gebhart/patrepeval huggingface dataset:
Patient engagement in research on dementia: Perceptions from researchers in a multidisciplinary research consortium (2020)

Abstract Background Patient ‘engagement’ or ‘involvement’ in health research refers to including people with lived experience (i.e. individuals with personal experience of a health issue and their friends, family and caregivers) in the research process – not as study subjects, but as collaborators in planning, conducting and communicating research. Patient engagement is being advanced by researchers, funding organisations, advocacy groups and others on both moral and methodological grounds. Although patient engagement in research on dementia is not new, it is becoming more common. Still, there are unresolved questions of how to incorporate, evaluate and adapt engagement activities for different types of research. Method We are reporting results of a survey of researchers who are members of the Canadian Consortium on Neurodegeneration in Aging (CCNA), conducted to understand their perceptions of engaging people with lived experience of dementia in research. Result There were 84 responses (27% response rate). Respondents included biomedical (n=10; 12%), clinical (n=35; 42%), health services (n=27; 32%) and social/cultural/environmental/population health (n=12; 14%) researchers. Overall, almost all (n=78; 93%) agreed that people with lived experience of dementia can contribute meaningfully to the research process. Nearly two thirds of respondents (n=54; 64%) indicated their research already included engagement activities and the most frequently reported motivations were to increase the quality and relevance of the research and empower people who have lived experience of dementia. They reported engagement activities took place most often in the context of knowledge translation, priority setting and study recruitment. Of those who indicated no current engagement activities (n=30; 36%), most were interested in opportunities for engagement and, for those who were not interested, the most common reason reported was that it was not relevant to their area of research. Limitations to these results include the low response rate that likely introduced some selection bias; researchers with an interest in engagement may have been more likely to respond. Conclusion Many CCNA researchers working in the area of dementia are engaging people with lived experience in their research. These data will be used to describe how researcher knowledge, attitudes and activities differ according to type of research.
Chromatin architecture reorganization during stem cell differentiation (2015)

Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.
CD271 antigen defines a subset of multipotent stromal cells with immunosuppressive and lymphohematopoietic engraftment-promoting properties (2010)

In vitro studies demonstrated that CD271-mesenchymal stromal cells differentiate along adipogenic, osteogenic and chondrogenic lineages (trilineage potential), produce significantly higher levels of cytokines than plastic adherence-mesenchymal stromal cells, and significantly inhibit the proliferation of allogeneic T-lymphocytes in mixed lymphocyte reaction assays. Elevated levels of prostaglandin E(2), but not nitric monoxide, mediated the majority of this immunosuppressive effect. In vivo studies showed that CD271-mesenchymal stromal cells promoted significantly greater lymphoid engraftment than did plastic adherence-mesenchymal stromal cells when co-transplanted with CD133(+) hematopoietic stem cells at a ratio of 8:1 in immunodeficient NOD/SCID-IL2Rgamma(null) mice. They induced a 10.4-fold increase in the number of T cells, a 2.5-fold increase in the number of NK cells, and a 3.6-fold increase in the number of B cells, indicating a major qualitative difference between these two mesenchymal stromal cell populations. Conclusions Our results indicate that CD271 antigen provides a versatile marker for prospective isolation and expansion of multipotent mesenchymal stromal cells with immunosuppressive and lymphohematopoietic engraftment-promoting properties. The co-transplantation of such cells together with hematopoietic stem cells in patients with hematologic malignancies may prove valuable in the prevention of impaired/delayed T-cell recovery and graft-versus-host disease.
Semantic Annotation of Experimental Methods in Analytical Chemistry (2022)

A major obstacle for reusing and integrating existing data is finding the data that is most relevant in a given context. The primary metadata resource is the scientific literature describing the experiments that produced the data. To stimulate the development of natural language processing methods for extracting this information from articles, we have manually annotated 100 recent open access publications in Analytical Chemistry as semantic graphs. We focused on articles mentioning mass spectrometry in their experimental sections, as we are particularly interested in the topic, which is also within the domain of several ontologies and controlled vocabularies. The resulting gold standard dataset is publicly available and directly applicable to validating automated methods for retrieving this metadata from the literature. In the process, we also made a number of observations on the structure and description of experiments and open access publication in this journal.
Organ Specific Storage of Dietary Pyrrolizidine Alkaloids in the Arctiid Moth Creatonotos transiens (1990)

