gebhart/patrepeval huggingface dataset:
Placebo non‐response measure in sequential parallel comparison design studies (2015)

The Sequential Parallel Comparison Design (SPCD) is one of the novel approaches addressing placebo response. The analysis of SPCD data typically classifies subjects as 'placebo responders' or 'placebo non-responders'. Most current methods employed for analysis of SPCD data utilize only a part of the data collected during the trial. A repeated measures model was proposed for analysis of continuous outcomes that permitted the inclusion of information from all subjects into the treatment effect estimation. We describe here a new approach using a weighted repeated measures model that further improves the utilization of data collected during the trial, allowing the incorporation of information that is relevant to the placebo response, and dealing with the problem of possible misclassification of subjects. Our simulations show that when compared to the unweighted repeated measures model method, our approach performs as well or, under certain conditions, better, in preserving the type I error, achieving adequate power and minimizing the mean squared error.
Structure and function in rhodopsin: high level expression of a synthetic bovine opsin gene and its mutants in stable mammalian cell lines. (1996)

Stable mammalian cell lines harboring a synthetic bovine opsin gene have been derived from the suspension-adapted HEK293 cell line. The opsin gene is under the control of the immediate-early cytomegalovirus promoter/enhancer in an expression vector that also contains a selectable marker (Neo) governed by a relatively weak promoter. The cell lines expressing the opsin gene at high levels are selected by growth in the presence of high concentrations of the antibiotic geneticin. Under the conditions used for cell growth in suspension, opsin is produced at saturated culture levels of more than 2 mg/liter. After reconstitution with 11-cis-retinal, rhodopsin is purified to homogeneity in a single step by immunoaffinity column chromatography. Rhodopsin thus prepared (> 90% recovery at concentrations of up to 15 microM) is indistinguishable from rhodopsin purified from bovine rod outer segments by the following criteria: (i) UV/Vis absorption spectra in the dark and after photobleaching and the rate of metarhodopsin II decay, (ii) initial rates of transducin activation, and (iii) the rate of phosphorylation by rhodopsin kinase. Although mammalian cell opsin migrates slower than rod outer segment opsin on SDS/polyacrylamide gels, presumably due to a different N-glycosylation pattern, their mobilities after deglycosylation are identical. This method has enabled the preparation of several site-specific mutants of bovine opsin in comparable amounts.
Ischemic induction of protooncogene expression in gerbil brain. (1991)

Cerebral ischemia and reperfusion results in an active series of metabolic events, eventually leading to cell death. The expression of specific genes during cerebral ischemia and reperfusion may play an important, determinant role in the mechanisms controlling cellular processes. Ten minutes of bilateral carotid occlusion in the Mongolian gerbil was found to increase the messenger RNA for both the c-fos and c-jun protooncogenes. The changes in gene expression were detected in the regions of ischemia, specifically the cortex and striatum, and no increases were seen in either the brain stem or the cerebellum, which possess a separate circulation. Induction of protooncogene mRNA is correlated to the duration of ischemia, i.e., the longer the time of ischemia, the greater the increase in c-fos expression. Pretreatment of animals with pentobarbital reduced the effect of the ischemic insult and prevented the increase in c-fos mRNA. Analysis of the c-fos and c-jun proteins after ischemia demonstrated an increase in the formation of a functional transcriptional complex and association with the AP-1 binding region. These findings suggest that ischemic cell death and recovery in neurodegenerative disorders such as stroke may involve the regulated expression of these protooncogenes early in the pathway of ischemia.
Migrants on the move in Asia (1996)

For more about the East-West Center, see <a href="http://www.eastwestcenter.org/">http://www.eastwestcenter.org/</a>
Differentiation and Expansion of Beta Cell Mass in Porcine Neonatal Pancreatic Cell Clusters Transplanted into Nude Mice (1999)

