gebhart/patrepeval huggingface dataset:
Inhibition of DNA Binding by Human Estrogen-Related Receptor 2 and Estrogen Receptor α with Minor Groove Binding Polyamides (2005)

Human estrogen-related receptor 2 (hERR2, ESRRB, ERRbeta, NR3B2) belongs to a class of nuclear receptors that bind DNA through sequence-specific interactions with a 5'-AGGTCA-3' estrogen response element (ERE) half-site in the major groove and an upstream 5'-TNA-3' site in the minor groove. This minor groove interaction is mediated by a C-terminal extension (CTE) of the DNA binding domain and is unique to the estrogen-related receptors. We have used synthetic pyrrole-imidazole polyamides, which bind specific sequences in the minor groove, to demonstrate that DNA binding by hERR2 is sensitive to the presence of polyamides in both the upstream minor groove CTE site and the minor groove of the ERE half-site. Thus, polyamides can inhibit hERR2 by two mechanisms, by direct steric blockage of minor groove DNA contacts mediated by the CTE and by changing the helical geometry of DNA such that major groove interactions are weakened. To confirm the generality of the latter approach, we show that the dimeric human estrogen receptor alpha (hERalpha, ESR1, NR3A1), which binds in the major groove of the ERE, can be inhibited by a polyamide bound in the opposing minor groove of the ERE. These results highlight two mechanisms for inhibition of protein-DNA interactions and extend the repertoire of DNA recognition motifs that can be inhibited by polyamides. These molecules may thus be useful for controlling expression of hERR2- or hERalpha-responsive genes.
Immunization of Cotton Rats with the Human Respiratory Syncytial Virus F Glycoprotein Produced Using a Baculovirus Vector (1989)

The F glycoprotein of respiratory syncytial virus in insect cells was produced using a baculovirus expression vector to examine its potential as a subunit vaccine. Two different forms of the F glycoprotein were expressed: the intact F (F) glycoprotein and the truncated (Ft) glycoprotein, in which the COOH-terminal anchor region was deleted. The F glycoprotein remained cell associated, whereas the Ft glycoprotein was secreted into the media of infected cells. In contrast to the processing of the F0 precursor into its F1 and F2 subunits that was observed in mammalian cells, a second cleavage site within the F1 subunit was recognized by the insect cell proteases and resulted in the formation of two F1 subunits. The baculovirus-expressed Ft glycoprotein induced neutralizing antibodies in cotton rats and protected vaccinated animals from challenge with respiratory syncytial virus.
Effects of dietary vitamin E on the quality of table eggs enriched with n-3 long-chain fatty acids (2000)

Because of the proposed cardioprotective benefits of n-3 fatty acids and vitamin E, a trial was carried out to investigate the possibility of enriching eggs with n-3 fatty acid and vitamin E added to the hen's diet. One hundred ninety-two Hy-Line Brown hens, 39-wk-old, were divided into eight groups: four groups received the basal diet supplemented with 3% lard and four doses of dl-alpha-tocopheryl acetate (0, 50, 100, and 200 ppm), whereas the diets of the other groups were supplemented with 3% of fish oil and the same doses of vitamin E. The performances of the hens and egg weights were not affected either by the type of lipid supplement or by the vitamin level. The treatment with fish oil caused a dramatic increase (P < 0.01) of all n-3 fatty acids of the yolk, particularly EPA (19.53 vs. 0.74 mg/egg) and DHA (143.70 vs. 43.66 mg/egg), and an appreciable decrease of arachidonic acid (25.54 vs. 67.72 mg/egg). The different levels of dietary vitamin E slightly affected the fatty acid composition of the yolk. Yolk alpha-tocopherol increased linearly as dietary dl-alpha-tocopheryl acetate increased (P < 0.01) from the control level of 90.93 microg/g of yolk to 313.84 microg/g of yolk when 200 ppm were added to the hen diets. Twenty-eight days of storage at room temperature (20 to 25 C) did not alter the yolk fatty acid profile, and, moreover, the levels of vitamin E remained still very close to those observed in fresh egg.
Inhibition of Serine Proteases by Arylboronic Acids (1971)

Arylboronic acids were found to be strong competitive inhibitors of subtilisin and chymotrypsin. The binding constants are strongly pH dependent and give a Hammett-type plot with a slope of -0.885. The pH dependence, the Hammett plot, and nmr model-system studies indicate that inhibition is due to electron-pair donation by the active site histidine to the bound inhibitor.
Making use of a two stage multiplexing scheme in a WDM network (2002)

