gebhart/patrepeval huggingface dataset:
Binding properties and DNA sequence-specific recognition of two bithiazole-linked netropsin hybrid molecules (1992)

We report the DNA binding properties of two hybrid molecules which result from the combination of the DNA sequence-specific minor groove ligand netropsin with the bithiazole moiety of the antitumor drug bleomycin. The drug-DNA interaction has been investigated by means of electric linear dichroism (ELD) spectroscopy and DNase I footprinting. In compound 1 the two moieties are linked by a flexible aliphatic tether while in compound 2 the two aromatic ring systems are directly coupled by a rigid peptide bond. The results are consistent with a model in which the netropsin moiety of compound 1 resides in the minor groove of DNA and where the appended bithiazole moiety is projected away from the DNA groove. This monocationic hybrid compound has a weak affinity for DNA and shows a strict preference for A and T stretches. ELD measurements indicate that in the presence of DNA compound 2 has an orientation typical of a minor groove binder. Similar orientation angles were measured for netropsin and compound 2. This ligand which has a biscationic nature tightly binds to DNA (Ka = 6.3 x 10(5) M-1) and is mainly an AT-specific groove binder. But, depending on the nature of the sequence flanking the AT site first targeted by its netropsin moiety, the bithiazole moiety of 2 can accommodate various types of nucleotide motifs with the exception of homooligomeric sequences. As evidenced by footprinting data, the bithiazole group of bleomycin acts as a DNA recognition element, offering opportunities to recognize GC bp-containing DNA sequences with apparently a preference (although not absolute) for a pyrimidine-G-pyrimidine motif. Thus, the bithiazole unit of bleomycin provides an additional anchor for DNA binding and is also capable of specifically recognizing particular DNA sequences when it is appended to a strongly sequence selective groove binding entity. Finally, a model which schematizes the binding of compound 2 to the sequence 5'-TATGC is proposed. This model readily explains the experimentally observed specificity of this netropsin-bithiazole conjugate.
Fibrinogen-endothelial cell interaction in vitro: a pathway mediated by an Arg-Gly-Asp recognition specificity (1989)

It has been previously shown that fibrinogen (FG) associates specifically with human umbilical vein and bovine aortic endothelial cells (EC) in culture and induces EC migration. In the present study, we have investigated whether the FG-EC interaction is mediated by an Arg-Gly-Asp (RGD) recognition specificity and whether EC membrane proteins related to platelet GPIIb-IIIa are involved. Highly purified radioiodinated human FG, containing no detectable fibronectin, interacted with cultured human and bovine EC in suspension in a time- dependent and specific manner. The binding was inhibited by EDTA. Two polyclonal antibodies to platelet GPIIb-IIIa, which immunoprecipitated a heterodimer molecule from EC, inhibited FG binding to EC. These same antibodies inhibited FG-induced EC migration in a dose-dependent manner as measured in a Boyden chamber. Preabsorption of the antibodies with purified platelet GPIIb-IIIa markedly reduced both inhibitory activities. A series of synthetic RGD-containing peptides inhibited FG binding to EC and FG-induced EC migration. Gly-Arg-Gly-Asp (GRGD) was the most active peptide tested in inhibiting FG binding and EC migration (ID50 of 30 microM), and conservative substitutions in the RGD sequence markedly reduced inhibitory activity (ID50 greater than 1,000 microM). These results indicate that FG binding and EC migration are events mediated by an RGD recognition specificity and that EC surface proteins immunologically related to the GPIIb-IIIa complex on platelets are involved in this recognition.
Serological relationship between reverse transcriptases from human T‐cell lymphotropic viruses denned by monoclonal antibodies (1986)

