-polymer of polyoxyethylene and polyoxypropylene. Aqueous solutions show thermo-reversible gelation, being liquid at temperatures < 15 degrees C and robust gels at temperatures > 15 degrees C. Chilled poloxamer solutions (30% w/v) were inoculated with approximately 10(4-5) cfu ml-1 of stationary phase cultures of Pseudomonas aeruginosa, Ps. fluorescens, Pantoea agglomerans, Micrococcus luteus, Staphylococcus epidermidis, Bacillus subtilis or Listeria innocua. Drops (200 microliters) of the inoculated poloxamers were placed on stainless steel coupons held in Petri dishes containing moistened cotton wool and incubated at 30 degrees C for 5 h. All strains grew well giving between 10(6-7) cfu ml-1 at 5-6 h. The cultured gels were readily applied to tests of biocide effectiveness as the stainless steel coupons could be removed and flooded with biocide solution for fixed exposure times. Provided that the temperature of the biocide solutions was > 15 degrees C, the integrity of the gels could be maintained during exposure. After exposure, the gels and their supports were removed to separate tubes containing neutralizer solution (< 15 degrees C). The gels rapidly dispersed within 5 min to ensure a complete recovery of the sample population. Biofilm-constructs and cell suspensions (10(7) cfu ml-1) were exposed to four commercial disinfectant formulations, based on hypochlorite, alcohol, hydrogen peroxide and a tenside, at recommended use levels. Cell suspensions, in the presence of bovine serum albumen (BSA; 0.03% w/v), were subject to a > 5-log kill within 5 min while the killing effected against the biofilm-constructs varied between 0.4 and 2-log reductions. The results indicate a high degree of reproducibility between replicate samples, with patterns of susceptibility varying both as a function of organism, biocide type and concentration. The experiments strongly support the view that poloxamer-constructs are suitable for application in trials and testing of disinfectant formulations.
Indoor multi-base stations system with simultaneous transmission using OFDM adaptive array antenna (2002)

We propose to set an OFDM adaptive array on a mobile terminal in order to collect the signals received from multi-base stations efficiently in an indoor wireless system. By doing so, the system will obtain some diversity gain when the received signals contain the same data. Moreover, when they contain different data, the mobile terminal is capable of mitigating the interferer waves and thus obtaining the desired signal. The performance of the proposed system is evaluated by computer simulations and the possibility of constructing a system without the use of frequency assignment or time assignment in wireless networks is discussed.
Single nucleotide polymorphism (SNP) genotyping in unprocessed whole blood and serum by real-time PCR: application to SNPs affecting homocysteine and folate metabolism. (2001)

Several single nucleotide polymorphisms (SNPs) have been identified that affect folate and homocysteine metabolism, which in turn are implicated in the pathogenesis of cardiovascular disease (1), neural tube defects (2), and colorectal cancer (3). These SNPs include methylenetetrahydrofolate ( MTHFR ) C677T (1), MTHFR A1298C (4), methionine synthase ( MTR ) A2756G (5)(6), and methionine synthase reductase ( MTRR ) A66G (7).

To determine the relationships of these and other SNPs with the risk of chronic diseases, along with possible interactions with environmental factors, large population-based epidemiologic studies are necessary. This requires high-throughput methodologies for SNP determination.

SNP genotyping can generally be divided into two steps: sample preparation, e.g., purification of DNA from blood, and allele detection. To date, great advances have been made in allele detection because novel technologies for DNA analysis have been developed (8). The DNA purification step is required because the enzymes used for manipulation of DNA (e.g., polymerases) are susceptible to inhibition by substrate impurities. Purification of DNA is often labor-intensive, time-consuming, and costly and enhances the risk of back- or cross-contamination of samples. The development of automated DNA purification methods has been aimed at alleviating some of these problems (9), but may increase the need for expensive equipment. Other researchers have investigated the feasibility of PCR amplification without prior DNA purification (10)(11)(12).

Allele-detection methods based on real-time PCR are attractive because signal amplification and allele detection are accomplished in a single, closed tube (13). For this type of assay, DNA purification seems mandatory because blood constituents such …
Major Histocompatibility Complex Class I Molecules Modulate Activation Threshold and Early Signaling of T Cell Antigen Receptor–γ/δ Stimulated by Nonpeptidic Ligands (1997)

Killer cell inhibitory receptors and CD94-NKG2-A/B heterodimers are major histocompatibility complex class I-specific inhibitory receptors expressed by natural killer cells, T cell antigen receptor (TCR)-gamma/delta cells, and a subset of TCR-alpha/beta cells. We studied the functional interaction between TCR-gamma/delta and CD94, this inhibitory receptor being expressed on the majority of gamma/delta T cells. When engaged by human histocompatibility leukocyte antigen class I molecules, CD94 downmodulates activation of human TCR-gamma/delta by phosphorylated ligands. CD94-mediated inhibition is more effective at low than at high doses of TCR ligand, which may focus T cell responses towards antigen-presenting cells presenting high amounts of antigen. CD94 engagement has major effects on TCR signaling cascade. It facilitates recruitment of SHP-1 phosphatase to TCR-CD3 complex and affects phosphorylation of Lck and ZAP-70 kinase, but not of CD3 zeta chain upon TCR triggering. These events may cause abortion of proximal TCR-mediated signaling and set a higher TCR activation threshold.
What is the most effective treatment for ADHD in children (2005)

