gebhart/patrepeval huggingface dataset:
Ulongamides A−F, New β-Amino Acid-Containing Cyclodepsipeptides from Palauan Collections of the Marine Cyanobacterium <i>Lyngbya</i> sp. (2002)

Six new beta-amino acid-containing cyclic depsipeptides, termed ulongamides A-F (1-6), have been isolated from collections of apratoxin-producing cyanobacteria from Palau. Their planar structures have been determined by NMR spectroscopic techniques. The absolute stereochemistry of the hydroxy acid and all the alpha-amino acid-derived units was ascertained to be S by chiral HPLC analysis of degradation products. The stereochemistry of the beta-amino acid moiety, 3-amino-2-methylhexanoic acid, was established by advanced Marfey analysis of the acid hydrolyzates and found to be 2R,3R in compounds 1-3 but 2S,3R in compounds 4-6. All compounds except 6, which lacks an aromatic amino acid moiety, were weakly cytotoxic against KB cells.
Testing the antagonistic effect of follistatin on BMP family members in ovine granulosa cells (2005)

Follistatin was first demonstrated as an activin-binding protein, neutralizing its actions. However, there is emerging evidence that follistatin inhibits the action of other members of the transforming growth factor beta(TGFbeta) / bone morphogenetic protein (BMP) superfamily. Recently, numerous BMP factors have been shown to play important roles in regulating folliculogenesis and ovulation rate in mammals, and such a potential antagonistic role of follistatin is of particular interest in the context of ovarian function. Using a biological test based on progesterone production by ovine primary granulosa cells in culture, we show that follistatin was a strong antagonist of activin A, but not BMP-2 or BMP-4 actions. In contrast, noggin, a known specific BMP antagonist, had no effect on activin A but strongly neutralized BMP-2 and BMP-4 actions. BMP-6 action was only slightly reduced by both follistatin and noggin. Our data led to the conclusion that follistatin would not represent a determinant physiological modulator of the biological effect of BMP factors on granulosa cells.
Neoadjuvant hormonal therapy in stage C adenocarcinoma of the prostate. (1993)

This report describes the effects of neoadjuvant hormonal therapy on 16 patients (mean age = 65 y) with clinical stage C adenocarcinoma of the prostate (CaP) who underwent radical prostatectomy from December 1991 to June 1993 at the University of Colorado Health Sciences Center. Staging of CaP was determined by digital rectal exam, transrectal ultrasonography (TRUS), radionuclide bone scanning, abdominal and pelvic computed tomography scanning, transrectal coil magnetic resonance imaging, and serum acid phosphatase. Most patients underwent a laparoscopic lymph node dissection to rule out micrometastasis. Every patient was treated for 4 months with a combination of a gonadotrophin-releasing hormone (GnRH) agonist (Lupron) and an anti-androgen (flutamide, Eulexin). Serial prostate-specific antigen (PSA) levels, post-treatment prostate volume measured by TRUS, and whole-mount sectioning of the surgical specimen were studied. The PSA levels decreased from a mean of 39.1 ng/ml (Hybritech method) to a mean of 0.43 ng/ml; (p < 0.0001). Prostate volumes in all patients demonstrated a mean decrease of 52% (p < 0.0001), and pathological effects of hormonal deprivation were observed in all patients. By whole-mount sectioning of the radical prostatectomy specimens, 3 patients had organ-confined disease (stage B), 6 showed invasion of the capsule with surgical margins free of tumor (stage C1), 3 had extracapsular extension with positive surgical margins (stage C2), and 4 had extracapsular extension with seminal vesicle involvement (stage C3). We conclude that by downsizing and markedly decreasing serum PSA values, neoadjuvant hormonal therapy offers an alternative treatment for stage C carcinoma of the prostate.(ABSTRACT TRUNCATED AT 250 WORDS)
Treatment of advanced malignancy with plasma perfused over staphylococcal protein A. (1983)

