gebhart/patrepeval huggingface dataset:
An analytical workflow for investigating cytokine profiles (2007)

Understanding cytokine profiles of disease states has provided researchers with great insight into immunologic signaling associated with disease onset and progression, affording opportunities for advancement in diagnostics and therapeutic intervention. Multiparameter flow cytometric assays support identification of specific cytokine secreting subpopulations. Bead-based assays provide simultaneous measurement for the production of ever-growing numbers of cytokines. These technologies demand appropriate analytical techniques to extract relevant information efficiently. We illustrate the power of an analytical workflow to reveal significant alterations in T-cell cytokine expression patterns in type 1 diabetes (T1D) and breast cancer. This workflow consists of population-level analysis, followed by donor-level analysis, data transformation such as stratification or normalization, and a return to population-level analysis. In the T1D study, T-cell cytokine production was measured with a cytokine bead array. In the breast cancer study, intracellular cytokine staining measured T cell responses to stimulation with a variety of antigens. Summary statistics from each study were loaded into a relational database, together with associated experimental metadata and clinical parameters. Visual and statistical results were generated with custom Java software. In the T1D study, donor-level analysis led to the stratification of donors based on unstimulated cytokine expression. The resulting cohorts showed statistically significant differences in poststimulation production of IL-10, IL-1 beta, IL-8, and TNF beta. In the breast cancer study, the differing magnitude of cytokine responses required data normalization to support statistical comparisons. Once normalized, data showed a statistically significant decrease in the expression of IFN gamma on CD4+ and CD8+ T cells when stimulated with tumor-associated antigens (TAAs) when compared with an infectious disease antigen stimulus, and a statistically significant increase in expression of IL-2 on CD8+ T cells. In conclusion, the analytical workflow described herein yielded statistically supported and biologically relevant findings that were otherwise unapparent.
Persulfoxide and thiadioxirane intermediates in the reaction of sulfides and singlet oxygen (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPersulfoxide and thiadioxirane intermediates in the reaction of sulfides and singlet oxygenYasumasa Watanabe, Nobuo Kuriki, Katsuya Ishiguro, and Yasuhiko SawakiCite this: J. Am. Chem. Soc. 1991, 113, 7, 2677–2682Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/ja00007a048https://doi.org/10.1021/ja00007a048research-articleACS PublicationsRequest reuse permissionsArticle Views236Altmetric-Citations51LEARN 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
Nanostructured polymers for photonics (2008)

We review recent progress in the development of polymer nanostructured materials with periodic structures and compositions having applications in photonics and optical data storage. This review provides a brief description of the microfabrication and self-assembly methods used for the production of polymer materials with periodic structures, and highlights the properties and applications of photonic materials derived from block copolymers, colloid crystals, and microfabricated polymers. We conclude with a summary of current and future research efforts and opportunities in the development of polymer materials for photonic applications.
Sequential shape-and-solder-directed self-assembly of functional microsystems (2004)

We demonstrate the fabrication of packaged microsystems that contain active semiconductor devices and passive components by using a directed self-assembly technique. The directed self-assembly is accomplished by combining geometrical shape recognition with site-specific binding involving liquid solder. Microfabricated components with matching complementary shapes, circuits, and liquid solder-coated areas were suspended in ethylene glycol and agitated by using a turbulent liquid flow to initiate the self-assembly. Microsystems were obtained by sequentially adding components of different types. Six hundred AlGaInP/GaAs light-emitting diode segments with a chip size of 200 microm were assembled onto device carriers with a yield of 100% in 2 min. Packaged light-emitting diodes formed with yields exceeding 97% as a result of two self-assembly steps in 4 min. This self-assembly procedure, based on geometrical shape recognition and subsequent binding to form mechanical and electrical connections, provides a high distinguishing power between different components and a route to nonrobotic parallel assembly of electrically functional hybrid microsystems in three dimensions.
Treatment for Abdominal Aortic Graft Infection: Irrigation with Electrolyzed Strong Aqueous Acid, In-situ Grafting, and Omentoplasty (2000)

We report on successful surgical treatment of consecutive three patients with infection of an abdominal aortic graft, Therapy involved a combination of removal of the infected graft, elaborate debridement, irrigation with electrolyzed strongly acidic aqueous solution (ESAAS), in-situ regrafting, and omentoplasty. The use of ESAAS is discussed.
High Efficiency Electroporation of Human Umbilical Cord Blood CD34 + Hematopoietic Precursor Cells (2001)