Stimulant medication therapy is the most effective treatment for attention deficit/ hyperactivity disorder (ADHD) in children, producing significant improvements in symptoms and modest improvements in academic achievement (strength of recommendation [SOR]: A, based on multiple randomized controlled trials [RCTs]). Nonpharmacologic therapies, such as behavior therapy, school- based interventions, and family therapy, are not as effective as stimulants but may add modest benefit to the effects of medication (SOR: B, based on 1 RCT).
Can Preoperative Spiral CT Scans Alone Determine the Feasibility of Endovascular AAA Repair? A Comparison to Angiographic Measurements (2000)

Considerable discrepancies exist between preoperative neck diameter and infrarenal aortic length measurements obtained from CT scans and angiograms used to evaluate candidates for endovascular aortic aneurysm repair. CT alone may not be adequate for predicting the feasibility of endovascular AAA repair.
Pneumococcal Polysaccharides Interact with Human Dendritic Cells (2006)

Dendritic cells (DCs) are critical antigen presentation cells whose influence on murine immune responses to polysaccharide antigens has only recently been elucidated. Little is known about human DC-polysaccharide interactions. We set out to study the interaction between human monocyte-derived DCs and pneumococcal capsular polysaccharides (PPS) in vitro. Immature DCs were generated from peripheral blood monocytes and incubated with fluorescein isothiocyanate-labeled PPS type 9N or 14 for assessment of uptake. DCs were exposed to PPS type 1, 6B, 9N, 14, 19F, or 23F in the absence or presence of Escherichia coli lipopolysaccharide (LPS) for assessment of phenotypic DC maturation and cytokine production. PPS were taken up by immature DCs and proceeded to HLA-DR+ and lysosome-associated membrane protein-1+ late endosomal compartments. Uptake was reduced in the presence of cytochalasin D and wortmannin, suggesting that both cytoskeletal rearrangements and phosphatidylinositol 3-kinase activation may be required for internalization. None of the PPS tested induced DC phenotype changes, maturation, or interleukin-12 (IL-12)/IL-10 production. However, PPS were capable of modulating the response of the DCs to a second signal such as LPS. Exposure of DCs to PPS in the presence of LPS resulted in an altered cytokine balance with significantly increased IL-10 production and reduced IL-12 production compared to LPS alone. This effect was not seen using the control antigen tetanus toxoid. DC-pneumococcus interaction may affect subsequent immune responses to pneumococci, as an altered cytokine balance may have a profound effect on DC-driven T-cell priming.
The type I insulin-like growth factor receptor is a motility receptor in human melanoma cells (1989)

Insulin-like growth factors I and II (IGF-I and II) and insulin are chemotactic agents for the human melanoma cell line A2058. As shown in this report, the motility receptor mediating this response is the heterodimeric type I IGF receptor. These three factors are able to compete with 125I-labeled IGF-I for binding to the cell surface with IC50 values equal to approximately 2 (IGF-I), approximately 150 (IGF-II), and approximately 300 nM (insulin). Cross-linking of 125I-IGF-I to the cell surface with disuccinimidyl suberate followed by analysis with sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography reveals a 130-kDa protein (reduced) consistent with the alpha component of a type I receptor and a 38-kDa protein which does not bind insulin, and thus could be another IGF-I cell surface binding protein. The anti-IGF-I receptor monoclonal antibody (alpha IR-3) also competes with labeled IGF-I in binding experiments. In contrast, a control monoclonal antibody, matched to alpha IR-3 with respect to IgG subclass, has no significant effect on IGF-I binding. While alpha IR-3 inhibits the motility induced by IGF-I, IGF-II, and insulin, pertussis toxin (0.01-1.0 micrograms/ml) has no significant effect on the motility induced by the insulin-like growth factors or insulin on this cell line. Therefore, the type I IGF receptor appears to mediate a highly potent pertussis toxin-insensitive motility response to IGF-I, IGF-II, and insulin. In contrast, motility induced by the autocrine motility factor, a cytokine produced by the A2058 cells, is not affected by alpha IR-3 but is extremely sensitive to pertussis toxin. When mixtures of autocrine motility factor and IGF-I are employed to induce chemotaxis, the resulting motility is greater than that induced by either agent alone. These data indicate that motility in this melanoma cell line can be initiated through multiple receptors that stimulate the cells by separate transduction pathways. This capability to respond to multiple stimuli could enhance the metastatic potential.
Varicella Zoster--Associated Neurologic Disease Without Skin Lesions (1989)