A total of 14 extensively pretreated patients with advanced and progressive malignancy were given 140 infusions of autologous plasma that had been perfused over staphylococcal protein A bound to an agarose gel (Sepharose). Infusions ranged in volume from 35 ml to 260 ml (mean, 70 ml), and the quantity of protein A used ranged from 1 to 30 mg per 100 ml of plasma (mean, 10 mg). Acute toxic reactions included fever (21%), chills (18%), nausea (17%), vomiting (8%), pain (9%) and bronchospasm (2%). Four patients did not have an acute toxic reaction and no chronic or cumulative toxic effects were identified. In two patients there was objective tumor regression and in five there was stabilization of disease lasting from 4 to 12 weeks. Further study of this treatment modality is warranted.
Characterization of silk proteins in the cocoon fibers of Cricula trifenestrata (2001)

Lower postoperative VAS scores and lower postoperative VAS scores and lower analgesic used requirements of EA, it is thought that EA can be safely applied in the TEP procedure as an alternative in patients who cannot be administered GA.
Genetic and phenotypic analysis of herpes simplex virus type 1 mutants conditionally resistant to immune cytolysis (1983)

Nine temperature-sensitive (ts) mutants of herpes simplex virus type 1 selected for their inability to render cells susceptible to immune cytolysis after infection at the nonpermissive temperature have been characterized genetically and phenotypically. The mutations in four mutants were mapped physically by marker rescue and assigned to functional groups by complementation analysis. In an effort to determine the molecular basis for cytolysis resistance, cells infected with each of the nine mutants were monitored for the synthesis of viral glycoprotein in total cell extracts and for the presence of these glycoproteins in plasma membranes. The four mutants whose ts mutations were mapped were selected with polypeptide-specific antiserum to glycoproteins gA and gB; however, three of the four mutations mapped to DNA sequences outside the limits of the structural gene specifying these glycoproteins. Combined complementation and phenotypic analysis indicates that the fourth mutation also lies elsewhere. The ts mutations in five additional cytolysis-resistant mutants could not be rescued with single cloned DNA fragments representing the entire herpes simplex virus type 1 genome, suggesting that these mutants may possess multiple mutations. Complementation tests with the four mutants whose ts lesions had been mapped physically demonstrated that each represents a new viral gene. Examination of mutant-infected cells at the nonpermissive temperature for the presence of viral glycoproteins in total cell extracts and in membranes at the cell surface demonstrated that (i) none of the five major viral glycoproteins was detected in extracts of cells infected with one mutant, suggesting that this mutant is defective in a very early function; (ii) cells infected with six of the nine mutants exhibited greatly reduced levels of all the major viral glycoproteins at the infected cell surface, indicating that these mutants possess defects in the synthesis or processing of viral glycoproteins; and (iii) in cells infected with one mutant, all viral glycoproteins were precipitable at the surface of the infected cell, despite the resistance of these cells to cytolysis. This mutant is most likely mutated in a gene affecting a late stage in glycoprotein processing, leading to altered presentation of glycoproteins at the plasma membrane. The finding that the synthesis of both gB and gC was affected coordinately in cells infected with six of the nine mutants suggests that synthesis of these two glycoproteins, their transport to the cell surface, or their insertion into plasma membranes is coordinately regulated.
Functional Nanocellulose, Alginate and Chitosan Nanocomposites Designed as Active Film Packaging Materials (2021)

The aim of the study was to characterize and compare films made of cellulose nanocrystals (CNC), nano-fibrils (CNF), and bacterial nanocellulose (BNC) in combination with chitosan and alginate in terms of applicability for potential food packaging applications. In total, 25 different formulations were made and evaluated, and seven biopolymer films with the best mechanical performance (tensile strength, strain)-alginate, alginate with 5% CNC, chitosan, chitosan with 3% CNC, BNC with and without glycerol, and CNF with glycerol-were selected and investigated regarding morphology (SEM), density, contact angle, surface energy, water absorption, and oxygen and water barrier properties. Studies revealed that polysaccharide-based films with added CNC are the most suitable for packaging purposes, and better dispersing of nanocellulose in chitosan than in alginate was observed. Results showed an increase in hydrophobicity (increase of contact angle and reduced moisture absorption) of chitosan and alginate films with the addition of CNC, and chitosan with 3% CNC had the highest contact angle, 108 ± 2, and 15% lower moisture absorption compared to pure chitosan. Overall, the ability of nanocellulose additives to preserve the structure and function of chitosan and alginate materials in a humid environment was convincingly demonstrated. Barrier properties were improved by combining the biopolymers, and water vapor transmission rate (WVTR) was reduced by 15-45% and oxygen permeability (OTR) up to 45% by adding nanocellulose compared to single biopolymer formulations. It was concluded that with a good oxygen barrier, a water barrier that is comparable to PLA, and good mechanical properties, biopolymer films would be a good alternative to conventional plastic packaging used for ready-to-eat foods with short storage time.
Incorporation of pyridazine rings in the structure of functionalized π-conjugated materials (2011)