Neonatal porcine pancreas has considerable capacity for growth and differentiation, making it an attractive potential source of islet tissue for xenotransplantation. Pancreases from 1-3-day-old newborn pigs were digested with collagenase and cultured for 8 days. The resulting cellular aggregates are called porcine neonatal pancreatic cell clusters (NPCCs). The mean yield of NPCCs from a newborn pig was 28,200 +/- 1700 islet equivalents. Cytokeratin 7 (CK7) was used as a marker for the immunostaining of pancreatic duct cells. In neonatal pancreas, 18% of the insulin-positive cells co-stained for CK7, thus being protodifferentiated. NPCCs also contained protodifferentiated cells; insulin/PP and insulin/somatostatin co-stained cells were more common than insulin/glucagon cells. Between 1 and 8 days of culture, the DNA content of the NPCCs fell to 16% and the insulin content to 33% of the starting value, mainly due to the preferential loss of exocrine cells. Transplantation of 2000 or 4000 NPCCs into diabetic nude mice typically normalized glucose values in 10-20 weeks. Mice with successful grafts had lower fasting blood glucose levels than normal mice and accelerated glucose clearance after an i.p. glucose load. The starting NPCCs consisted of 17% insulin-staining cells, but the grafts of mice with reversed diabetes consisted of 94% beta cells, with some co-stained for CK7, indicating that the grafts still contained immature cells. The mass of insulin-producing cells rose from 0.22 +/- 0.08 mg 1 week after transplantation to 4.34 +/- 0.27 mg in mice sacrificed at 27-35 weeks. In summary, NPCCs contain mostly islet precursor cells, which when transplanted into nude mice undergo striking differentiation and beta cell expansion.
Blood screening using Diffraction Phase Cytometry (2010)

We demonstrate an automatic interferometry based blood smear analysis technique known as Diffraction Phase Cytometry (DPC) which provides detailed physiologically relevant information on the 2D and 3D morphology of individual blood cells.
Amino acid sequences of α-helical segments from S-carboxymethylkerateine-A. Statistical analysis (1978)

The distribution of the different types of amino acid residue within two helical segments isolated from the low-sulphur fraction of wool keratin was examined for periodicity and larger sequence repeats. Both were detected, the former corresponding to the geometry of the proposed coiled=coil structure and the latter suggesting a distant gene duplication, though the existence of the repeat might equally well be related to interactions within the microfibril.
A Polyoxometalate-Assisted Electrochemical Method for Silicon Nanostructures Preparation:  From Quantum Dots to Nanowires (2007)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Polyoxometalate-Assisted Electrochemical Method for Silicon Nanostructures Preparation: From Quantum Dots to NanowiresZhenhui Kang, Chi Him A. Tsang, Zhendong Zhang, Mingliang Zhang, Ning-bew Wong, J. Antonio Zapien, Yueyue Shan, and Shuit-Tong LeeView Author Information Department of Biology and Chemistry and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China, and Centre of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Hong Kong, P. R. China Cite this: J. Am. Chem. Soc. 2007, 129, 17, 5326–5327Publication Date (Web):April 4, 2007Publication History Received13 December 2006Published online4 April 2007Published inissue 1 May 2007https://pubs.acs.org/doi/10.1021/ja068894whttps://doi.org/10.1021/ja068894wrapid-communicationACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views4420Altmetric-Citations154LEARN 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 SUBJECTS:Electrical properties,Nanoparticles,Nanostructures,Silicon,Transmission electron microscopy Get e-Alerts
Cloning and Primary Sequence of a Mouse Candidate Prohormone Convertase PC1 Homologous to PC2, Furin, and Kex2: Distinct Chromosomal Localization and Messenger RNA Distribution in Brain and Pituitary Compared to PC2 (1991)

Using a 796-basepair cDNA fragment obtained from a mouse pituitary library we have screened two mouse insulinoma libraries and isolated a full-length cDNA clone (2516 basepairs; 753 amino acids), designated mPC1. The cDNA sequence of mPC1 codes for a protein containing 753 amino acids and three potential N-glycosylation sites. This cDNA encodes a putative novel subtilisin-like proteinase, exhibiting within its presumed catalytic domain 64%, 55%, and 47% amino acid sequence identity to the recently characterized candidate prohormone convertases human Furin, mouse PC2, and yeast Kex2 gene products, respectively. An identical sequence to mPC1 was derived from a cDNA library of mouse corticotroph AtT-20 tumor cells. An ArgGlyAsp tripeptide identical to the recognition sequence of integrins was observed in the structures of the mammalian PC1, PC2, and Furin. In situ hybridization results demonstrated a distinct localization of the mPC1 and mPC2 transcripts in pituitary and brain. Thus, whereas both mPC1 and mPC2 are found in the intermediate lobe of the pituitary, only mPC1 is easily detected in the anterior lobe. In extrahypothalamic regions of the brain, including cortex, hippocampus, thalamus, and spinal cord, mPC2 transcripts predominate over mPC1. Both mRNAs are found in only a fraction of hypothalamic neurons, with greater abundance of mPC1 over mPC2 in the supraoptic nucleus. The genes coding for mPC1 and mPC2 map to the murine chromosomes 13 (band 13c) and 2 (2F3-2H2 region), respectively.
Differential Activation of T Cells by Natural Antigen Peptide Analogues: Influence on Autoimmune and Alloimmune In Vivo T Cell Responses (1998)