Abstract Larvae of the arctiid moth Creatonotos transiens obtained each 5 mg of heliotrine, a pyrrolizidine alkaloid, via an artificial diet. 7 S-H eliotrine is converted into its enantiomer, 7 R 1 -heliotrine, and some minor metabolites, such as callimorphine. 7 S- and 7 R-heliotrine are present in the insect predominantly (more than 97%) as their N-oxides. The distribution of heliotrine in the organs and tissues of larvae, prepupae, pupae and imagines was analyzed by capillary gas-liquid chromatography. A large proportion of the alkaloid is stored in the integument of all developmental stages, where it probably serves as a chemical defence compound against predators. Female imagines had transferred substantial amounts of heliotrine to their ovaries and subsequently to their eggs; males partly directed it to their pheromone biosynthesis.
Support cluster machine (2007)

For large-scale classification problems, the training samples can be clustered beforehand as a downsampling pre-process, and then only the obtained clusters are used for training. Motivated by such assumption, we proposed a classification algorithm, Support Cluster Machine (SCM), within the learning framework introduced by Vapnik. For the SCM, a compatible kernel is adopted such that a similarity measure can be handled not only between clusters in the training phase but also between a cluster and a vector in the testing phase. We also proved that the SCM is a general extension of the SVM with the RBF kernel. The experimental results confirm that the SCM is very effective for largescale classification problems due to significantly reduced computational costs for both training and testing and comparable classification accuracies. As a by-product, it provides a promising approach to dealing with privacy-preserving data mining problems.
Evaluating the Generalizability of a Large Streamlined Cardiovascular Trial (2014)

http://www.clinicaltrials.gov. Unique identifier: NCT00977938.
Emergent Graphs with PCA-features for Improved Face Recognition (2006)

Built on the principles of “Learning from Nature” and “Self‐organization” Elastic Bunch Graph Matching for face recognition is a defining example for Organic Computing methodology. Here, we follow these principles further to advance the method in two respects. First, the requirement for manual annotation of landmarks is reduced to one single face, from which a self‐organizing selection process gradually builds up the bunches by adding the most similar face to the bunch graph and then recalculating the matching. Second, the resulting bunches are replaced by the principal components of the nodes of all persons in the database. The similarity function is restricted to a suitable subset of these components. The additional self‐organizing processes lead to improved precision of landmark localization and recognition rates. Altogether, an improved data structure for face storage has emerged from the simple presentation of examples in a minimally supervised way.
Runtime Design Space Exploration and Mapping of DCNNs for the Ultra-Low-Power Orlando SoC (2020)

Recent trends in deep convolutional neural networks (DCNNs) impose hardware accelerators as a viable solution for computer vision and speech recognition. The Orlando SoC architecture from STMicroelectronics targets exactly this class of problems by integrating hardware-accelerated convolutional blocks together with DSPs and on-chip memory resources to enable energy-efficient designs of DCNNs. The main advantage of the Orlando platform is to have runtime configurable convolutional accelerators that can adapt to different DCNN workloads. This opens new challenges for mapping the computation to the accelerators and for managing the on-chip resources efficiently. In this work, we propose a runtime design space exploration and mapping methodology for runtime resource management in terms of on-chip memory, convolutional accelerators, and external bandwidth. Experimental results are reported in terms of power/performance scalability, Pareto analysis, mapping adaptivity, and accelerator utilization for the Orlando architecture mapping the VGG-16, Tiny-Yolo(v2), and MobileNet topologies.
ChemInform Abstract: Oxidation of Primary Amines to Ketones. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Abstract C237: Merkel cell polyomavirus infection-related Merkel cell carcinomas have intratumoral lymphocyte infiltrates and favorable survival. (2011)