Throughout the past few decades, the development of new π-conjugated organic compounds has received a lot of attention due to their potential applications ranging from liquid crystals, light-emitting and nonlinear optical applications to self-assembly and supramolecular chemistry. Most of these applications rely on electron transfer (ET) and excitation energy transfer (EET). Introduction in these conjugated structures of N-heterocycles such as the highly electronegative pyridazine ring appeared particularly interesting since the π-deficient character of the pyridazine, used as a dipolar moiety, favored the electron transfer. Moreover, the presence of nitrogen atoms with free electron pairs allows the pyridazine ring to act like as an effective and stable complexing agent for transition metal ions and to be used in supramolecular chemistry for the construction of highly sophisticated architectures. This review highlights recent π-conjugated materials including pyridazine ring and their applications in various fields.
Teaching Uncomfortable Topics: An Action-Oriented Strategy for Addressing Racism and Related Forms of Difference (2001)

The purpose of this article is to provide one pedagogical model for addressing uncomfortable topics in the classroom. More concretely, the model reconceptualizes the process of teaching and learning and generates an action-oriented strategy for dealing with a topic that typically creates classroom discomfortrace and racism. Traditional modes of learning are critically evaluated, highlighting how elements of these approaches can negatively impact one's understanding of race and racial differences. The paper then offers an alternative, action-oriented strategy grounded in the notions of collective responsibility, dialogue, and intersubjectivity, the Gramscian (1971) intellectual, the dialectic, and praxis. This strategy is concretized using examples of teaching and learning about racism and related forms of difference that occur both in and outside of the classroom.
A Versatile Amino Acid Analogue of the Solvatochromic Fluorophore 4-<i>N,N</i>-Dimethylamino-1,8-naphthalimide: A Powerful Tool for the Study of Dynamic Protein Interactions (2008)

We have developed a new unnatural amino acid based on the solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide (4-DMN) for application in the study of protein-protein interactions. The fluorescence quantum yield of this chromophore is highly sensitive to changes in the local solvent environment, demonstrating "switch-like" emission properties characteristic of the dimethylaminophthalimide family of fluorophores. In particular, this new species possesses a number of significant advantages over related fluorophores, including greater chemical stability under a wide range of conditions, a longer wavelength of excitation (408 nm), and improved synthetic accessibility. This amino acid has been prepared as an Fmoc-protected building block and may readily be incorporated into peptides via standard solid-phase peptide synthesis. A series of comparative studies are presented to demonstrate the advantageous properties of the 4-DMN amino acid relative to those of the previously reported 4-N,N-dimethylaminophthalimidoalanine and 6-N,N-dimethylamino-2,3-naphthalimidoalanine amino acids. Other commercially available solvatochromic fluorophores are also include in these studies. The potential of this new probe as a tool for the study of protein-protein interactions is demonstrated by introducing it into a peptide that is recognized by calcium-activated calmodulin. The binding interaction between these two components yields an increase in fluorescence emission greater than 900-fold.
MCM2–7 Complexes Bind Chromatin in a Distributed Pattern Surrounding the Origin Recognition Complex inXenopus Egg Extracts (2002)