The immunological relationship between reverse transcriptases purified from human T-cell lymphotropic viruses (HTLV-I, HTLV-II, HTLV-III) was defined using monoclonal antibodies specific for HTLV-III reverse transcriptase, secreted by a mouse/mouse hybridoma clone (4F8) developed in our laboratory. The viral proteins from HTLV-I and HTLV-II do not bear any cross-reactive epitope to antibodies secreted by this clone. These antibodies specifically cross-react with HTLV-III reverse transcriptase. The antibodies failed to neutralize the catalytic activity of reverse transcriptase; however, after immunoprecipitation with a magnetic conjugate of goat anti-mouse IgG, the residual activity was completely inhibited. This shows that the antibodies are not directed towards the catalytic active center of the enzyme. Using an immunoblotting technique (Western blotting), we have found two cross-reactive proteins with HTLV-III lysate with molecular masses of 53 and 66 kDa. This suggests that HTLV-III possesses two reverse transcriptase activities with a common determinant recognized by the same epitope.
Neonatal Screening for Hearing Disorders in Infants at Risk: Incidence, Risk Factors, and Follow-up (1999)

Objective. To determine the incidence and risk factors for hearing disorders in a selected group of neonates and the feasibility of selective hearing screening. Settings. Multicenter prospective trial at five centers in Germany. Methods. Enrollment criteria: in addition to previously defined risk factors by the Joint Committee on Infant Hearing (family history of hearing loss, in utero infections, craniofacial anomalies, birth weight &lt;1500 g, critical hyperbilirubinemia, ototoxic medications, bacterial meningitis, postnatal asphyxia, mechanical ventilation &gt;5 days, stigmata, or syndromes associated with hearing loss), the impact of maternal drug abuse, birth weight &lt;10th percentile, persistent pulmonary hypertension, and intracranial hemorrhage more than or equal to grade III or periventricular leukomalacia on infant hearing were evaluated. The screening procedure was performed by automated auditory brainstem response (A-ABR; ALGO 1-plus; Natus Med Inc, San Carlos, CA). Statistics: univariate analyses of risk factors versus A-ABR results and a multivariate regression analysis were used; additionally, the total test time was recorded. Results. Seven hundred seventy recordings from 777 infants enrolled consecutively constitute the basis of this analysis. Mean gestational age was 33.8 ± 4.3 weeks, birth weight 2141 ± 968 g; 431 infants being male and 339 female; 41 (5.3%) infants exhibited pathologic A-ABR results (16 bilateral and 25 unilateral). Meningitis or sepsis, craniofacial malformations, and familial hearing loss were independent significant risk factors. Median total test time was 25 minutes. Follow-up examinations in 31 infants revealed persistent hearing loss in 18 infants (13 infants sensorineural, 5 from mixed disorders), 7 requiring amplification. Conclusion. Hearing screening in high-risk neonates revealed a total of 5% of infants with pathologic A-ABR (bilateral 2%). Significant risk factors were familial hearing loss, bacterial infections, and craniofacial abnormalities. Other perinatal complications did not significantly influence screening results indicating improved perinatal handling in a neonatal population at risk for hearing disorders.
Gas Separation with Polymer Membranes (1998)

Gas-selective polymer membranes have long been used in industrial applications. Studies of polymers with well-defined flexible phenyl ether segments such as 1 should contribute to the understanding of the selection mechanism and thus ultimately lead to the synthesis of optimized membrane materials. Various different bridging groups X were used in the studies.
Plant Foods, Antioxidants, and Prostate Cancer Risk: Findings From Case-Control Studies in Canada (1999)

Epidemiological data on most cancer sites suggest that consumption of plant foods, which contain high levels of antioxidants, might slow or prevent the appearance of cancer. We used data from three case-control studies to test this hypothesis. The total study population consisted of 617 incident cases of prostate cancer and 636 population controls from Ontario, Quebec, and British Columbia. Dietary information was collected by an in-person interview with a detailed quantitative dietary history. Unconditional logistic regression analyses were performed to estimate odds ratios (ORs) and 95% confidence intervals (CIs). A decreasing, statistically significant association was found with increasing intakes of green vegetables (OR = 0.54, 95% CI = 0.40-0.71 for 4th quartile), tomatoes (OR = 0.64, 95% CI = 0.45-0.91), beans/lentils/nuts (OR = 0.69, 95% CI = 0.53-0.91), and cruciferous vegetables (OR = 0.69, 95% CI = 0.52-0.91 for 3rd quartile). Higher intakes of fruit were associated with higher ORs (OR = 1.51, 95% CI = 1.14-2.01 for 4th quartile), an effect that was seen for total fruit and citrus fruit, as well as for all other noncitrus fruits. Among the grains, refined-grain bread intake was associated with a decrease in risk (OR = 0.65 for 4th quartile), whereas whole-grain breakfast cereals were associated with a higher risk for prostate cancer. Of all the antioxidant nutrients studied, the ORs were higher with higher intakes of cryptoxanthin (OR = 1.44, 95% CI = 1.09-1.89 for 4th quartile). Exposure to certain dietary components of plant origin, which are potentially modifiable, indicates the theoretical scope for reducing the risk from prostate cancer. Future experimental studies or trials are warranted for further understanding.
Experimental Quantum Teleportation of Laser Beams (2002)

