gebhart/patrepeval huggingface dataset:
Crystal structure of the TRANCE/RANKL cytokine reveals determinants of receptor-ligand specificity (2001)

RANK, the receptor activator of NF-kappaB, and its ligand RANKL (initially termed TRANCE, also termed ODF and OPGL), are a TNF superfamily receptor-ligand pair that govern the development and function of osteoclasts, lymphoid tissue, and mammary epithelium. While TNF family cytokines share a common structural scaffold, individual receptor-ligand pairs associate with high specificity. Given the low level of amino acid conservation among members of the TNF superfamily, the means by which these molecules achieve specificity cannot be completely understood without knowledge of their three-dimensional structures. To determine the elements of RANKL that mediate RANK activation, we have crystallized the ectodomain of murine RANKL and solved its structure to a resolution of 2.6 A. RANKL self-associates as a homotrimer with four unique surface loops that distinguish it from other TNF family cytokines. Mutagenesis of selected residues in these loops significantly modulates RANK activation, as evidenced by in vitro osteoclastogenesis, thereby establishing their necessity in mediating the biological activities of RANKL. Such structural determinants of RANKL-RANK specificity may be of relevance in the pharmacologic design of compounds to ameliorate osteopenic disorders of bone.
Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction. (1990)

We have developed an approach for screening ordered arrays of yeast artificial-chromosome (YAC) clones containing human DNA that is based on the polymerase chain reaction (PCR). This approach is designed to determine the locations of positive clones within a YAC library that is stored as individual clones in 96-well microtiter plates. The high sensitivity and specificity of the PCR allow the detection of target sequences in DNA prepared from pools of 1920 or more YAC clones. The PCR-based screening protocol is performed in two successive stages, which effectively limit the location of a positive clone to four microtiter plates (384 clones). Final localization of each positive clone is accomplished by conventional DNA.DNA hybridization using a single filter containing the YAC clones from the appropriate four microtiter plates. This PCR-based screening strategy has proven highly efficient, allowing the identification and isolation of numerous YAC clones containing specific human genes. The prospects of developing a strategy for screening YAC libraries based completely on PCR assays are discussed, as are the potential applications of this approach to the systematic analysis of the human genome.
A review of Campath in autoimmune disease: Biologic therapy in the gray zone between immunosuppression and immunoablation (2005)

Campath, the subject of this review, is an example of a broadly targeted biologic agent, approved for patients with B-CLL, which may combine immunosuppressive as well as immunoablative properties. For many years Campath has been in clinical use as an immunosuppressive agent for various autoimmune diseases and as part of the preparative regimes for allogeneic HSCT, successfully preventing graft-versus-host-disease (GVHD). This review summarizes the experience of 24 studies including a total of 323 patients treated with Campath for various autoimmune diseases such as arthritis, MS, vasculitis, autoimmune cytopenias and others. The results demonstrate that Campath is fairly safe and 75% of the patients experienced clinical improvement and 15% of the patients were reported in clinical remission even though improvements were often transient.While other biologic drugs may have to narrow targets, Campath, is able to bridge the gap between immunosuppression and immunoablation and may offer an alternative to human stem cell transplantation avoiding the risks of chemotherapy and radiation.
DAF Optimization Using Taguchi Methods and the Effect of Thermal Cycling Parameters on DNA Amplification (1998)

Taguchi methods, which are widely applied in industrial process design, were used to optimize DNA amplification finger-printing (DAF). Quadratic loss functions that penalize deviations from prediction values and L9 (3(4)) and L18 (3(8)) orthogonal arrays revealed effects and interactions of amplification reaction components and thermal cycling parameters. Analysis of variance (ANOVA) decomposed the contribution of individual factors to the experimental response (amplification yield and product number), while verification experiments established that optimum conditions were predictable, verifiable and reproducible. While several amplification components (primer, magnesium and enzyme) conditioned the amplification reaction, annealing temperature and time were the only important thermal cycling contributing factors. The Taguchi strategy defined a robust and transportable amplification protocol based on high annealing temperatures (typically 48 degrees C) and primer concentrations (typically 8 microM), which can be applied to the fingerprinting of a wide range of DNA templates of plant and fungal origin. The general strategy of robust experimental design holds potential as an optimization tool for other methods in molecular biology.
Liquid crystalline surfactant phases in chemical applications (1998)