Human umbilical cord blood provides an alternative source of hematopoietic cells for purposes of transplantation or ex vivo genetic modification. The objective of this study was to evaluate electroporation as a means to introduce foreign genes into human cord blood CD34+ cells and evaluate gene expression in CD34+/CD38(dim) and committed myeloid progenitors (CD33+, CD11b+). CD34+ cells were cultured in X-VIVO 10 supplemented with thrombopoietin, stem cell factor, and Flt-3 ligand. Electroporation efficiency and cell viability measured by flow cytometry using enhanced green fluorescent protein (EGFP) as a reporter indicated 31% +/- 2% EGFP+ /CD34+ efficiency and 77% +/- 3% viability as determined 48 hours post-electroporation. The addition of allogeneic cord blood plasma increased the efficiency to 44% +/- 5% with no effect on viability. Of the total CD34+ cells 48 hours post-electroporation, 20% were CD38(dim)/EGFP+. CD34+ cells exposed to interleukin-3, GM-CSF and G-CSF for an additional 11 days differentiated into CD33+ and CD11b+ cells, and 9% +/- 3% and 8% +/- 7% were expressing the reporter gene, respectively. We show that electroporation can be used to introduce foreign genes into early hematopoietic stem cells (CD34+/CD38(dim)), and that the introduced gene is functionally expressed following expansion into committed myeloid progenitors (CD33+, CD11b+) in response to corresponding cytokines. Further investigation is needed to determine the transgene expression in functional terminal cells derived from the genetically modified CD34+ cells, such as T cells and dendritic cells.
Specific accumulation of tumor-derived adhesion factor in tumor blood vessels and in capillary tube-like structures of cultured vascular endothelial cells. (1996)

Tumor-derived adhesion factor (TAF) was previously identified as a cell adhesion molecule secreted by human bladder carcinoma cell line EJ-1. To elucidate the physiological function of TAF, we examined its distribution in human normal and tumor tissues. Immunochemical staining with an anti-TAF monoclonal antibody showed that TAF was specifically accumulated in small blood vessels and capillaries within and adjacent to tumor nests, but not in those in normal tissues. Tumor blood vessel-specific staining of TAF was observed in various human cancers, such as esophagus, brain, lung, and stomach cancers. Double immunofluorescent staining showed apparent colocalization of TAF and type IV collagen in the vascular basement membrane. In vitro experiments demonstrated that TAF preferentially bound to type IV collagen among various extracellular matrix components tested. In cell culture experiments, TAF promoted adhesion of human umbilical vein endothelial cells to type IV collagen substrate and induced their morphological change. Furthermore, when the endothelial cells were induced to form capillary tube-like structures by type I collagen, TAF and type IV collagen were exclusively detected on the tubular structures. The capillary tube formation in vitro was prevented by heparin, which inhibited the binding of TAF to the endothelial cells. These results strongly suggest that TAF contributes to the organization of new capillary vessels in tumor tissues by modulating the interaction of endothelial cells with type IV collagen.
High-resolution whole genome tiling path array CGH analysis of CD34+ cells from patients with low-risk myelodysplastic syndromes reveals cryptic copy number alterations and predicts overall and leukemia-free survival (2008)

Myelodysplastic syndromes (MDSs) pose an important diagnostic and treatment challenge because of the genetic heterogeneity and poorly understood biology of the disease. To investigate initiating genomic alterations and the potential prognostic significance of cryptic genomic changes in low-risk MDS, we performed whole genome tiling path array comparative genomic hybridization (aCGH) on CD34(+) cells from 44 patients with an International Prognostic Scoring System score less than or equal to 1.0. Clonal copy number differences were detected in cells from 36 of 44 patients. In contrast, cells from only 16 of the 44 patients displayed karyotypic abnormalities. Although most patients had normal karyotype, aCGH identified 21 recurring copy number alterations. Examples of frequent cryptic alterations included gains at 11q24.2-qter, 17q11.2, and 17q12 and losses at 2q33.1-q33.2, 5q13.1-q13.2, and 10q21.3. Maintenance of genomic integrity defined as less than 3 Mb total disruption of the genome correlated with better overall survival (P = .002) and was less frequently associated with transformation to acute myeloid leukemia (P = .033). This study suggests a potential role for the use of aCGH in the clinical workup of MDS patients.
Localized surface plasmon resonance effects on the magneto-optical activity of continuous Au/Co/Au trilayers (2008)

