gebhart/patrepeval huggingface dataset:
Regulation of Cancer Germline Antigen Gene Expression: Implications for Cancer Immunotherapy (2010)

Cancer germline (CG; also known as cancer-testis) antigen genes are normally expressed in germ cells and trophoblast tissues and are aberrantly expressed in a variety of human malignancies. CG antigen genes have high clinical relevance as they encode a class of immunogenic and highly selective tumor antigens. CG antigen-directed immunotherapy is undergoing clinical evaluation for the treatment of a number of solid tumor malignancies and has been demonstrated to be safe, provoke immune responses and be of therapeutic benefit. Achieving an improved understanding of the mechanisms of CG antigen gene regulation will facilitate the continued development of targeted therapeutic approaches against tumors expressing these antigens. Substantial evidence suggests epigenetic mechanisms, particularly DNA methylation, as a primary regulator of CG antigen gene expression in normal and cancer cells as well as in stem cells. The roles of sequence-specific transcription factors and signal transduction pathways in controlling CG antigen gene expression are less clear but are emerging. A combinatorial therapeutic approach involving epigenetic modulatory drugs and CG antigen immunotherapy is suggested based on these data and is being actively pursued. In this article, we review the mechanisms of CG antigen gene regulation and discuss the implications of these mechanisms for the development of cancer immunotherapy approaches targeting CG antigens.
Arrays of parametric receiving arrays (1973)

Theory is presented to describe the response of arrays whose elements consist of parametric end-fire receivers. The results of measurements on arrays containing up to four elements are presented in support of the theory. Electronic steering of this type of array is also addressed. The use of very small transducers in the formation of narrow receiver beams at low frequencies is demonstrated.
Estimation of the systemic availability and other pharmacokinetic parameters of naltrexone in man after acute and chronic oral administration. (1977)

First pass metabolism, metabolic clearance, volume of distribution and steady state plasma levels were estimated in man following acute and chronic 100 mg oral doses of naltrexone. Essentially no statistical differences was observed in these values between the acute and chronic physiologic state. The values for the first pass effect were 79.6 +/- 4.6% and 78.0 +/- 3.0% for acute and chronic treatment respectively. From our pharmacokinetic data an apparent chronic release rate (ACRR) for a sustained release preparation of naltrexone was calculated as 11.8 microgram/kg/hr. In practice a release rate of one half the ACRR should be sufficient to provide continuous antagonism of 25 mg i.v. heroin. In conclusion our data clearly indicate that naltrexone is an effective and safe narcotic antagonist in man.
Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system. (1996)

Many biological processes rely upon protein-protein interactions. Hence, detailed analysis of these interactions is critical for their understanding. Due to the complexities involved, genetic approaches are often needed. In yeast and phage, genetic characterizations of protein complexes are possible. However, in multicellular organisms, such characterizations are limited by the lack of powerful selection systems. Herein we describe genetic selections that allow single amino acid changes that disrupt protein-protein interactions to be selected from large libraries of randomly generated mutant alleles. The strategy, based on a yeast reverse two-hybrid system, involves a first-step negative selection for mutations that affect interaction, followed by a second-step positive selection for a subset of these mutations that maintain expression of full-length protein (two-step selection). We have selected such mutations in the transcription factor E2F1 that affect its ability to heterodimerize with DP1. The mutations obtained identified a putative helix in the marked box, a region conserved among E2F family members, as an important determinant for interaction. This two-step selection procedure can be used to characterize any interaction domain that can be tested in the two-hybrid system.
Universal Health Insurance and Health Care Access for Homeless Persons (2010)

Within a system of universal health insurance, homeless people still encounter barriers to obtaining health care. Strategies to reduce nonfinancial barriers faced by homeless women with children, younger adults, and recent victims of physical assault should be explored.
Pedestrian Detection with Local Feature Assistant (2007)

Until now, existing pedestrian detection systems usually use global features (e.g. appearance or motion) of human body to detect pedestrian; however, the detection rate needs to be improved in many situations since sometimes the global features can not be obtained. For example, a pedestrian may be partly covered by a car or his/her part may hide into the background. Therefore it is essential to adopt some local features of key parts of human body to assist pedestrian detection. In this paper, we propose a method using some key local features of human body to help pedestrian detection. Since the introduction of additional features will cost the system more time, in order to ensure the detection speed, we firstly use both appearance and motion global features of human body to select candidates, and then use local features of head and leg to do further confirmation. In the confirmation stage, we use three kinds of local features (head appearance, face color and hair color) to detect the head of each candidate; at the same time, we also choose some particular local appearance features to detect the leg. The experimental results indicate that this method can improve detection rate with almost the same detection speed; additionally, it can reduce false alarm sometimes.
Life Cycle Assessment (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLife Cycle AssessmentAllen White and Karen ShapiroCite this: Environ. Sci. Technol. 1993, 27, 6, 1016–1017Publication Date (Print):June 1, 1993Publication History Published online21 July 2005Published inissue 1 June 1993https://pubs.acs.org/doi/10.1021/es00043a614https://doi.org/10.1021/es00043a614research-articleACS PublicationsRequest reuse permissionsArticle Views1439Altmetric-Citations20LEARN 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
Precise and efficient genome editing in zebrafish using the CRISPR/Cas9 system (2014)