The importance of lyotropic liquid crystalline structures is shown for two selected surfactant applications,i.e. cosmetics and detergency. The properties of lyotropic liquid crystals are demonstrated for binary surfactant–water systems, ternary surfactant–oil–water systems and multicomponent systems. Detailed knowledge of the phase behavior is crucial for tailor-made product development.
Coadsorption of ferrocene-terminated and unsubstituted alkanethiols on gold: electroactive self-assembled monolayers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoadsorption of ferrocene-terminated and unsubstituted alkanethiols on gold: electroactive self-assembled monolayersChristopher E. D. Chidsey, Carolyn R. Bertozzi, T. M. Putvinski, and A. M. MujsceCite this: J. Am. Chem. Soc. 1990, 112, 11, 4301–4306Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/ja00167a028https://doi.org/10.1021/ja00167a028research-articleACS PublicationsRequest reuse permissionsArticle Views5344Altmetric-Citations961LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Prophylactic glutamine protects the intestinal mucosa from radiation injury (1990)

Glutamine may be an essential dietary component, especially for the support of intestinal mucosal growth and function. This study evaluated the effects of a glutamine-enriched elemental diet, administered before whole-abdominal radiation on gut glutamine metabolism, mucosal morphometrics, and bacterial translocation. Rats were randomized to receive a nutritionally complete elemental diet that was glutamine-enriched or glutamine-free for 4 days. The animals were then subjected to a single dose of 1000 cGy x-radiation to the abdomen. After irradiation, all animals received the glutamine-free diet. Four days later the animals underwent laparotomy for sampling of arterial and portal venous blood, culture of mesenteric lymph nodes, and removal of the small intestine for microscopic examination. There was no difference in arterial glutamine or gut glutamine extraction between the two groups, but body weight loss was significantly diminished in the glutamine-fed rats. Rats receiving the glutamine-enriched elemental diet before radiation had a significant increase in jejunal villous number, villous height, and number of metaphase mitoses per crypt. Scanning electron microscopy confirmed the presence of an intact gut epithelium in eight of eight rats receiving prophylactic glutamine compared to one of eight animals in the glutamine-free group. Three of eight rats fed glutamine had culture positive mesenteric lymph nodes compared with five of seven rats receiving the glutamine-free diet. Glutamine exerts a protective effect on the small bowel mucosa by supporting crypt cell proliferation effect on accelerate healing of the acutely radiated bowel.
NOTE ON PLATO'S REPUBLIC, VI. 510 C 2–5 (1934)

NOTE ON PLATO'S REPUBLIC, VI. 510 C 2–5 Get access A. E. TAYLOR A. E. TAYLOR Search for other works by this author on: Oxford Academic Google Scholar Mind, Volume XLIII, Issue 169, January 1934, Pages 81–84, https://doi.org/10.1093/mind/XLIII.169.81 Published: 01 January 1934
Estimating tempo, swing and beat locations in audio recordings (2002)

The problem of estimating the tempo of audio recordings (the number of beats per minute, or BPM) has received an increasing amount of attention in the past few years. Applications include the synchronization of multiple audio tracks for simultaneous playback, "tempo-synchronous" audio effects, automatic looping of audio tracks etc. This article presents techniques for estimating the tempo and the swing, and locating the beats in audio recordings, under the assumption that the tempo is constant. The techniques rely on a preliminary transient detection stage where note onsets/offsets, percussion hits and other time-localized events are detected. This first step is followed by a maximum likelihood estimation of the tempo, swing and downbeat. Suggestions are given to minimize the computation load of the methods.
Stable propagation of cosmid sized human DNA inserts in an F factor based vector (1992)

Instability of complex mammalian genomic DNA inserts is commonplace in cosmid libraries constructed in conventional multicopy vectors. To develop a means to construct stable libraries, we have developed a low copy number cosmid vector based on the E. coli F factor replicon (Fosmid). We have tested relative stability of human DNA inserts in Fosmids and in two conventional multicopy vectors (Lawrist 16 and Supercos) by comparing the frequency of changes in restriction patterns of the inserts after propagating randomly picked human genomic clones based on these vectors. We found that the clones based on Fosmid vector undergo detectable changes at a greatly reduced frequency. We also observed that sequences that undergo drastic rearrangements and deletions during propagation in a conventional vector were stably propagated when recloned as Fosmids. The results indicate that Fosmid system may be useful for constructing stable libraries from complex genomes.
Amyloid P-component is a constituent of normal human glomerular basement membrane. (1980)