We experimentally demonstrate quantum teleportation for continuous variables by using squeezed-state entanglement. A fidelity expression for a real experimental system is presented, where all the imperfection factors are considered, including losses and phase fluctuations. The measured fidelity for input coherent states is 0.62 and the prospective result with our measured entanglement and efficiencies is 0.69. We will show the details of the quantum teleportation for continuous variable and discuss the problems for further improvement in this experiment.
(Invited) Tunable Thermoelectric Power Factor in Semiconducting Single-Walled Carbon Nanotube Networks (2015)

Single-walled carbon nanotubes (SWCNTs) are a versatile electronic material being explored as cost-effective, high-performance active materials in a variety of renewable energy applications such as transparent conducting or light-harvesting layers in photovoltaics and inclusions in thermoelectric composites. We present a series of experiments focused on understanding the thermoelectric performance of enriched semiconducting SWCNT networks dispersed in a semiconducting polymer matrix. Rational choice of the semiconducting polymer allows us to sensitively tune the s-SWCNT diameter and band gap distributions within the composites. We use a stable charge-transfer dopant to control the density of carriers in the s-SWCNT network, as determined by the bleach of the absorption corresponding to the S 11 excitonic transition. The performance of these transparent conducting s-SWCNT composite networks is comparable to neat p-type and n-type s-SWCNT networks doped by either nitric acid or hydrazine treatments. By varying the carrier density we are able to probe the relationship between the electrical conductivity and Seebeck coefficient (thermopower) in the s-SWCNT networks as a function of the carrier density and position of the Fermi energy. Although the electrical conductivity of the s-SWCNT networks is poor at very low carrier densities we have measured a colossal thermopower as high as ~2,500 µV/K, which is more than an order of magnitude larger than has been previously reported for SWCNT-based material systems and is consistent with theoretical calculations that consider the density of electronic states in individual s-SWCNTs. As we tune the carrier density, we are able to maintain a thermopower above 200 µV/K over almost the entire range of hole densities, corresponding to conductivities up to 1885 S/m, resulting in a thermoelectric power factor of ~100 µW/m·K 2 . These studies suggest that the low dimensionality of the SWCNTs has a stronger impact on the electrical conductivity than the thermopower, implying that they are less strongly coupled in these systems than is observed for compound inorganic semiconductors. These observations demonstrate the ability to exert exquisite control of the thermoelectric performance by tuning the carrier density and/or Fermi energy, and touts SWCNTs as an avenue for realizing thermally stable room temperature thermoelectric devices fashioned from inexpensive and abundant organic constituents.
C H 4 monitoring in ambient air by communication band laser diode based difference frequency generation in a quasi-phase-matched LiNbO3 waveguide (2006)

Methane in ambient air is detected by difference frequency generation in a direct-bonded quasi-phase-matched LiNbO3 ridge waveguide using near infrared communication band laser diodes as pump and signal sources. Absorption lines for the Q branch in the 3.3μm ν3 band are measured by using a Hanst configuration multipass cell with a 107m path length. The authors detect 35ppb CH4 in 2kPa ambient air with a single wavelength scan of a signal external cavity laser diode by suppressing various spectroscopic fringes and stabilizing the pump laser diode oscillation mode with a fiber Bragg grating.
Genome-Wide Identification, Structure and Expression Studies, and Mutant Collection of 22 Early Nodulin-Like Protein Genes in Arabidopsis (2009)