The MCM2-7 complex is believed to function as the eukaryotic replicative DNA helicase. It is recruited to chromatin by the origin recognition complex (ORC), Cdc6, and Cdt1, and it is activated at the G(1)/S transition by Cdc45 and the protein kinases Cdc7 and Cdk2. Paradoxically, the number of chromatin-bound MCM complexes greatly exceeds the number of bound ORC complexes. To understand how the high MCM2-7:ORC ratio comes about, we examined the binding of these proteins to immobilized linear DNA fragments in Xenopus egg extracts. The minimum length of DNA required to recruit ORC and MCM2-7 was approximately 80 bp, and the MCM2-7:ORC ratio on this fragment was approximately 1:1. With longer DNA fragments, the MCM2-7:ORC ratio increased dramatically, indicating that MCM complexes normally become distributed over a large region of DNA surrounding ORC. Only a small subset of the chromatin-bound MCM2-7 complexes recruited Cdc45 at the onset of DNA replication, and unlike Cdc45, MCM2-7 was not limiting for DNA replication. However, all the chromatin-bound MCM complexes may be functional, because they were phosphorylated in a Cdc7-dependent fashion, and because they could be induced to support Cdk2-dependent Cdc45 loading. The data suggest that in Xenopus egg extracts, origins of replication contain multiple, distributed, initiation-competent MCM2-7 complexes.
Contamination in Expressed Breast Milk Following Breast Cleansing (1997)

The purpose of this study was to determine if preexpression breast cleansing reduced the bacterial count in expressed breast milk. The study involved the collection of 178 breast milk samples (89 matched samples); 38 matched samples were from mothers of term infants and 51 matched samples were from mothers of preterm infants. One half of the samples were collected following breast cleansing with Phisoderm and tap water. The other half were collected following breast cleansing with tap water only. Hand and equipment washing with Phisoderm and tap water preceded all sample collections. Storage containers were sterile. Samples were cultured for pathogenic and nonpathogenic bacteria and examined at 24 and 48 hours. Data were analyzed by Wilcoxon Matched-Pairs sign test and Chi square. Breast cleansing with Phisoderm and water was not more effective than water alone at reducing nonpathogenic bacteria or eliminating pathogenic bacteria. Mothers of preterm infants had higher levels of both nonpathogenic and pathogenic bacteria than mothers of full-term infants. The most common form of bacterial contamination was coagulase-negative Staphylococcus epidermidis. This particular bacteria is found in higher levels in the stools of breast fed infants than formula fed infants and it also the most common contaminant found in the blood of preterm infants who develop sepsis. The findings of this study reveal that chemical interventions may not be effective at rendering breast milk free from pathogenic bacteria. More research is needed to determine the optimal cleansing protocol to achieve bacterial decontamination of breast milk or to determine the clinically acceptable level of contamination based on the effects on infants.
Encryption technology other than PKI (2002)

TECSEC Inc. invented and demonstrated a COTS cryptographic key management system called Constructive Key Management (CKM). This technology is a complete system with the ability to also manage multiple algorithms and the flexibility to provide encryption for Data-at-Rest and Data-in-Transit. Although August 1997 DoD policy is to establish a DoD public key infrastructure (PKI), there are indications that other technologies that can incorporate public private key (PK) functions could become acceptable to DoD. The paper discusses the CKM technology and considers role-based access control.
Identification of 5–7 Defects in a Copper Oxide Surface (2011)

A topological defect in a Cu(2)O surface oxide grown on Cu(111) has been identified. Using scanning tunneling microscopy, we observed the formation of pentagonal and heptagonal rings within the Cu(2)O surface oxide. These structures break the symmetry of the hexagonal oxide surface and are a consequence of the presence of oxygen vacancies in the Cu(2)O surface. We propose that the pentagonal and heptagonal rings are formed through the rotation of a -O-Cu-O- chain in a manner similar to the Stone-Wales transformation. The proposed transformation is supported by the results of density functional theory calculations.
Organocatalyzed atom transfer radical polymerization driven by visible light (2016)