We have investigated a group of cases with inflammatory neurologic disease and serologic evidence of varicella zoster virus activity without cutaneous vesicles. In agreement with experience, a case of cranial polyneuropathy with facial palsy and cases of aseptic meningitis were found. However, cases of acute polyneuropathy, myelitis, and encephalitis were also identified. Thus, it seems that the spectrum of neurologic disease associated with varicella zoster virus in the absence of skin lesions is considerably broader than previously recognized.
A Small Interfering RNA Targeting Vascular Endothelial Growth Factor Inhibits Ewing's Sarcoma Growth in a Xenograft Mouse Model (2005)

Angiogenesis plays an essential role in tumor growth and metastasis and is a promising therapeutic target for cancer. Vascular endothelial growth factor (VEGF) is a key regulator in vasculogenesis as well as in angiogenesis. TC71 human Ewing's sarcoma cells overexpress VEGF, with a shift in isoform production from membrane-bound VEGF189 to the more soluble VEGF165. Transfection of TC71 cells with a vector-based VEGF targeted small interfering RNA expression system (VEGFsi) inhibited VEGF165 expression by 80% and VEGF165 protein production by 98%, with no alteration in VEGF189 expression. Human microvascular endothelial cell proliferation and migration induced by conditioned medium from VEGFsi-transfected TC71 cells was significantly less than that induced by conditioned medium from TC71 cells and control vector-transfected TC71 cells. Furthermore, after s.c. injection into athymic nu/nu mice, the tumor growth of VEGFsi-expressing TC71 cells was significantly less than that of parental or control vector-transfected cells. Vessel density as assessed by CD31 immunohistochemical analysis and VEGF165 expression as assessed by Northern blotting were also decreased. Intratumor gene therapy with polyethylenimine/VEGFsi also resulted in tumor growth suppression. When inoculated into the tibias of nude mice, VEGFsi-expressing TC71 cells induced osteolytic bone lesions that were less severe than those induced by control groups. These data suggest that targeting VEGF165 may provide a therapeutic option for Ewing's sarcoma.
Alteration of Polysaccharide Size Distribution of a Vertebrate Hyaluronan Synthase by Mutation (2003)

Hyaluronan (HA) is a nonsulfated glycosaminoglycan that has long been known to play structural roles in vertebrates. Recently, it has become increasingly obvious that this linear polysaccharide has many more uses than simply scaffolding or space filler. HA has been found to be involved in development, cell signaling, cell motility, and metastasis. These roles are often dictated by the length of the HA polymer, which can vary from a few to about 10,000 sugar residues in length. Three distinct isoforms of HA synthase exist in mammals. It has been shown previously by others that each isoform produces HA that differs in size distribution, but the regulatory mechanism is not yet known. Mutations have been described that alter the size distribution of the HA produced by the streptococcal HA synthases. We show that by mutating one particular amino acid residue of a vertebrate HA synthase, depending on the introduced side chain, the size of HA produced can be either reduced or increased. We postulate that several cysteine residues and a serine residue may be involved in binding directly or indirectly to the nascent HA chain. These data support the theory that the relative strength of the interaction between the catalyst and the polymer may be a major factor in HA size control.
Observation by fluorescence microscopy of transcription on single combed DNA (2002)

Molecular combing is a powerful procedure for aligning a large array of DNA molecules onto a surface. This technique usually leads to an overstretching of about 150% of the molecules' contour length. By changing the magnitude of capillary forces during the combing process, we were able to reduce the relative extension of the DNA molecules. Thus we achieved combing of T7 DNA with an extension close to its molecule contour length. We checked the ability of combed DNA to interact with DNA binding proteins. Using the T7 bacteriophage transcription system, we investigated the transcription activity of RNA polymerase on combed DNA by direct visualization of newly synthesized fluorescent RNAs. Our experiments show that no transcription activity occurs on overstretched DNA molecules, whereas we observe a transcription activity for nonoverstretched molecules. This activity is observed both in multiple initiation experiments and for one immobilized T7 RNA polymerase per promoter. These results open possibilities for the study of single enzyme actions on combed DNA by optical methods.
Layer-based supervised classification of moving objects in outdoor dynamic environment using 3D laser scanner (2014)

In this paper, we present a layered approach for classification of moving objects from 3D range data based on supervised learning technique. Our approach combines the model based classification in 2D with boosting for classifying the objects into four classes of interest namely bus, car, bike and pedestrian. In contrast to most of the existing work on 3D classification which involves extensive feature extraction and description, this combination uses simple single-valued features and allows our system to perform efficiently. The proposed method can be used in conjunction with any type of range sensors, however, we have demonstrated its performance using the data acquired from a Velodyne HDL-64E laser scanner.
Deuterium kinetic isotope effects in the 1,4-dimethylenecyclohexane boat Cope rearrangement (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDeuterium kinetic isotope effects in the 1,4-dimethylenecyclohexane boat Cope rearrangementJoseph J. Gajewski and Jose Leonardo. JimenezCite this: J. Am. Chem. Soc. 1986, 108, 3, 468–474Publication Date (Print):February 1, 1986Publication History Published online1 May 2002Published inissue 1 February 1986https://pubs.acs.org/doi/10.1021/ja00263a017https://doi.org/10.1021/ja00263a017research-articleACS PublicationsRequest reuse permissionsArticle Views721Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts