gebhart/patrepeval huggingface dataset:
High Performance Liquid Chromatography of Small and Large Molecules with Nonporous Silica-Based Stationary Phases (1997)

Abstract Nonporous monodispersed, microspherical silica particles, having mean particle diameters of 0.8 and 1.1 μm, were surfacel-modified with octadecyl or triphenyl functions as well as with lectin proteins for high performance liquid chromatography of small and large molecules. “Monomeric” or “polymeric” octadecyl-silica (C18-silica) bonded phases were formed, depending on the silane compounds used. Monomeric C18-silica stationary phases yielded high resolution in the separation of 2-pyridylamino derivatives of xyloglucan oligosaccharides and proteins. The effect of particle size of the support on resolution was also examined. For comparative study, the chromatographic behavior of large molecular weight proteins on a triphenyl-silica stationary phase was also conducted. Polymeric C18-silica stationary phases yielded higher phase ratios and better support surface coverage which proved useful in the separation of small hydrophilic species such as derivatized chitooligosaccharides of lower degree of polymerization (d.p.). The slopes of the linear dependence of logarithmic retention factor on volume percent of organic modifier were determined for the monomelic and polymeric C18-silica stationary phases with low molecular weight aromatic compounds. Lectin affinity stationary phases with lens culinaris agglutinin and wheat germ agglutinin covalently bound to nonporous silica support were examined for the applications of nonporous stationary phases in lectin affinity chromatography of glycoproteins. In all cases, rapid separations in the time scales of seconds and minutes could be obtained because of the absence of mass transfer resistance in the nonporous stationary phase matrices.
Primary results from a randomized (1:1), open-label phase II study of talimogene laherparepvec (T) and ipilimumab (I) vs I alone in unresected stage IIIB- IV melanoma. (2017)

9509 Background: T is a HSV-1-based oncolytic virus designed to selectively replicate in tumors and produce GM-CSF to stimulate antitumor immune responses. I is an anti-CTLA-4 Ab that blocks inhibition of activated T cells. This is the first randomized study to evaluate the addition of an oncolytic virus to a checkpoint inhibitor. Methods: The 1 o endpoint was ORR by immune-related response criteria. Key 2 o endpoints: duration of response, disease control rate (DCR), PFS, OS, and safety. Prior treatment was allowed but not required. Pts had unresected stage IIIB-IV melanoma with measurable/injectable tumor(s) and no evidence of immunosuppression. T was given at approved dosing until no injectable tumors, disease progression (PD), or intolerance. I was started at w6 in T+I and at w1 in I at 3 mg/kg IV q3w x 4. Primary analysis occurred 6 m after last pt enrolled. Results: 198 pts were randomized: 98 T+I; 100 I. Characteristics were similar: 54% stage IIIB-IVM1a, 46% IVM1b/c. Median follow up time was 68 w (T+I) and 58 w (I). ORR was 38.8% (T+I) and 18.0% I, P = 0.002, Odds ratio (OR) 2.9. 89% T+I and 83% I pts remain in response. Unconfirmed visceral lesion response was 35.5% T+I vs 13.6% I. OS is immature. Of 190 pts (safety set: 95 T+I, 95 I), most common adverse events (AEs) for T+I, I (%) were fatigue (59, 42), chills (53, 3), and diarrhea (42, 35). 28% T+I and 18% I pts had gr ≥3 tx-related AE. There were 3 deaths (all unrelated) in T+I: 1 myocardial infarction and 2 PD. Conclusions: The study met the 1 o endpoint. ORR was significantly higher for T+I vs I; responses were not limited to injected lesions. Toxicity of T+I combination was tolerable with no unexpected AEs. Clinical trial information: NCT01740297. [Table: see text]
Monoclonal antibody reactive with the sialyl-sugar residue of a high molecular weight glycoprotein in sera of cancer patients. (1984)

A monoclonal antibody, ST-4-39, was obtained by means of a unique immunization procedure using a gastric cancer xenograft as an immunogen. ST-4-39 reacted immunohistochemically with various cancers and a limited number of normal tissues. The antigen reactive with ST-4-39 was detected in sera of cancer patients, and possessed a molecular weight of greater than or equal to 1 X 10(6). The antigenic determinant was a sialyl-sugar residue different from sialyl-Lewis a recognized by NS 19-9.
Molecular Imprinting in Crosslinked Polymers - The Role of the Binding Sites (1996)