The paper explores the implications of using a two stage optical multiplexing scheme in optical WDM nodes. This allows to keep bands of adjacent wavelengths intact, thereby reducing the cost of multiplexing, increasing the number of hops and simplifying network management.
A Minimal Nitrogen Fixation Gene Cluster from <i>Paenibacillus</i> sp. WLY78 Enables Expression of Active Nitrogenase in <i>Escherichia coli</i> (2016)

&lt;div&gt;&lt;p&gt;Most biological nitrogen fixation is catalyzed by molybdenum-dependent nitrogenase, an enzyme complex comprising two component proteins that contains three different metalloclusters. Diazotrophs contain a common core of nitrogen fixation &lt;i&gt;nif&lt;/i&gt; genes that encode the structural subunits of the enzyme and components required to synthesize the metalloclusters. However, the complement of &lt;i&gt;nif&lt;/i&gt; genes required to enable diazotrophic growth varies significantly amongst nitrogen fixing bacteria and archaea. In this study, we identified a minimal &lt;i&gt;nif&lt;/i&gt; gene cluster consisting of nine &lt;i&gt;nif&lt;/i&gt; genes in the genome of &lt;i&gt;Paenibacillus&lt;/i&gt; sp. WLY78, a gram-positive, facultative anaerobe isolated from the rhizosphere of bamboo. We demonstrate that the &lt;i&gt;nif&lt;/i&gt; genes in this organism are organized as an operon comprising &lt;i&gt;nifB&lt;/i&gt;, &lt;i&gt;nifH&lt;/i&gt;, &lt;i&gt;nifD&lt;/i&gt;, &lt;i&gt;nifK&lt;/i&gt;, &lt;i&gt;nifE&lt;/i&gt;, &lt;i&gt;nifN&lt;/i&gt;, &lt;i&gt;nifX&lt;/i&gt;, &lt;i&gt;hesA&lt;/i&gt; and &lt;i&gt;nifV&lt;/i&gt; and that the &lt;i&gt;nif&lt;/i&gt; cluster is under the control of a σ&lt;sup&gt;70&lt;/sup&gt; (σ&lt;sup&gt;A&lt;/sup&gt;)-dependent promoter located upstream of &lt;i&gt;nifB&lt;/i&gt;. To investigate genetic requirements for diazotrophy, we transferred the &lt;i&gt;Paenibacillus nif&lt;/i&gt; cluster to &lt;i&gt;Escherichia coli&lt;/i&gt;. The minimal &lt;i&gt;nif&lt;/i&gt; gene cluster enables synthesis of catalytically active nitrogenase in this host, when expressed either from the native &lt;i&gt;nifB&lt;/i&gt; promoter or from the T7 promoter. Deletion analysis indicates that in addition to the core &lt;i&gt;nif&lt;/i&gt; genes, &lt;i&gt;hesA&lt;/i&gt; plays an important role in nitrogen fixation and is responsive to the availability of molybdenum. Whereas &lt;i&gt;nif&lt;/i&gt; transcription in &lt;i&gt;Paenibacillus&lt;/i&gt; is regulated in response to nitrogen availability and by the external oxygen concentration, transcription from the &lt;i&gt;nifB&lt;/i&gt; promoter is constitutive in &lt;i&gt;E. coli&lt;/i&gt;, indicating that negative regulation of &lt;i&gt;nif&lt;/i&gt; transcription is bypassed in the heterologous host. This study demonstrates the potential for engineering nitrogen fixation in a non-nitrogen fixing organism with a minimum set of nine &lt;i&gt;nif&lt;/i&gt; genes.&lt;/p&gt;&lt;/div&gt;
Structural Studies of Position 2 Modified Endomorphin-2 Analogs by NMR Spectroscopy and Molecular Modeling (2009)