Early nodulin-like proteins (ENODLs) are chimeric arabinogalactan proteins (AGPs) related to the phytocyanin family. Although they show similarities with other phytocyanins, they lack amino acid residues for copper binding. Despite the existence of other phytocyanins, information about the function of ENODLs in plants is largely lacking. In this study, we characterized ENODL genes consisting of 22 members in Arabidopsis thaliana. Structure prediction indicated that most ENODLs are glycosylphosphatidylinositol-anchored chimeric AGPs. Expression analysis by real-time reverse transcription polymerase chain reaction indicated that most ENODL genes showed spatially specific expression, mainly in the flower organs. Furthermore, we obtained and analyzed 26 homozygous T-DNA insertion lines of 15 ENODL genes, but novel biological roles were not uncovered, probably due to functional redundancy. The detailed phylogenetic and expression analyses and characterization of the available insertion lines in this study might facilitate future studies to elucidate the biological roles of ENODLs.
IN VITRO STUDIES TO EXPLAIN HIGH RENAL ALLOGRAFT SURVIVAL IN IGA NEPHROPATHY PATIENTS (1993)

The pretransplant sera of 27 IgA nephropathy (N) kidney transplant patients were investigated for antibodies to the HLA molecule, together with 104 sera from non-IgA N patients and 60 controls. IgA antibodies to HLA were found in 61% of IgA N patients and 2% of non-IgA N patients. IgA N patients with IgA antibodies to HLA had a 100% 2-year cadaver donor graft survival rate compared with 70% in those without IgA antibodies. Patients with IgG antibodies to HLA without accompanying IgA antibodies had the worst graft survival rates. We propose that IgA anti-HLA contributes to the high kidney graft survival in IgA N patients by blocking IgG antibodies or inhibiting cellular immune response.
Gefitinib (Iressa, ZD1839): a novel targeted approach for the treatment of solid tumors. (2004)

Recent advances in cancer therapy have resulted in the development of drugs that target mechanisms involved in neoplastic change and angiogenesis. One example is gefitinib ('Iressa', ZD1839), an orally-active epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) that blocks EGFR signaling in vitro, thereby inhibiting the growth, proliferation and survival of many solid tumors. Clinical trial data show that gefitinib monotherapy is generally well tolerated in patients with a wide range of tumor types (including lung, head and neck, colon, breast, and prostate cancers). The most common adverse events (AEs) were mild and reversible skin and gastrointestinal disorders (National Cancer Institute common toxicity criteria grade 1/2). Few drug-related grade 3/4 skin and gastrointestinal disorders were observed, and drug-related hematologic AEs were uncommon. The clinical benefit of gefitinib in non-small-cell lung cancer (NSCLC), head and neck, colon, breast, and prostate cancer is being investigated, as antitumor activity has been observed in a range of solid tumors, including NSCLC. In two large phase II NSCLC trials (IDEAL ['Iressa' Dose Evaluation in Advanced Lung Cancer] 1 and 2) objective tumor responses of 18.4% and 11.8%, and disease control rates (complete and partial responses plus stable disease) of 54.4% and 42.2%, respectively, were seen in patients given 250 mg/day gefitinib. Additionally, disease-related symptoms improved in 40.3% and 43.1% of patients, and improved quality of life was experienced by 23.9% and 34.3% patients in IDEAL 1 and 2, respectively. Furthermore, the majority of patients who had an objective response also experienced symptom improvement. Gefitinib has been approved for the treatment of advanced NSCLC in Japan, the USA, and other countries. This review discusses the potential of gefitinib in a wide range of solid tumors. 'Iressa' is a trademark of the AstraZeneca group of companies.
Diffractive multifocal intraocular lens image quality (1992)

The diffractive multifocal intraocular lens is implanted in the eye to replace a cataractous crystalline lens. Axially separated images from two diffraction orders provide near and distance vision. Overall image quality is affected by both the quality of the in-focus component and the energy distribution between images. Modulation transfer function and energy distribution data are presented. Measurement accuracy is limited by the diameter of the point spread function and by the difficulty in separating the focused and defocused components.
Nitration of Tyrosine Residues in the Pancreatic Trypsin Inhibitor with Tetranitromethane (1968)