Abstract Introduction: Merkel cell carcinoma (MCC) is rare and often aggressive skin cancer that manifests mainly in elderly white people. The majority of MCCs contain Merkel cell polyomavirus (MCPyV) DNA. Patients with MCPyV-positive MCC have favorable survival as compared to those with MCPyV-negative tumor. The reasons for this remain speculative, but host immune defence might influence outcome of patients with MCPyV infection. Material and Methods: Tumor infiltrating T-lymphocytes (CD3+ cells) and macrophages (CD68+ cells) were stained using immunohistochemistry from 116 MCCs. The numbers of stained cells were counted at 400× magnification of the microscope. Presence of MCPyV infection was assessed by detecting MCPyV DNA using quantitative PCR and the viral large T antigen using immunohistochemistry. The associations between the tumor immune cell counts, presence of MCPyV DNA, clinicopatholocial factors and patient survival were examined using the Mann-Whitney test and the Kaplan-Meyer survival analysis. Results: MCPyV-positive tumors contained more CD3+ and CD68+ cells as compared to MCPyV-negative cancers (5.3 vs. 3.3 cells/high-power field [HPF], p=0.014; and 5.3 vs. 4.0 cells/HPF, p=0.028, respectively). Similar results were obtained when presence of MCPyV infection was efined by expression of the viral large T-antigen (5.9 vs. 2.7 cells/HPF, p&amp;lt;0.001; and 5.6 vs. 3.9 cells/HPF, p=0.003, respectively). Patients with regional nodal metastases had fewer CD3+ cells in the primary tumor as compared to those without metastases (2.3 vs. 5.3 cells/HPF, p=0.006). Patients who had MCC with a higher than the median number of CD3+ cells had better MCC-specific survival (55.2% vs. 82.1%, log-rank test p=0.003) and overall survival (22.4% vs. 50.0%, p=0.002) as compared to those with a smaller than the median tumor CD3+ cell count. Tumor CD3+ count was an independent prognostic factor for overall survival in a Cox multivariable analysis that included the presence of regional nodal etastases, gender and MCPyV large T-antigen expression as covariates (HR=0.55, 95% CI, 0.35 to 0.88, p=0.012). Conclusions: MCCs with evidence of MCPyV infection harbor high numbers of tumor infiltrating T-lymphocytes. A high number of CD3+ cells in the tumor is associated with generally favorable survival. Host immune response to MCPyV might explain in part the favorable survival associated with MCCs with MCPyV infection. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C237.
Did Tim Paint a Vermeer? (2020)

Tim’s Vermeer is a recent documentary feature film following engineer and self-described non-artist Tim Jenison’ extensive efforts to “paint a Vermeer” by means of a novel optical telescope and mirror-comparator procedure. His efforts were inspired by the controversial claim that some Western painters as early as 1420 secretly built optical devices and traced passages in projected images during the execution of some of their works, thereby achieving a novel and compelling “optical look.” The authors examine the proposed telescope optics in historical perspective, the particular visual evidence adduced in support of the comparator hypothesis, and the difficulty and efficacy of the mirror-comparator procedure as revealed by an independent artist/copyist’s attempts to replicate the procedure. Specifically, the authors find that the luminance gradient along the rear wall in the duplicate painting is far from being rare, difficult, or even “impossible” to achieve as proponents claimed; in fact, such gradients appear in numerous Old Master paintings that show no ancillary evidence of having been executed with optics. There is indeed a slight bowing of a single contour in the Vermeer original, which one would normally expect to be straight; however, the optical explanation for this bowing implies that numerous other lines would be similarly bowed, but in fact all are straight. The proposed method does not explain some ofthe most compelling “optical” evidence in Vermeer’s works suchas the small disk-shaped highlights, which appear like the blur spots that arise in an out-of-focus projected image. Likewise, the comparator-based explanations for the presence of pinprick holes at central vanishing points and the presence of underdrawings and pentimenti in several of Vermeer’s works have more plausible non-optical explanations. Finally, an independent experimentalattempt to replicate the procedure fails overall to provide support for the telescope claim. In light of these considerations and evidence, the authors conclude that it is extremely unlikely that Vermeer used the proposed mirror-comparator procedure.
Functional lung MRI using matrix pencil decomposition and N2 multiple-breath washout measurements in cystic fibrosis. (2017)

This study examines a correlation between the functional lung MRI using matrix pencil decomposition and lung function tests in patients with cystic fibrosis. A strong correlation between the global ventilation inhomogeneity index (LCI) from multiple breath washout and ventilation/perfusion impairment in the lung determined by functional MRI is observed. The results of our study support the potential of functional MRI as a diagnostic tool in monitoring disease progression in cystic fibrosis.
Elimination of Doppler broadening at coherently driven quantum transitions (1999)

Possibilities of elimination of Doppler broadening by making use of atomic coherence in ladder- and folded-type configurations of quantum transitions are considered. A simple physical analysis in terms of modification of the frequency-correlation factor for cascade and multiphoton processes in strong driving fields is developed.
Cerenkov Luminescence Endoscopy: Improved Molecular Sensitivity with β−-Emitting Radiotracers (2014)

The use of (90)Y for Cerenkov endoscopic imaging enabled superior results compared with an (18)F radiotracer.
Synthesis of optically active teleocidin derivatives. Absolute configuration of teleocidin B and olivoretin A. (1984)

Optically active 3, 4, 5, 6, 7, 8-hexahydro-4 (S)-hydroxymethyl-7 (S)-isopropyl-8-methyl-6-oxo [1, 4] diazonino [7, 6, 5-cd] indole was synthesized from N-Boc-4-nitro-L-tryptophanol and a circular dichroism study of the compound shows that the nine-membered ring of teleocidin B and olivoretin A is S, S configuration.
ChemInform Abstract: Iron‐Mediated One‐Pot Synthesis of 3,5‐Diarylpyridines from β‐Nitrostyrenes. (2016)