Endomorphin-2 (EM-2, Tyr-Pro-Phe-Phe-NH 2 ) is an endogenous ligand for the μ-opioid receptor. To examine the importance of Pro 2 in EM-2 structure, we synthesized a series of analogs incorporating piperidine-2-, 3- and 4-carboxylic acids (Pip, Nip and Inp, respectively) in position 2. Pip, Nip and Inp are six-membered mimics of Pro and can be considered as α-, β- and γ-amino acids, respectively. Receptor binding studies revealed that [(R)-Nip 2 ]EM-2 had greatly increased μ-opioid receptor affinity compared with the parent peptide, while two other analogs were inactive. In order to determine which structural elements of [(R)-Nip 2 ]EM-2 could be responsible for the outstanding affinity of this analog, the solution conformations of EM-2 analogs incorporating Pro mimics were investigated by the combination of 2D 1 H NMR measurements and molecular modeling calculations. Evaluating the ratios of cis/trans rotamers, aromatic interactions and dihedral angles we have found that all three analogs exist as a mixture of cis/trans rotamers of the Tyr-Xaa peptide bond and have flexible, extended conformations, with no intramolecular hydrogen bonds or aromatic ring interactions observed for EM-2. The obtained results do not allow to draw conclusions on the bioactive conformation ofthe most active analog. We can suggest that a well known preference of the substituents to occupy equatorial positions in six-membered rings, together with a greater distance between Tyr 1 and Phe 3 aromatic rings, in Nip, which is a β-amino acid, as compared with EM-2, are the main differentiating factors which are responsible for the exceptional affinity of [(R)-Nip 2 ]EM-2.
Definition of Myasthenogenic Sites of the Human Acetylcholine Receptor Using Synthetic Peptidesa (1987)

Experimental autoimmune myasthenia gravis (EAMG) and antibodies that modulate AChRs from cultured human muscle are induced by a disulfide-looped peptide comprising the human acetylcholine receptor (AChR) alpha-subunit residues 125-147 (H alpha 125-147). To delineate the essential antigenic requirements for induction of EAMG by this peptide, a series of peptides was synthesized: (a) a nonlooped analog (Cys 128 replaced by Ser) stimulated modulating autoantibodies, induced EAMG, and bound antibodies induced by native AChR; (b) H alpha 131-147, a heptadecylpeptide shorter by 6 N-terminal residues, induced modulating antibodies, EAMG, and T cells that responded to H alpha 125-147, but not to H alpha 137-147; (c) H alpha 137-147, an undecapeptide shorter than H alpha 125-147 by 12 N-terminal residues, did not stimulate T cells or induce antibody production, but it bound antibodies generated by the longer peptides. Thus, when coupled to an epitope that could stimulate helper T cells, the region 137-147 was able to stimulate B cells. This study has defined a myasthenogenic region of the human AChR's alpha-subunit, 17 amino acids long, that contains several distinct epitopes, including at least one N-terminal site inducing T-cell responses (region 131-136) and two possibly overlapping sites that induce antibodies (regions 131-136 and 137-147). Further definition of antigenic sites inducing helper and suppressor T-cell responses and stimulating production of autoantibodies to AChR is essential to the goal of antigen-specific immunotherapy for myasthenia gravis.
Estimating Net Realizable Value for Distressed Real Estate (1990)

This paper provides a framework for adjusting distressed real estate properties for liquidating discounts. We estimate the probability of receiving an offer on a property in any particular short interval of time. Our empirical evidence allows us to predict the average rate at which offers will occur in any particular interval of time. Further, it allows us to arrive at an estimate of net realizable value, adjusted for selling expenses.
Monoterpenoids and Their Synthetic Derivatives as Leads for New Insect-Control Agents (1995)

Monoterpenoids are natural substances which are found in many higher plant species. These plant secondary metabolites are generally considered as self-defense tactics against the plants' enemies. Our study was aimed at the anticipation of improved biological activities through the synthesis of derivatives of the natural monoterpenoids. We have also developed a systematic bioassay system to evaluate the spectrum of toxicities of the monoterpenoids. The results show that the monoterpenoids, either natural or synthetic, have a relatively wide spectrum of activity against agricultural and public health insect pests. Derivatization, especially, to the acyl derivatives of the monoterpenoids, has significantly improved the acute, fumigant, larvicidal and ovicidal activities against the above insects. The ether derivatives also showed enhanced insecticidal activity. When mosquito larvae were treated with the monoterpenoids at sublethal dosages, insect growth and development activity was observed. The enhanced biological activity of the synthetic derivatives of monoterpenoids indicates that optimal chemical structures for insecticides can be possibly elucidated through the study of structure-activity relationships.
Preliminary Results of the Use of Indole‐3‐Carbinol for Recurrent Respiratory Papillomatosis (1998)

The preliminary results of treating recurrent respiratory papillomatosis with indole-3-carbinol holds promise. Longer follow-up of this patient group and a blinded, controlled trial are required. We conclude that indole-3-carbinol appears to be safe and well tolerated and may be an efficacious treatment for recurrent respiratory papillomatosis.
Crystallization Behavior of Poly(ethylene oxide) and Its Blends Using Time-Resolved Wide- and Small-Angle X-ray Scattering (2000)