Nitration of pancreatic trypsin inhibitor with tetranitromethane affords a mono‐and a disubstituted derivative which was shown by sequential analysis to contain nitrotyrosine in position 10 and in positions 10 and 21, respectively. Both retain full trypsin inhibitor activity. Measurements of optical rotatory dispersion in the 230 nm region indicate that the secondary structure of the protein is unaffected by nitration. The nitrated derivatives exhibit a conformation‐dependent side‐chain Cotton effect in the region of nitroaromatic absorption. No such Cotton effect is shown by a nitrotyrosine‐containing pentadecapeptide isolated from the tryptic digest from the nitrated and oxidized inhibitor.
Low cost solar array project 1: Silicon material (1980)

The low cost production of silicon by deposition of silicon from a hydrogen/chlorosilane mixture is described. Reactor design, reaction vessel support systems (physical support, power control and heaters, and temperature monitoring systems) and operation of the system are reviewed. Testing of four silicon deposition reactors is described, and test data and consequently derived data are given. An 18% conversion of trichlorosilane to silicon was achieved, but average conversion rates were lower than predicted due to incomplete removal of byproduct gases for recycling and silicon oxide/silicon polymer plugging of the gas outlet. Increasing the number of baffles inside the reaction vessel improved the conversion rate. Plans for further design and process improvements to correct the problems encountered are outlined.
Endocytic pH‐Triggered Degradation of Nanoengineered Multilayer Capsules (2013)

The synthesis of cross-linker free layer-by-layer (LbL) capsules that solely utilize cellular pH variations as a trigger to specifically deconstruct and subsequently release cargo in cells is reported. These capsules demonstrate retention of water-soluble therapeutic molecules as small as 500 Da at extracellular pH. Triggered capsule degradation and release of cargo is observed within 30 min of cell uptake.
Comparative Performance of High-Density Oligonucleotide Sequencing and Dideoxynucleotide Sequencing of HIV Type 1 <i>pol</i> from Clinical Samples (1998)

The performance of the high-density oligonucleotide array methodology (GeneChip) in detecting drug resistance mutations in HIV-1 pol was compared with that of automated dideoxynucleotide sequencing (ABI) of clinical samples, viral stocks, and plasmid-derived NL4-3 clones. Sequences from 29 clinical samples (plasma RNA, n = 17; lymph node RNA, n = 5; lymph node DNA, n = 7) from 12 patients, from 6 viral stock RNA samples, and from 13 NL4-3 clones were generated by both methods. Editing was done independently by a different investigator for each method before comparing the sequences. In addition, NL4-3 wild type (WT) and mutants were mixed in varying concentrations and sequenced by both methods. Overall, a concordance of 99.1% was found for a total of 30,865 bases compared. The comparison of clinical samples (plasma RNA and lymph node RNA and DNA) showed a slightly lower match of base calls, 98.8% for 19,831 nucleotides compared (protease region, 99.5%, n = 8272; RT region, 98.3%, n = 11,316), than for viral stocks and NL4-3 clones (protease region, 99.8%; RT region, 99.5%). Artificial mixing experiments showed a bias toward calling wild-type bases by GeneChip. Discordant base calls are most likely due to differential detection of mixtures. The concordance between GeneChip and ABI was high and appeared dependent on the nature of the templates (directly amplified versus cloned) and the complexity of mixes.
Human Embryonic Origin Early Pregnancy Factor Before and After Implantation (1990)

Early pregnancy factor (EPF) is a factor that has been shown to be involved in the maintenance of the fetal allograft in several mammalian species including man. In that capacity it serves as a link between fertilization and immunomodulation. In the present study we have investigated the secretion of EPF by the human conceptus before and after implantation using rosette inhibition antibody concentration (T11 monoclonal antibody). In isolated trophoblastic cells at gestational week 7-9 there was a significant secretion of EPF. For the first 8 days in culture, secretion was maximal; later, however, at days 13 and 21 these levels declined. Further the EPF content of human embryonal extracts was examined. In various organs, spinal cord, liver, and kidney, significant EPF activity was detected. In women undergoing in vitro fertilization/embryo transfer, a total of 52 preimplantational embryos were cultured for 36 hours. No significant EPF activity was detected in the surrounding media. Two of the 11 patients studied became pregnant during the same cycle after embryo transfer. In conclusion, the preimplantational origin of EPF is maternal, while that of the post-implantational embryo is of embryonal origin.