We study how the magneto-optical activity in polar configuration of continuous Au/Co/Au trilayers is affected by the excitation of localized plasmon resonances of an array of Au nanodiscs fabricated on top of them over a dielectric SiO(2) spacer. We show that the effect of the nanodiscs array is twofold. First, it optimizes the absorption of light at specific photon energies corresponding to the localized surface plasmon excitation of the array, modifying the reflectivity of the system (we define this effect as the purely optical contribution). Second, upon localized plasmon resonance excitation, the electromagnetic field in the whole system is redistributed, and an enhanced magneto-optical activity occurs at those energies where the electromagnetic field in the magnetic layer is increased (this effect is identified as the purely magneto-optical contribution of the nanodiscs array).
Plasma HIV Viral Rebound following Protocol-Indicated Cessation of ART Commenced in Primary and Chronic HIV Infection (2012)

Stopping ART initiated in PHI and CHI was associated with viral rebound to levels conferring increased transmission risk, although the level of rebound was significantly lower and sustained in PHI compared to CHI.
Genetic analysis of the colicin V secretion pathway. (1995)

Colicin V (ColV) is peptide antibiotic secreted by Escherichia coli through a dedicated exporter composed of three proteins, CvaA, CvaB, and TolC. ColV secretion is independent of the E. coli general secretory pathway (Sec) but requires an N-terminal export signal specific for the CvaAB/TolC exporter. ColV secretion was characterized using genetic and biochemical methods. When the ColV N-terminal extension is replaced with the OmpA signal sequence, the Sec system can localize ColV to the periplasm. Periplasmic ColV is lethal to cells lacking the ColV immunity protein, Cvi. Based on this result, a genetic assay was designed to monitor for the presence of periplasmic ColV during normal CvaAB/TolC mediated secretion. Results indicate that low levels of ColV may be present in the periplasm during secretion. Precursor and mature ColV were also characterized from the wild-type system and in various exporter mutant backgrounds using immunoprecipitation. ColV processing is rapid in wild-type cells, and CvaA and CvaB are critical for processing to occur. In contrast, processing occurs normally, albeit more slowly, in a TolC mutant.
Destruction and Detection of Chemical Warfare Agents (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTDestruction and Detection of Chemical Warfare AgentsKibong Kim†, Olga G. Tsay†, David A. Atwood‡, and David G. Churchill*†View Author Information† Molecular Logic Gate Laboratory, Department of Chemistry, KAIST, Daejeon, 305-701, Republic of Korea‡ Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United StatesE-mail: [email protected]. Phone: +82-42-350-2845. Fax: +82-42-350-2810.Cite this: Chem. Rev. 2011, 111, 9, 5345–5403Publication Date (Web):June 13, 2011Publication History Received25 June 2010Published online13 June 2011Published inissue 14 September 2011https://pubs.acs.org/doi/10.1021/cr100193yhttps://doi.org/10.1021/cr100193yreview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views20187Altmetric-Citations782LEARN 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:Hydrolysis,Ions,Metals,Organophosphorus compounds,Peptides and proteins Get e-Alerts
The reverse two-hybrid system: a genetic scheme for selection against specific protein/protein interactions (1996)

The yeast two-hybrid system is a powerful experimental approach for the characterization of protein/ protein interactions. A unique strength of the yeast two-hybrid system is the provision for genetic selection techniques that enable the identification of specific protein/protein interactions. We now report the development of a modified yeast two-hybrid system which enables genetic selection against a specific protein/protein interaction. This reverse two-hybrid system utilizes a yeast strain which is resistant to cycloheximide due to the presence of a mutant cyh2 gene. This strain also contains the wild-type CYH2 allele under the transcriptional control of the Gal1 promoter. Expression of the wild-type Gal4 protein is sufficient to restore growth sensitivity to cycloheximide. Growth sensitivity towards cycloheximide is also restored by the coexpression of the avian c-Rel protein and its I kappa B alpha counterpart, p40, as Gal4 fusion proteins. Restoration of growth sensitivity towards cycloheximide requires the association of c-Rel and p40 at the Gal1 promoter and correlates with the ability of the c-Rel/p40 interaction to activate expression from the Gal1 promoter. A genetic selection scheme against specific protein/protein interactions may be a valuable tool for the analysis of protein/protein interactions.
Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals after mRNA vaccination (2021)