Time-resolved synchrotron wide- and small-angle X-ray scattering experiments were used to investigate the crystallization behavior and microstructure development of poly(ethylene oxide) and several melt-miscible PEO blends. Model blends were prepared with both weakly interacting poly(methyl methacrylate) and two strongly interacting random copolymers. Average SAXS long periods and lamellar thicknesses decreased at early crystallization times: by 2−3 nm for PEO and blends containing the low Tg diluent and by ∼5−9 nm for blends containing higher Tg diluents. The latter appears to arise in part from additional restrictions placed on the growing lamellae by the stiff, high Tg amorphous polymeric diluents. The increase in final long period over that of neat PEO was ∼2−4 nm for the weakly interacting blends, as opposed to as large as 10 nm for the strongly interacting mixtures. In the former case, the changes are associated with interlamellar diluent placement, while in the latter they result primarily from an increase in lamellar thickness due to reduction in degrees of supercooling. In line with previous observations, there was a significant decrease in crystallization rates for blends containing strongly interacting diluents. Two Avrami expressions were generally required to fit the WAXD crystallinity−time data for PEO and as many as three for the blends. For neat PEO, the behavior is reminiscent of crystallization in mixtures of high and low molecular weight PEO fractions.
IEEE 802.22: An Introduction to the First Wireless Standard based on Cognitive Radios (2006)

In November/2004, we witnessed the formation of the first worldwide effort to define a novel wireless air interface (i.e., MAC and PHY) standard based on Cognitive Radios (CRs): the IEEE 802.22 Working Group (WG). The IEEE 802.22 WG is chartered with the development of a CR-based Wireless Regional Area Network (WRAN) Physical (PHY) and Medium Access Control (MAC) layers for use by license-exempt devices in the spectrum that is currently allocated to the Television (TV) service. Since 802.22 is required to reuse the fallow TV spectrum without causing any harmful interference to incumbents (i.e., the TV receivers), cognitive radio techniques are of primary importance in order to sense and measure the spectrum and detect the presence/absence of incumbent signals. On top of that, other advanced techniques that facilitate coexistence such as dynamic spectrum management and radio environment characterization could be designed. In this paper, we provide a detailed overview of the 802.22 draft specification, its architecture, requirements, applications, and coexistence considerations. These not only form the basis for the definition of this groundbreaking wireless air interface standard, but will also serve as foundation for future research in the promising area of CRs.
Complexes of grass pollen allergens and specific antibodies reduce allergic symptoms and inhibit the seasonal increase of IgE antibody (1990)

Complexes made from antigen and specific antibodies have been used to suppress specific antibody production. This property is of potential therapeutic interest in immediate hypersensitivity states which are characterized by hyperproduction of IgE antibodies. We report here on the use of antigen-antibody complexes in patients with hypersensitivity to grass pollen. Specific anti-allergen antibodies were prepared by immunoadsorption from the serum of hypersensitive individuals and mixed with grass pollen allergens to form complexes in antibody excess. These complexes were used in a strictly autologous manner for inoculating patients prior to and during a pollen season. The study comprised two randomly defined groups of 15 patients who were inoculated intradermally either with a preparation of allergen-antibody complexes or with the carrier buffer, according to a double-blind protocol. Diary cards were used to follow nasal and ocular symptoms, bronchial asthma and medication intake. Specific IgE antibodies were assayed during the trial and 1 year afterwards. Inoculation of allergen-autologous antibody complexes was well tolerated. It significantly reduced ocular symptoms (Mann-Whitney U-test, P less than 0.05), bronchial asthma during the first part of the season (Mann-Whitney U-test, P less than 0.001) and drug intake (Mann-Whitney U-test, P less than 0.001). This treatment prevented the seasonal increase in specific IgE antibodies, whose production continued to decrease after the pollen season. These effects were obtained within a few weeks of treatment, using a cumulative amount of allergen 100-fold lower than the amount which would have been used for a conventional hyposensitization.(ABSTRACT TRUNCATED AT 250 WORDS)
Preparation of Bi-Sr-Ca-Cu-O thin film by coevaporation and its thermal stability (1989)

Thin film with a high Tc single phase was prepared on a (100)MgO substrate at a substrate temperature of about 620 °C by coevaporation of Bi2O3, Sr, Ca, and Cu metal. The resistive superconducting transition with onset Tc of 80 K was observed for this film. By post-deposition annealing at 850 °C, the high Tc phase was transformed into a low Tc phase, while films annealed at a higher temperature such as 890 °C maintained the high Tc phase. These results indicated that the high Tc phase can exist only at the high-temperature region (∼890 °C) while the stable phase existing at the low-temperature region (∼850 °C) is the low Tc phase.
NF-κB-dependent synergistic regulation of CXCL10 gene expression by IL-1β and IFN-γ in human intestinal epithelial cell lines (2007)