Glomerular and other vascular basement membranes were found to contain an antigen that was immunochemically indistinguishable from serum amyloid P-component. There was no immunological cross-reactivity between antisera to serum amyloid P-component and to collagen types I, III, IV, or V. The amyloid P-component antigen was confined to the endothelial aspect, the lamina rara interna, of glomerular basement membrane. It could not be eluted by high-ionic-strength saline, EDTA, dithiothreitol, or either polar or nonpolar detergents, but was released into solution when isolated glomerular basement membrane was digested by highly purified bacterial collagenase. Most of these P-component molecules and their constituent polypeptide chains were of higher molecular weight and lower isoelectric point than serum amyloid P-component. These findings indicate that, as well as being a normal plasma protein and a universal constituent of amyloid deposits, P-component is also a normal matrix glycoprotein of basement membrane in which it is covalently linked to collagen and/or other matrix proteins. This may be relevant both to the pathogenesis of amyloidosis and to other aspects of physiology and pathology of basement membranes.
Convenient synthesis of optically active 2,2,2-trifluoro-1-phenylethylamine. (2000)

Amination of aryl trifluoromethyl ketones with ammonium formate readily gave racemic 2,2,2-trifluoro-1-arylethylamines in good yields. Resolution of 2,2,2-trifluoro-1-phenylethylamine was carried out with the Pseudomonas fluorescens lipase via enantioselective alcoholysis of its chloroacetamide.
Structural Development and Adhesion of Acrylic ABA Triblock Copolymer Gels (1999)

Relationships between the structure, properties, and processing techniques of model polymer gels are investigated. The mechanical properties of the gels are determined by a thermally reversible aggregation of the syndiotactic PMMA end blocks of an acrylic triblock copolymer, which is diluted with a selective solvent for the center block. The adhesive and mechanical properties of these gels are related to their structural features, which are quantified by small-angle X-ray scattering experiments. The gels are significantly strengthened by the addition of low molecular weight isotactic PMMA homopolymers. These polymers form complexes with the syndiotactic PMMA end blocks of the triblock copolymer. In addition, we employ an axisymmetric adhesion test to demonstrate that the equilibrium gelation process can be utilized to reproducibly control the structure and adhesive properties of "dried" polymers. Acrylic acid moieties increase the adhesive performance of these materials without affecting their structure. By employing a unique gel casting process, a network structure with the desired properties can be formed, giving materials that are ideally suited for use as pressure-sensitive adhesives.
Human immunodeficiency virus reverse transcriptase substitutes for DNA polymerase I in Escherichia coli. (1995)

We present evidence that human immunodeficiency virus (HIV) reverse transcriptase (RT) can substitute for DNA polymerase I in bacteria. Expression of HIV RT enables an Escherichia coli mutant, polA12 recA718, containing a temperature-sensitive mutation in DNA polymerase I, to grow at a nonpermissive temperature. The plasmid pBR322 contains a DNA polymerase I-dependent origin of replication. Expression of HIV RT enables the same E. coli mutant to maintain this plasmid at a nonpermissive temperature. Furthermore, expression of HIV RT in this mutant renders it sensitive to 3'-azido-3'-deoxythymidine, a commonly used anti-AIDS drug that targets HIV RT. These combined findings on the genetic complementation of DNA polymerase I by HIV RT provide a bacterial assay to screen for drugs directed against HIV RT. Genetic complementation provides a method for positive selection of large numbers of functional HIV RT mutants for studies on structure-function relationships.
Two-Person Cooperative Games (1953)

In this paper, the autor extends his previous treatment of «The Bargaining Problem» to a wider class of situations in which threats can play a role/ A new approach is introduced involving the elaboration of the threat concept.
Conducting Polymetallorotaxanes:  A Supramolecular Approach to Transition Metal Ion Sensors (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTConducting Polymetallorotaxanes: A Supramolecular Approach to Transition Metal Ion SensorsS. Sherry Zhu, Patrick J. Carroll, and Timothy M. SwagerView Author Information Department of Chemistry and Laboratory for Research on the Structure of Matter University of Pennsylvania Philadelphia, Pennsylvania 19104 Cite this: J. Am. Chem. Soc. 1996, 118, 36, 8713–8714Publication Date (Web):September 11, 1996Publication History Received11 June 1996Published online11 September 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9619667https://doi.org/10.1021/ja9619667rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views1307Altmetric-Citations175LEARN 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 SUBJECTS:Electrical conductivity,Ions,Plastics,Polymers,Redox reactions Get e-Alerts
Absence of retinoids can induce motoneuron disease in the adult rat and a retinoid defect is present in motoneuron disease patients (2002)

We generated retinoid-deficient adult rats by the removal of retinoids from their diet. We show that their motoneurons undergo neurodegeneration and that there is an accumulation of neurofilaments and an increase in astrocytosis, which is associated with motoneuron disease. These effects are mediated through the retinoic acid receptor alpha. The same receptor deficit is found in motoneurons from patients suffering from spontaneous amyotrophic lateral sclerosis. Furthermore, we show that there is a loss of expression of the retinaldehyde dehydrogenase enzyme II in motoneurons. Therefore, we propose that a defect in the retinoid signalling pathway is in part be responsible for some types of motoneuron disease.
Viral-Induced Self-Assembly of Magnetic Nanoparticles Allows the Detection of Viral Particles in Biological Media (2003)