The introduction of engineered site-specific DNA endonucleases has brought precise genome editing in many model organisms and human cells into the realm of possibility. In zebrafish, loss-of-function alleles have been successfully produced; however, germ line transmission of functional targeted knock-ins of protein tags or of SNP exchanges have not been reported. Here we show by phenotypic rescue that the CRISPR/Cas system can be used to target and repair a premature stop codon at the albino (alb) locus in zebrafish with high efficiency and precision. Using circular donor DNA containing CRISPR target sites we obtain close to 50% of larvae with precise homology-directed repair of the alb(b4) mutation, a small fraction of which transmitted the repaired allele in the germ line to the next generation (3/28 adult fish). The in vivo demonstration of germ line transmission of a precise SNP exchange in zebrafish underscores its suitability as a model for genetic research.
The Craft of Information Visualization: Readings and Reflections (2003)

Since the beginning of the computer age, researchers from many disciplines have sought to facilitate people's use of computers and to provide ways for scientists to make sense of the immense quantities of data coming out of them. One gainful result of these efforts has been the field of information visualization, whose technology is increasingly applied in scientific research, digital libraries, data mining, financial data analysis, market studies, manufacturing production control, and data discovery.

This book collects 38 of the key papers on information visualization from a leading and prominent research lab, the University of Maryland's Human-Computer Interaction Lab (HCIL). Celebrating HCIL's 20th anniversary, this book presents a coherent body of work from a respected community that has had many success stories with its research and commercial spin-offs. 

Each chapter contains an introduction specifically written for this volume by two leading HCI researchers, to describe the connections among those papers and reveal HCIL's individual approach to developing innovations.

*Presents key ideas, novel interfaces, and major applications of information visualization tools, embedded in inspirational prototypes.

*Techniques can be widely applied in scientific research, digital libraries, data mining, financial data analysis, business market studies, manufacturing production control, drug discovery, and genomic studies.

*Provides an insider view to the scientific process and evolution of innovation, as told by the researchers themselves.

*This work comes from the prominent and high profile University of Maryland's Human Computer Interaction Lab

Table of Contents

Preface
Acknowledgments
Introduction
Chapter 1. Database Discovery with Dynamic Queries
Chapter 2. Seeing the World Through Image Libraries
Chapter 3. Preserving Context with Zoomable User Interfaces 
Chapter 4. The World's Information in Digital Libraries 
Chapter 5. Making Sense of the World Wide Web 
Chapter 6. Understanding Hierarchical Data 
Chapter 7. Innovating the Interaction 
Chapter 8. Theories for Understanding Information Visualization 
Appendix A: Video Reports
Appendix B: Project Pages
Appendix C: Software for Downloading
Appendix D: Full Tech Report Index
Author Index
Key Terms Index
Tunable, Gap-State Lasing in Switchable Directions for Opal Photonic Crystals (2002)

A photonic crystal laser that is tunable throughout the visible in three-dimensionally switchable directions is demonstrated. This photo-pumped laser utilizes a dye-infiltrated, single-crystal SiO2 opal having incomplete bandgaps. Our results support a gap-state-enhanced distributed feedback mechanism for lasing. Three different types of wavelength tunability are demonstrated, each applicable over a different frequency range and involving either single or multiple bandgaps. The many independent laser cavities that exist in one photonic crystal are demonstrated by simultaneously obtaining lasing in various colors and directions from an opal crystal. The observation of characteristic laser emission lines provides a new spectroscopy for characterizing intra-gap photonic states, which may be useful for developing the photonic crystal analogues of electronic circuitry.
PAICS, a De Novo Purine Biosynthetic Enzyme, Is Overexpressed in Pancreatic Cancer and Is Involved in Its Progression (2020)

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with an extremely poor prognosis. There is an urgent need to identify new therapeutic targets and also understand the mechanism of PDAC progression that leads to aggressiveness of the disease. To find therapeutic targets, we analyzed data related to PDAC transcriptome sequencing and found overexpression of the de novo purine metabolic enzyme phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS). Immunohistochemical analysis of PDAC tissues showed high expression of the PAICS protein. To assess the biological roles of PAICS, we used RNA interference and knock down of its expression in PDAC cell lines that caused a reduction in PDAC cell proliferation and invasion. Furthermore, results of chorioallantoic membrane assays and pancreatic cancer xenografts demonstrated that PAICS regulated pancreatic tumor growth. Our data also showed that, in PDAC cells, microRNA-128 regulates and targets PAICS. PAICS depletion in PDAC cells caused upregulation in E-cadherin, a marker of the epithelial-mesenchymal transition. In PDAC cells, a BET inhibitor, JQ1, reduced PAICS expression. Thus, our investigations show that PAICS is a therapeutic target for PDAC and, as an enzyme, is amenable to targeting by small molecules.
Distributed-feedback, surface-emitting laser diode with lateral double heterostructure (1987)