These data demonstrate that in colonic epithelial cells, depending on the cellular context and utilizing the NF-kappaB pathway, IL-1beta alone and/or in synergism with IFN-gamma may play a major role in the induction of CXCL10.
Nanomechanical Architecture of Strained Bilayer Thin Films: From Design Principles to Experimental Fabrication (2005)

Design principles for nanostructures are proposed based on the controlled folding of strained thin bilayer films. By controlling the geometry of the bilayer films, calculations can predict formation of structures such as nanorings, nanodrills, and nanocoils (see Figure). In theory, this approach could be applied to the fabrication of nanostructures from other combinations of different classes of materials.
Characterization of moenomycin antibiotic complex by multistage MALDI-IT/RTOF-MS and ESI-IT-MS (2006)

Flavomycin is a commercially available antimicrobial growth promoter and an authorized additive for feeding stuffs in the EU and in the USA. As most antibiotically active products biosynthesized by microorganisms, it contains not only a single active compound but is a complex mixture of structurally closely related substances. Multistage matrix-assisted laser desorption/ionization-ion trap/reflectron time-of-flight mass spectrometry (MALDI-IT/RTOF-MS) and liquid chromatography-electrospray ionization-ion trap-mass spectrometry (LC-ESI-IT-MS) were utilized for a detailed analysis of the constituents of the Flavomycin complex based on low-energy collision induced dissociation (CID). An optimal sample preparation for negative ion vacuum MALDI-MS for this compound class was developed. The MALDI-IT/RTOF-MS2 and -MS3 analysis starting with the precursor [M - H]- ions of these interesting phosphoglycolipids, named moenomycins, yielded a large variety of product ions that facilitated the structural characterization of this class of compounds. Based on the derived CID fragmentation pathway of the five known major constituents, namely moenomycin A, moenomycin A12, moenomycin C4, moenomycin C3. and moenomycin C1, four not yet described moenomycin-type constituents could be characterized. They were assigned as 4F-demethyl-6E-O-de-beta-D-glucopyranosyl-moenomycin A, 6B-N-de(2-hydroxy-5-oxo-1-cyclopenten-1-yl)-moenomycin A, 6B-hydroxy-6B-de[N-(2-hydroxy-5-oxo-1-cyclopenten-1-yl)amino]-moenomycin A, and 6C-hydroxy-moenomycin A. In addition, a moenomycin A carrying an oxygen in the moenocinol-group was found, which is most probably a chemical degradation product. These new compounds were verified by LC-ESI-IT-MS.
Cluster headache (2008)

Cluster headache (CH) is a primary headache disease characterized by recurrent short-lasting attacks (15 to 180 minutes) of excruciating unilateral periorbital pain accompanied by ipsilateral autonomic signs (lacrimation, nasal congestion, ptosis, miosis, lid edema, redness of the eye). It affects young adults, predominantly males. Prevalence is estimated at 0.5-1.0/1,000. CH has a circannual and circadian periodicity, attacks being clustered (hence the name) in bouts that can occur during specific months of the year. Alcohol is the only dietary trigger of CH, strong odors (mainly solvents and cigarette smoke) and napping may also trigger CH attacks. During bouts, attacks may happen at precise hours, especially during the night. During the attacks, patients tend to be restless. CH may be episodic or chronic, depending on the presence of remission periods. CH is associated with trigeminovascular activation and neuroendocrine and vegetative disturbances, however, the precise cautive mechanisms remain unknown. Involvement of the hypothalamus (a structure regulating endocrine function and sleep-wake rhythms) has been confirmed, explaining, at least in part, the cyclic aspects of CH. The disease is familial in about 10% of cases. Genetic factors play a role in CH susceptibility, and a causative role has been suggested for the hypocretin receptor gene. Diagnosis is clinical. Differential diagnoses include other primary headache diseases such as migraine, paroxysmal hemicrania and SUNCT syndrome. At present, there is no curative treatment. There are efficient treatments to shorten the painful attacks (acute treatments) and to reduce the number of daily attacks (prophylactic treatments). Acute treatment is based on subcutaneous administration of sumatriptan and high-flow oxygen. Verapamil, lithium, methysergide, prednisone, greater occipital nerve blocks and topiramate may be used for prophylaxis. In refractory cases, deep-brain stimulation of the hypothalamus and greater occipital nerve stimulators have been tried in experimental settings. The disease course over a lifetime is unpredictable. Some patients have only one period of attacks, while in others the disease evolves from episodic to chronic form.