Novel mRNA vaccines for SARS-CoV-2 have been authorized for emergency use. Despite their efficacy in clinical trials, data on mRNA vaccine-induced immune responses are mostly limited to serological analyses. Here, we interrogated antibody and antigen-specific memory B cells over time in 33 SARS-CoV-2 naïve and 11 SARS-CoV-2 recovered subjects. SARS-CoV-2 naïve individuals required both vaccine doses for optimal increases in antibodies, particularly for neutralizing titers against the B.1.351 variant. Memory B cells specific for full-length spike protein and the spike receptor binding domain (RBD) were also efficiently primed by mRNA vaccination and detectable in all SARS-CoV-2 naive subjects after the second vaccine dose, though the memory B cell response declined slightly with age. In SARS-CoV-2 recovered individuals, antibody and memory B cell responses were significantly boosted after the first vaccine dose; however, there was no increase in circulating antibodies, neutralizing titers, or antigen-specific memory B cells after the second dose. This robust boosting after the first vaccine dose strongly correlated with levels of pre-existing memory B cells in recovered individuals, identifying a key role for memory B cells in mounting recall responses to SARS-CoV-2 antigens. Together, our data demonstrated robust serological and cellular priming by mRNA vaccines and revealed distinct responses based on prior SARS-CoV-2 exposure, whereby COVID-19 recovered subjects may only require a single vaccine dose to achieve peak antibody and memory B cell responses. These findings also highlight the utility of defining cellular responses in addition to serologies and may inform SARS-CoV-2 vaccine distribution in a resource-limited setting.
Blood lactate and ammonia in short-term anaerobic work following induced alkalosis. (1995)

This study was designed to investigate the effect of an induced metabolic alkalosis on a 300 m sprinting time in six elite 400 m runners. The subjects competed as pairs, on two separate occasions, in a standard racing format, three hours after ingestion of either an alkaline (sodium citrate, 0.5 g.kg-1 body weight) or a placebo solution (calcium carbonate, 0.5 g.kg-1 body weight). The results showed that following alkaline ingestion mean sprinting time was not improved. Peak blood lactate during recovery was higher after sodium citrate administration than after placebo (19.88 +/- 2.09 vs 18.82 +/- 1.84 mmol.l-1, p < 0.01). No difference was observed in peak blood ammonia between the alkaline and placebo treatments (187.0 +/- 37.0 vs 188.8 +/- 49.0 mumol.l-1). The absence of effects on performance confirms that when exercise of short duration (30 to 40 s) is used, alkaline agents have minor or no effects on performance. The altered relationship observed between blood lactate and ammonia under placebo and buffering loading conditions suggests that the regulation of lactate and ammonia metabolism is unrelated.
Connectionist temporal classification (2006)

Many real-world sequence learning tasks require the prediction of sequences of labels from noisy, unsegmented input data. In speech recognition, for example, an acoustic signal is transcribed into words or sub-word units. Recurrent neural networks (RNNs) are powerful sequence learners that would seem well suited to such tasks. However, because they require pre-segmented training data, and post-processing to transform their outputs into label sequences, their applicability has so far been limited. This paper presents a novel method for training RNNs to label unsegmented sequences directly, thereby solving both problems. An experiment on the TIMIT speech corpus demonstrates its advantages over both a baseline HMM and a hybrid HMM-RNN.
Activity model: (2000)

In order to accomplish the project's objective, it is important to understand the practices that are commonly used by the industry.This document presents an activity model that identifies the functions involved in the ship repair and conversion industry, and the information flows required to perform those functions.The model presented in this report has been developed primarily based on information gathered during visits to both ship repairs and conversion facilities of AMHC, in Mobile, Alabama, and Jacksonville, Florida.Although the model describes all types of repairs/conversions, it puts special emphasis on those processes associated with steel systems, pipe systems, and paint.The document also includes two appendices: a node tree that describes functional hierarchy, and a glossary that provides definitions of all terms, including activity names and data/objects, used in the activity model.The activity model presented in this document uses the IDEFO 3 methodology.In the IDEFO diagrams, activities/functions are represented by "boxes," data/objects, such as inputs, controls, outputs, and mechanisms (Icom), are represented by "arrows," tunneling is represented by a tunnel (a pair of parentheses, or sign "()") around the arrow's head or arrow's tail, and boxes and arrows are labeled.Tunneling an arrow implies that the arrow does not appear on a child or parent diagram.When a tunnel appears around the arrow's head, there is no corresponding Icom connected to the parent box.Similarly, when a tunnel appears on the arrow's tail, no corresponding Icom connected to the child box.IDEFO does not model the timing of activities, nor does the ordering of the activities by label-number imply time of precedence.