Abstract Highly selective microcavities are formed in crosslinked polymers by polymerizing around a molecule that acts as a template and subsequently removing this template. The function of the binding sites within the cavities is discussed more in detail.
Synchrotron SAXS studies of segmented polyurethanes (2007)

It has been reported by us, for the first time, that segmented polyurethanes (SPUs) based on 4,4′-diphenylmethane diisocyanate (MDI) and 1,4-butanediol (BD) as the hard segment could form spherulite structures upon melt-quenching to an annealing temperature (T A) above 120°C. Synchrotron small-angle x-ray scattering (SAXS) experiments were performed to investigate the microphase separated structures corresponding to the spherulite formation. With increasing hard-segment content, both the integrated scattered intensity (Q) and the interdomain spacing (d) increased first and then decreased when the hard segment was above 50%, possibly due to phase inversion. With increasing T A, the Q values increased first, reached a maximum at ∼107°C, and then decreased with further increase in T A; the d values showed a monotonic increase. The kinetics of phase separation was investigated after the samples were quenched from the melt to 140°C. Interdomain spacing remained unchanged throughout the whole process. The results indicated that the hard-segment mobility and the system viscosity were the two key factors controlling the phase structure.
Single-Cell DNA Barcoding Using Sequences from the Small Subunit rRNA and Internal Transcribed Spacer Region Identifies New Species of Trichonympha and Trichomitopsis from the Hindgut of the Termite Zootermopsis angusticollis (2013)

To aid in their digestion of wood, lower termites are known to harbour a diverse community of prokaryotes as well as parabasalid and oxymonad protist symbionts. One of the best-studied lower termite gut communities is that of Zootermopsis angusticollis which has been known for almost 100 years to possess 3 species of Trichonympha (T. campanula, T. collaris, and T. sphaerica), 1 species of Trichomitopsis (T. termopsidis), as well as smaller flagellates. We have re-assessed this community by sequencing the small subunit (SSU) rRNA gene and the internal transcribed spacer (ITS) region from a large number of single Trichonympha and Trichomitopsis cells for which morphology was also documented. Based on phylogenetic clustering and sequence divergence, we identify 3 new species: Trichonympha postcylindrica, Trichomitopsis minor, and Trichomitopsis parvus spp. nov. Once identified by sequencing, the morphology of the isolated cells for all 3 new species was re-examined and found to be distinct from the previously described species: Trichonympha postcylindrica can be morphologically distinguished from the other Trichonympha species by an extension on its posterior end, whereas Trichomitopsis minor and T. parvus are smaller than T. termopsidis but similar in size to each other and cannot be distinguished based on morphology using light microscopy. Given that Z. angusticollis has one of the best characterized hindgut communities, the near doubling of the number of the largest and most easily identifiable symbiont species suggests that the diversity of hindgut symbionts is substantially underestimated in other termites as well. Accurate descriptions of the diversity of these microbial communities are essential for understanding hindgut ecology and disentangling the interactions among the symbionts, and molecular barcoding should be a priority for these systems.
[Searching for retroviral sequences related to human breast cancer]. (1997)

The participation of viruses in mammary carcinogenesis has been largely studied in animals. A model similar to the mouse mammary tumor virus (MMTV) was previously proposed. Several lines of research supported the participation of MMTV in human breast cancer, but these evidences were contradicted when further research was performed. One major issue was the presence of human endogenous retroviral sequences that confounded results reporting MMTV-like sequences in human breast cancer. To overcome this problem we selected a 660 bp sequence of the MMTV env gene with low homology to endogenous sequences and search for a sequence to it using the polymerase chain reaction (PCR). The sequence was found in 38% of the human breast cancers and in 2% of the normal breasts studied. The sequence was not present in tumors from other organs. It was 90-98% homologous to MMTV and only 18% to human endogenous retrovirus (HERV) K-10. It was also detected in some of the positive tumors by Southern blot hybridization using one of the cloned 660 bp as a probe. Using reverse transcriptase PCR, it was possible to demonstrate that the 660 bp sequence is expressed in the majority of the tumors. Also, preliminary experiments revealed that sequences related to the LTR and gag genes of MMTV were present in the DNA of breast tumors. The origin of the MMTV-like sequences in tumor DNA could be the result of integrated MMTV-like sequences derived from a human mammary virus or may represent unknown endogenous sequences that can only be detected in breast tumors.
One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections (2016)

Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis.
Heterogeneity of Heparan Sulfates in Human Lung (2003)

Heparan sulfates (HS), a class of glycosaminoglycans, are long linear complex polysaccharides covalently attached to a protein core. The HS molecules are made up of repeating disaccharides onto which modification patterns are superimposed. This results in a large structural heterogeneity and forms the basis of specific interactions of HS toward a vast array of proteins, including growth factors and proteases. To study HS heterogeneity in the lung, we used phage display technology to select seven antibodies against human lung HS. Antibodies reacted with HS/heparin, but not with other glycosaminoglycans or polyanions. Sulfate groups were essential for antibody binding. The amino acid sequence of the antibodies was established, the complementarity determining region 3 of the heavy chain containing basic amino acids. The antibodies defined HS epitopes with a characteristic tissue distribution. Antibody EV3A1 primarily stained macrophages. Other antibodies primarily stained basement membranes, but with different preference toward type of basement membrane. Antibody EV3C3 was the only antibody which clearly reacted with bronchiolar epithelial cells. In human lung parenchyma, basic fibroblast growth factor and vascular endothelial growth factor were largely bound by HS. Some antibodies blocked a basic fibroblast growth factor-binding site of HS, and one antibody blocked a vascular endothelial growth factor-binding site of heparin. Taken together, these data suggest a specific role for HS epitopes in human lung. The antibodies obtained may be valuable tools to study HS in pulmonary diseases.
Genetic and proteomic analysis of the role of <i>luxS</i> in the enteric phytopathogen, <i>Erwinia carotovora</i> (2005)

SUMMARY Erwinia carotovora is a Gram-negative phytopathogen that is an important cause of soft rot disease, including stem and tuber rot in potatoes. Quorum sensing is the process by which bacteria detect their population density and regulate gene expression accordingly. Quorum sensing, an important example of intercellular communication, involves the production and detection of chemical signal molecules. The enzyme LuxS is responsible for the production of Autoinducer-2 (AI-2), a molecule that has been implicated in quorum sensing in many bacterial species. In this study, the role of luxS in Erwinia carotovora ssp. carotovora strain ATTn10 and Erwinia carotovora ssp. atroseptica SCRI1043 has been examined. Both strains have been shown to produce luxS-dependent extracellular AI-2 activity and the phenotypes of defined luxS mutants in these strains have been characterized. Inactivation of luxS in Er. carotovora was found to have a strain-dependent impact on the intracellular proteome (using two-dimensional difference in gel electrophoresis), secreted proteins, motility and virulence in planta. No link was detected with the N-acyl-l-homoserine lactone quorum sensing system in these organisms. Although the molecular mechanism(s) of luxS regulation in Erwinia remain to be determined, this is the first report of any luxS-dependent phenotypes in a plant pathogen.
1-Pyrenyldiazomethane as a fluorescent labeling reagent for liquid chromatographic determination of carboxylic acids (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1-Pyrenyldiazomethane as a fluorescent labeling reagent for liquid chromatographic determination of carboxylic acidsNoriyuki. Nimura, Toshio. Kinoshita, Tsuguchika. Yoshida, Atsuhiro. Uetake, and Chie. NakaiCite this: Anal. Chem. 1988, 60, 19, 2067–2070Publication Date (Print):October 1, 1988Publication History Published online1 May 2002Published inissue 1 October 1988https://pubs.acs.org/doi/10.1021/ac00170a017https://doi.org/10.1021/ac00170a017research-articleACS PublicationsRequest reuse permissionsArticle Views1445Altmetric-Citations98LEARN 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 Get e-Alerts
AN INVESTIGATION INTO THE PRIOR ECONOMIC EXPERIENCE OF PRIMARY EDUCATION STUDENTS (1992)

Abstract This paper summarises the findings of an analysis of primary education students' backgrounds and economic experiences, relating this to their economic and industrial understanding. The research was conducted in the 1990‐91 period by the Primary Schools and Industry Centre of the Polytechnic of North London, under the sponsorship and aegis of E ATE. The project team consisted of the present writer with Merryn Hutchings (PNL) and John Ahier (Homerton College). The full research report is published by EATE as The Economic and Industrial background, understanding and attitudes of Student Primary Teachers: EATE Research Report No. 1.
Creation and Translation Virtual 3D Architectural Environments (2021)