Abstract A convenient one‐pot approach to both symmetrical and unsymmetrical 3,5‐diarylpyridines is reported.
1-Sulfonyl-4-acylpiperazines as Selective Cannabinoid-1 Receptor (CB1R) Inverse Agonists for the Treatment of Obesity (2009)

A novel series of 1-sulfonyl-4-acylpiperazines as selective cannabinoid-1 receptor (CB1R) inverse agonists was discovered through high throughput screening (HTS) and medicinal chemistry lead optimization. Potency and in vivo properties were systematically optimized to afford orally bioavailable, highly efficacious, and selective CB1R inverse agonists that caused food intake suppression and body weight reduction in diet-induced obese rats and dogs. It was found that the receptor binding assay predicted in vivo efficacy better than functional antagonist/inverse agonist activities. This observation expedited the structure-activity relationship (SAR) analysis and may have implications beyond the series of compounds presented herein.
Instruments à vent : formulation intégrale ou différentielle ? (1994)

Depuis une dizaine d'années les modélisations d'instruments à vent ont mis l'accent sur le caractère non linéaire de ces systèmes. Les équations de base écrites dans le domaine temporel font apparaître une intégrale de convolution couplée à une équation non linéaire. Nous montrerons que dans des cas simples ce système peut se ramener à une équation différentielle non linéaire à retard, plus facile à résoudre numériquement, et qui possède en outre l'avantage de mettre plus facilement en évidence les comportements accessibles en termes d'oscillations périodiques et de bifurcations.
Unsupervised capture and profiling of rare immune cells using multi-directional magnetic ratcheting (2018)

Correction for 'Unsupervised capture and profiling of rare immune cells using multi-directional magnetic ratcheting' by Coleman Murray et al., Lab Chip, 2018, 18, 2396-2409.
Post-ERCP pancreatitis: still a major issue despite all efforts (2021)

SCOPUS: ed.j
Optimization of flexible filter banks based on fast-convolution (2014)

Multirate filter banks can be implemented very efficiently using fast-convolution (FC) processing. The main advantage of the FC filter banks compared with the conventional polyphase implementations is their increased flexibility, that is, the number of channels, their bandwidths, and the center frequencies can be independently selected. In this paper, an approach for optimizing the FC filter banks is proposed. First, a subband representation of the adjustable FC filter banks is derived. Then, the optimization problems are formulated with the aid of the subband model. Finally, these problems are conveniently solved with the aid of a nonlinear optimization algorithm. Two examples are included to illustrate the performance of the proposed overall scheme.
Regressive channel coding with sequential decoding for embedded source coders (2002)

An adaptive error protection scheme for embedded source coders is presented. Convolutional codes of very high memory and regressive redundancy are applied to encode the data frame of the source. The channel decoder with scalable complexity and delay employs modified sequential decoding. In contrast to conventional coding systems, the principal idea of this new algorithm, the 'far end error decoder (FEED)' is to delay the first error as far to the end of the frame as possible rather than to aim at a low average error rate. The proposed system is particularly appropriate for transmitting over strongly varying channels.
C-band microstrip based bandpass filter with design oriented transmission zeros allocation (2011)

This paper presents microstrip band pass filter design which is orientated towards positioning of transmission zeros at particular frequencies as a design goal. This flexibility of choosing these transmission zeros helps in suppressing unwanted spurious or intermodulation components which otherwise requires higher order sharp skirt filter to achieve the stop-band rejection. If there are limited number of such spurious components, and a high rejection rate is required, this filter provides better design choice in terms of size and rejection level, rather using a conventional polynomial based cross-coupled filters. The design methodology is validated with a design of 4.5 GHz bandpass filter of 20 MHz bandwidth with attenuation zeros placed at ±500 MHz from the center frequency.
Semisynthesis of Erythropoietin Analog Having Three Oligosaccharides (2011)

An erythropoietin (EPO) analog having three complex-type biantennary sialyloligosaccharides was prepared. The full-length EPO glycopeptide was prepared through native chemical ligation of a triglycosylated peptide-αthioester corresponding to EPO 1–32 amino acid residues, which was synthesized chemically, and a polypeptide corresponding to EPO 33–166 amino acid residues, which was prepared by E. coli expression. Oxidative folding of the full-length glycopolypeptide afforded the biologically active EPO analog.