Atom transfer radical polymerization (ATRP) has become one of the most implemented methods for polymer synthesis, owing to impressive control over polymer composition and associated properties. However, contamination of the polymer by the metal catalyst remains a major limitation. Organic ATRP photoredox catalysts have been sought to address this difficult challenge but have not achieved the precision performance of metal catalysts. Here, we introduce diaryl dihydrophenazines, identified through computationally directed discovery, as a class of strongly reducing photoredox catalysts. These catalysts achieve high initiator efficiencies through activation by visible light to synthesize polymers with tunable molecular weights and low dispersities.
Multiple RNase H activities in mammalian type C retravirus lysates (1978)

Lysates of Moloney murine sarcoma-leukemia virus [M-MSV(MLV)], a virus complex grown in the rat cell line 78A-1, were found to contain three RNase H species separable by polycytidylic acid[poly(C)]-agarose chromatography. RNase H activity (RNase H I) associated with RNA-directed DNA polymerase eluted at 0.23 M KCI from poly(C)-agarose. RNase H II, which eluted from poly(C)-agarose at 0.12 M KCI and was not associated with DNA polymerase activity, was shown to be identical to an RNase H species (designated RNase H II) previously isolated from M-MSV(MLV) by a different procedure (G. F. Gerard and D. P. Grandgenett, J. Virol. 15:785-797, 1975). M-MSV(MLV) RNase H II was established to be a random exohybridase that requires free-chain termini in its hybrid substrate for activity. Lysates of Rickard feline leukemia virus also contained RNase H activity not associated with DNA polymerase activity that eluted from poly(C)-agarose at 0.12 M KCl. A third species of enzyme from M-MSV(MLV) lysates, called RNase H III, did not bind to poly(C)-agarose in 0.06 M KCl. RNase H III was purified from lysates of M-MSV(MLV) and M-MLV (grown in mouse cells) by sequential chromatography on poly(C)-agarose, DEAE-cellulose, phosphocellulose, and polyuridylic acid-Sepharose. Purified RNase H III (i) was free of any associated DNA polymerase activity, (ii) had an apparent molecular weight of 30,000 determined by Sephadex G-100 gel filtration, (iii) had an absolute requirement for Mn2+ (1 mM optimum) for the degradation of [3H](A)n.(dT)n, (iv) was inhibited by the presence of any salt in reaction mixtures, and (v) was endoribonucleolytic in its mode of action as indicated by the size distribution of limited degradation products of [3H](A)n.(dT)n. RNase H III was inhibited by antisera prepared against Rauscher MLV and simian sarcoma virus reverse transcriptase, and the quantity of RNase H III and RNase H I present in lysates of M-MLV were reduced and increased proportionately if virus was lysed in the presence of the protease inhibitor phenylmethylsulfonyl fluoride. These results indicate that RNase H III is a proteolytic cleavage product of DNA polymerase-RNase H. Substantial RNase H activity that did not bind to poly(C)-agarose in 0.06 M KCl was also found in lysates of Harvey MSV(MLV), Rauscher MLV, and Rickard feline leukemia virus, but not in lysates of avian myeloblastosis virus.
Enhanced solar water-splitting efficiency using core/sheath heterostructure CdS/TiO<sub>2</sub>nanotube arrays (2007)

A novel fabrication route for core/sheath heterostructure CdS/TiO(2) nanotube arrays is proposed using ac electrodeposition for application in photoelectrochemical cells. The morphologies of the CdS/TiO(2) electrodes, which were prepared by electrochemically depositing CdS directly into anodic titanium nanotubes from an electrolyte containing Cd(2+) and S in dimethyl sulfoxide, were characterized by a field emission scanning electron microscope (FESEM). The deposited material was found to be in a hexagonal CdS structure by x-ray diffraction (XRD). The synthesized CdS/TiO(2) electrodes showed much higher photocurrent density in the visible wavelength region than pure TiO(2) nanotube arrays. We demonstrate that ac deposition voltage and time can control the CdS/TiO(2) composite architecture, which is crucial in determining the overall efficiency of the water-splitting reaction. The maximum photocurrent density was obtained with the core/sheath heterostructure CdS/TiO(2) nanotube arrays, which were fabricated by deposition of CdS at 5 V for 30 min with 2.5 microm tube length.