In this paper, we describe the research we undertake to investigate the perception and comprehension of spatial volumes within immersive, non-immersive virtual environments and physical models and their translation to a tangible representation. We set up two related design experiments to investigate the outcome of creation, interpretation and communication of architectural design. One, being the analysis of a cubic structure, based on three-dimensional (3D) interlocking volumes and spaces; and the other, being the design of a 3D-maze together with text -based communication. Collaboratively participants create, assess and analyse spatial relationships of volumes and spaces of a 3D maze structure or construct models of these spaces. The objective of our study is to identify how designers perceive space in Virtual Environments (VE) and communicate design ideas by using VE versa conventional methods of two-dimensional depictions such as paper and pen or 3D representations such as physical models. We investigate issues of quality, accuracy, understanding, communicating and rebuilding of designed or experienced architectural compositions.
Beneficial Effect of Muscarinic-2 Antagonist on Dilated Cardiomyopathy Induced by Autoimmune Mechanism against Muscarinic-2 Receptor (2001)

We have previously shown that a peptide corresponding to the sequence of the second extracellular loop of the human muscarinic-2 (M2) receptor (M2-peptide) was able to induce an autoimmune cardiomyopathy in rabbits. In this study, we investigated the effect of M2-antagonist (otenzepad) on M2-peptide-induced cardiomyopathy in rabbits. New Zealand White rabbits were divided into four groups: 1) control group, saline injection; 2) M2-peptide group, M2-peptide injection; 3) M2-antagonist group, otenzepad (30 mg/day) orally and saline injection; and (4) M2-antagonist + M2-peptide group, otenzepad (30 mg/day) orally and M2-peptide injection. The study duration was 1 year. Saline or peptide was injected once a month. All rabbits in both the M2-peptide group and the M2-antagonist + M2-peptide group had high titers of anti-M2-autoantibodies in their sera. Rabbits in the M2-peptide group showed an increase in heart weight, wall thinning and dilatation of the right ventricle. On the contrary, rabbits in the M2-antagonist + M2-peptide group had normal heart weight and shape. All rabbits in the M2-peptide group showed multifocal degeneration and necrosis of myocardial cells with moderate infiltration of inflammatory cells, while four rabbits in the M2-antagonist + M2-peptide group showed slight infiltration of inflammatory cells with normal myocardial cells and interstitium, and another three showed no histological changes in the hearts. In conclusion, M2-antagonist protects the myocardium from injury induced by autoimmune mechanism against M2-muscarinic receptor.
Modeling the energy cost of applications on portable wireless devices (2008)

Extending the battery life of portable wireless devices has been in the focus of researchers for close to a decade. Several energy management techniques have been investigated at different levels of system design -- starting from silicon at the bottom to application design at the top, with communication protocols and operating system in between. In this paper, we present a model to estimate the energy cost of an application running on a portable wireless device. To develop the cost model, we partition a wireless device into two components, namely, computation and communication. Each component is modeled by a state-transition diagram. Two attributes are associated with each state: an average power cost and a state residence time. The cost of each state of the state-transition diagrams is validated by actual measurements. For a constant voltage supply, the average power cost of a state is denoted by the average current drawn by the component. The state residence times are estimated from the behavior of applications. The cost model has been validated by performing actual measurement of energy cost. We find that the estimated cost and the actual energy cost are within 5-10% of each other. This study will help us in improving the design of energy efficient software for portable devices. Moreover, the energy consumption breakdown into components will be an essential guide for future research in energy management of hardware and software systems.
Distributed online learning of the shortest path under unknown random edge weights (2013)

We consider the distributed shortest path problem in an undirected graph where the edge weights are random variables with unknown distributions. The objective is to design a distributed online learning algorithm to find the shortest path from a source node to a destination node where each node only knows its neighbors but not the entire network topology. The performance of the learning algorithms is measured by regret defined as the additional cost incurred over a time horizon of length T when compared to a centralized shortest path algorithm carried out under known edge weight distributions. We propose a distributed learning algorithm that achieves a regret logarithmic with the number of packets and polynomial with the network size. The same order with time and network size holds for the message complexity of the proposed algorithm. This result finds applications in cognitive radio and ad hoc networks under unknown and dynamic communication environments.
Commonsense-based interfaces (2000)

article Commonsense-based interfaces Share on Author: Marvin Minsky Massachusetts Institute of Technology, Cambridge Massachusetts Institute of Technology, CambridgeView Profile Authors Info & Claims Communications of the ACMVolume 43Issue 8Aug. 2000 pp 66–73https://doi.org/10.1145/345124.345145Online:01 August 2000Publication History 58citation1,923DownloadsMetricsTotal Citations58Total Downloads1,923Last 12 Months101Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access