Recent studies using synthetic altered peptide ligands (Analogues) have led to the fine dissection of TCR-mediated T cell functions elicited by Ag recognition. Certain Analogues behave as full agonists of the antigenic peptide while others are partial agonists in that they only trigger selected T cell functions. Additionally, peptide Analogues can behave as antagonists by inhibiting functions of T cell clones when coincubated with the wild-type peptide. In fetal thymic organ cultures, synthetic altered peptide ligands can impact T cell repertoire selection. However, the influence of naturally occurring peptide Analogues on T cell immunity in vivo remains hypothetical. We previously reported that, in B10.A mice, immunogenicity and tolerogenicity of the self-MHC class I peptide, Ld 61-80, were influenced by the presentation of a cross-reactive self-peptide, Kk 61-80. Here, we show that Kk 61-80 self-peptide represents a partial agonist of Ld 61-80 in that it induced the proliferation but not the lymphokine production of Ld 61-80-primed T cells. Next, we showed that presentation of Kk 61-80 Analogue peptide mediated T cell tolerance toward Ld 61-80 self-peptide. Alternatively, when Ld protein represented an alloantigen displayed on transplanted cells, immunization with Kk 61-80 Analogue sensitized recipient mice to Ld 61-80 peptide, thus inducing potent immune responses to donor cells. These results show that the presentation of natural Analogue peptides may represent an essential component of T cell responses involved in autoimmunity and transplant rejection.
Investigation of actinomycete diversity in the tropical rainforests of Singapore (1999)

Five thousand actinomycetes were isolated from soil samples collected from rainforests in Singapore and the generic identities of these isolates were determined by using a procedure that combined morphological, chemotaxonomic and 16S rDNA sequence-based phylogenetic analyses. Actinomycetes belonging to a total of 36 genera were identified. The most abundant isolates are members of Streptomyces, Micromonospora, Actinoplanes, Actinomadura, Nonomuria, Nocardia and Streptosporangium. By phylogenetic analysis of 16S rDNA sequences of our isolates together with those of known actinomycete species, we also evaluated the species diversity of several genera including Streptomyces, Micromonospora, Nonomuria, and Actinomadura. We found that: first, the tropical isolates are present in most clades represented by known species; and second, many tropical isolates form new clades distant from the known species, indicating the presence of unidentified taxa at both species and genus levels. Based on these results, we conclude that actinomycete diversity in the tropical rainforest is very great and should represent an excellent source for discovery of novel bioactive compounds.
Noninvasive gene targeting to the brain (2000)

Gene therapy of the brain is hindered by the presence of the blood-brain barrier (BBB), which prevents the brain uptake of bloodborne gene formulations. Exogenous genes have been expressed in the brain after invasive routes of administration, such as craniotomy or intracarotid arterial infusion of noxious agents causing BBB disruption. The present studies describe the expression of an exogenous gene in brain after noninvasive i.v. administration of a 6- to 7-kb expression plasmid encoding either luciferase or beta-galactosidase packaged in the interior of neutral pegylated immunoliposomes. The latter are conjugated with the OX26 mAb to the rat transferrin receptor, which enables targeting of the plasmid DNA to the brain via the endogenous BBB transferrin receptor. Unlike cationic liposomes, this neutral liposome formulation is stable in blood and does not result in selective entrapment in the lung. Luciferase gene expression in the brain peaks at 48 h after a single i.v. administration of 10 microg of plasmid DNA per adult rat, a dose that is 30- to 100-fold lower than that used for gene expression in rodents with cationic liposomes. beta-Galactosidase histochemistry demonstrated gene expression throughout the central nervous system, including neurons, choroid plexus epithelium, and the brain microvasculature. In conclusion, widespread gene expression in the brain can be achieved by using a formulation that does not employ viruses or cationic liposomes, but instead uses endogenous receptor-mediated transport pathways at the BBB.
[Clostridium difficile-associated diarrhea treated with homologous feces]. (1998)

The incidence of Clostridium difficile-associated diarrhoea has increased during the last few years. Treatment with vankomycin or metronidazol is usually effective, but relapses are not uncommon. Some good results have been reported with faecal enemas, but it is a controversal form of treatment. 18 patients with C. difficile-associated diarrhoea were given homologous faeces from one healthy donor. In 17 patients faeces was instillated via a coloscope and in one patient via a gastrostoma. C. difficile toxin was detected in all patients. Three patients with severe colitis did not respond to the treatment. The remaining patients were clinically cured, and no relapses were observed. Treatment of C. difficile-associated diarrhoea with faeces appears to be an alternative in moderate cases. In our limited number of patients we observed a poor correlation between the clinical picture, the endoscopic findings and the histological findings in colon biopsies. The ethical aspects of treatment with faeces will continue to be subject to discussion.
Structure and Functions of the Bacterial Microbiota of Plants (2013)

Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype-dependent fine-tuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth-promoting and plant health-promoting bacteria.
Polypyrrole-Entrapped Quinohemoprotein Alcohol Dehydrogenase. Evidence for Direct Electron Transfer via Conducting-Polymer Chains (1999)

It is reported for the first time that direct electron-transfer processes between a polypyrrole (PPY) entrapped quinohemoprotein alcohol dehydrogenase from Gluconobacter sp. 33 (QH-ADH) and a platinum electrode take place via the conducting-polymer network. The cooperative action of the enzyme-integrated prosthetic groups--pyrroloquinoline-quinone and hemes--is assumed to allow this electron-transfer pathway from the enzyme's active site to the conducting-polymer backbone. A hypothetical model of the electron transfer is proposed which is supported by the influence of various parameters, such as, e.g., ionic strength and nature of the buffer salts. This unusual electron-transfer pathway leads to an accentuated increase of the K M app value (102 mM) and hence to a significantly increased linear detection range of an ethanol sensor based on this enzyme.
The phenotypically variable surface protein of Trichomonas vaginalis has a single, tandemly repeated immunodominant epitope (1991)

Trichomonas vaginalis is a sexually transmitted protozoan parasite that undergoes phenotypic variation for numerous surface proteins. A monoclonal antibody (MAb) was used to isolate an approximately 400-bp cDNA encoding a fragment of an important phenotypically varying immunogen of T. vaginalis (Mr = 270 kDa; P270). The MAb completely inhibited the binding of P270 by antibody in sera of patients and by antibody in monospecific antiserum obtained toward purified P270, indicating that P270 contained only one immunodominant epitope. Hydrophilicity plot analysis of the deduced amino acid sequence of the recombinant protein predicted the hexapeptide sequence DREGRD as the antigenic determinant of P270. Synthetic peptides synthesized to this region demonstrated that the amino acid sequence DREGRD is important for antibody binding. Seven adjacent amino acids also contributed substantially to maximal recognition of the epitope by the MAb. A single transcript of approximately 9.5 kb, a size compatible with the reported Mr of the immunogen, hybridized to the cDNA in Northern blots of total RNA from T. vaginalis. DNA sequence and Southern blot analysis determined the epitope to be encoded by a 339-bp unit, which was found to be tandemly repeated at least 12 times within the single-copy gene. This 12-mer unit would only constitute approximately 50% of the protein, yet it is responsible for all of the serum antibody to the immunogen produced by animals and humans. The epitope sequence was found in all fresh and long-term-grown organisms examined to date, demonstrating the stability and conservation of this gene.
Preparation and properties of chiral titanocene and zirconocene dichloride complexes of a chiral ligand (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and properties of chiral titanocene and zirconocene dichloride complexes of a chiral ligandArnold L. Rheingold, N. P. Robinson, John Whelan, and B. BosnichCite this: Organometallics 1992, 11, 5, 1869–1876Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/om00041a021https://doi.org/10.1021/om00041a021research-articleACS PublicationsRequest reuse permissionsArticle Views564Altmetric-Citations53LEARN 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
Constitutive and antibody-induced internalization of prostate-specific membrane antigen. (1998)

Prostate-specific membrane antigen (PSMA) is a cell surface glycoprotein expressed predominantly by prostate cancer cells. We have characterized four monoclonal antibodies that bind to the extracellular domain of PSMA (Liu et al., Cancer Res., 57: 3629-3634, 1997). Here we report that viable LNCaP cells internalize these antibodies. Laser scanning confocal microscopy reveals that the internalized antibodies accumulate in endosomes, and immunoelectron microscopy reveals that endocytosis of the PSMA-antibody complex occurs via clathrin-coated pits. In addition, a quantitative cell surface biotinylation assay demonstrates that PSMA is constitutively endocytosed in LNCaP cells and that anti-PSMA antibodies increase the rate of internalization of PSMA. These studies suggest that PSMA might function as a receptor mediating the internalization of a putative ligand. The availability of prostate-specific internalizing antibodies should aid the development of novel therapeutic methods to target the delivery of toxins, drugs, or short-range isotopes specifically to the interior of prostate cancer cells.