Monodisperse magnetic nanoparticles conjugated with virus-surface-specific antibodies self-assemble in the presence of specific viral particles to create supramolecular structures with enhanced magnetic properties, as detected by magnetic resonance methods (NMR/MRI). The observed magnetic relaxation changes that occur upon viral-induced assembly allowed for highly sensitive and selective detection of a virus in complex biological media. The developed method was shown to specifically detect adenovirus-5 and herpes simplex virus-1 at concentrations of 5 viral particles/10 muL without the need of extensive sample preparation. The applications of this new method span from high-throughput NMR detection of viruses in biological samples to potential MR imaging of viral distribution in vivo.
Adjuvant Galantamine Administration Improves Negative Symptoms in a Patient With Treatment-Refractory Schizophrenia (2002)

Because of the demonstration of a selective alpha nicotinic receptor abnormality in patients with schizophrenia, galantamine was added to the stable regimen of atypical and other antipsychotic medications in a 43-year-old man manifesting severe and persistent positive and negative symptoms, as well as mood disturbance and cognitive dysfunction. Galantamine is an inhibitor of acetylcholinesterase and a positive allosteric modulator of nicotinic cholinergic receptors (with a FDA-approved indication for the treatment of patients with mild to moderate Alzheimer disease (AD) under the trade name Reminyl). Galantamine HBr was initiated at a dose of 4 mg po BID, which was maintained for the first week of adjuvant therapy, and eventually was increased to 12 mg po BID during the final weeks of his 2-month trial. Remarkably, within 1 week of its initiation, there was a dramatic and clinically significant decrease of negative symptoms, as reflected in formal ratings on the Scale for the Assessment of Negative Symptoms. Moreover, within a few days of galantamine discontinuation, negative symptoms worsened, returning to the baseline level of severity. In addition to targeting memory dysfunction in AD, acetylcholinesterase inhibitors may have an expanded range of targets and clinical indications, including behavioral and psychotic symptoms. Galantamine is distinguished from other acetylcholinesterase inhibitors by its positive allosteric modulatory properties, improving the efficiency of transduction of the acetylcholine signal at nicotinic receptors. This latter property may have contributed to the observed improvement in negative symptoms observed in this patient. Importantly, positive symptoms were unchanged during this 2-month trial.(7)
Modulation of Erbb2 signaling during development: a threshold level of Erbb2 signaling is required for development (2004)

We have generated a series of Erbb2 cDNA knock-in animals to explore the role of signaling pathways coupled to Erbb2 during development. Although this knock-in allele was hypomorphic, expressing tenfold less Erbb2 protein than wild type, the knock-in animals were healthy. However, a further twofold reduction in Erbb2 levels in hemizygous knock-in animals resulted in perinatal lethality with defects in the innervation of the diaphragm. Genetic rescue of this hypomorph was accomplished by expression of the Erbb2-Y1028F mutant in a comparable knock-in allele. Interestingly, hemizygous Y1028F animals were viable with normal innervation of the diaphragm. Molecular analyses revealed that the Y1028F allele expressed higher levels of Erbb2 and that Y1028 promoted the turnover of the receptor. In addition, ablation of the Shc-binding site in Erbb2 (Y1227) resulted in subtle defects in the sensory nerves not observed in the other mutant erbb2 strains. Thus, we have established how Erbb2 levels may be modulated through development and that a minimum threshold level of Erbb2 is required.
<title>Calibration of the device simulation program suitable for low-temperature application</title> (1998)

Temperature dependent mobility in the device simulation program has been used to check whether they are adequate to simulate device characteristics under low temperature operation. The study here shows that although the mobility models in the simulation program can be used to simulate room temperature device characteristics, care should be taken for the low temperature simulation. By substituting the extracted mobility table or the suitable mobility model into the simulation program, better simulation results can be obtained. To this point, we believe that there is still a need to develop a better and more concentrated and temperature dependent mobility model.
Intrinsic Resistance of Tumorigenic Breast Cancer Cells to Chemotherapy (2008)

These studies provide clinical evidence for a subpopulation of chemotherapy-resistant breast cancer-initiating cells. Lapatinib did not lead to an increase in these tumorigenic cells, and, in combination with conventional therapy, specific pathway inhibitors may provide a therapeutic strategy for eliminating these cells to decrease recurrence and improve long-term survival.