The distributed-feedback, surface-emitting laser diode with lateral double heterostructure (LDH) is realised with the combination of molecular beam epitaxy (MBE) and selective liquid-phase-epitaxial (LPE) techniques. Stimulated emission with a spectrum width of 2–3 nm was observed at the operating current of 100mA at −50°C, and 400 mA at room temperature.
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach (2001)

Phylogenetic inference from amino acid sequence data uses mainly empirical models of amino acid replacement and is therefore dependent on those models. Two of the more widely used models, the Dayhoff and JTT models, are estimated using similar methods that can utilize large numbers of sequences from many unrelated protein families but are somewhat unsatisfactory because they rely on assumptions that may lead to systematic error and discard a large amount of the information within the sequences. The alternative method of maximum-likelihood estimation may utilize the information in the sequence data more efficiently and suffers from no systematic error, but it has previously been applicable to relatively few sequences related by a single phylogenetic tree. Here, we combine the best attributes of these two methods using an approximate maximum-likelihood method. We implemented this approach to estimate a new model of amino acid replacement from a database of globular protein sequences comprising 3,905 amino acid sequences split into 182 protein families. While the new model has an overall structure similar to those of other commonly used models, there are significant differences. The new model outperforms the Dayhoff and JTT models with respect to maximum-likelihood values for a large majority of the protein families in our database. This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates. Potentially, this matrix, and the methods used to generate it, may also be useful in other areas of research, such as biological sequence database searching, sequence alignment, and protein structure prediction, for which an accurate description of amino acid replacement is required.
Prolonged Clinical and Molecular Remission in Patients With Low-Grade or Follicular Non-Hodgkin's Lymphoma Treated With Rituximab Plus CHOP Chemotherapy: 9-Year Follow-Up (2004)

Although a cure has not been found yet for follicular NHL, the R-CHOP combination provides a lengthy response duration in patients with relapsed or newly diagnosed indolent NHL.
Molecular Genetics of Familial Alzheimer’s Disease (1989)

A proportion of cases of Alzheimer disease show familial aggregation with a pattern of vertical transmission compatible with autosomal dominant inheritance. Isolation of the genetic defect causing this form of Alzheimer disease, which may elucidate the biochemical mechanisms underlying the pathogenesis of the Alzheimer disease phenotype, can theoretically be achieved by first defining the chromosomal location of the disease gene(s) by classical genetic linkage studies in large families segregating this disorder. Subsequently, other cloning strategies can be applied to isolate the disease gene from the chromosomal region showing tight linkage to the disease phenotype. This paper reports some recent results of such studies, and discusses some of the potential confounding events which must be considered when approaching inherited neuropsychiatric disorders using these strategies.
Equine connective tissue tumors contain unintegrated bovine papilloma virus DNA (1980)

Bovine papilloma virus (BPV) appears to be the etiological agent of common equine connective tissue tumors. We investigated the physical state of the viral DNA within such tumors and found no indication for integration into the host genome. The BPV genomes were present as free circular episomes. Two equine sarcoids were shown to contain multiple copies of free circular BPV type 1 (BPV-1) DNA. When the tumors were digested with several single-cut restriction enzymes, there were only form III BPV-1 DNA sequences could be revealed. One of the sarcoids contained, apart from wild-type BPV-1 DNA, a class of smaller BPV-1 circular DNA molecules bearing a deletion of approximately 9% of the BPV-1 genome. This deletion is located in the physical map between the relative units 0 and 0.32.
Multivariate Adaptive Regression Splines (Preprint) (1990)

Abstract : A new method is presented for flexible regression modeling of high dimensional data. The model takes the form of an expansion in product spline basis functions, where the number of basis functions as well as the parameters associated with each one (product degree and knot locations) are automatically determined by the data. This procedure is motivated by the recursive partitioning approach to regression and shares its attractive properties. Unlike recursive partitioning, however this method produces continuous models with continuous derivatives. It has more power and flexibility to model relationships that are nearly additive or involve interactions in at most a few variables. In addition, the model can be represented in a form that separately identifies the additive contributions and those associated with the different multivariable interactions.
Friedel-Crafts reaction with 1-bromo-1-phenyl-2-propanone (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFriedel-Crafts reaction with 1-bromo-1-phenyl-2-propanoneRussell Kwok, Bobbi Chamberlain, and S. C. MuthaCite this: J. Org. Chem. 1972, 37, 8, 1275–1276Publication Date (Print):April 1, 1972Publication History Published online1 May 2002Published inissue 1 April 1972https://pubs.acs.org/doi/10.1021/jo00973a050https://doi.org/10.1021/jo00973a050research-articleACS PublicationsRequest reuse permissionsArticle Views79Altmetric-Citations1LEARN 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
Syndecan4 coordinates Wnt/JNK and BMP signaling to regulate foregut progenitor development (2016)

Temporally and spatially dynamic Wnt and BMP signals are essential to pattern foregut endoderm progenitors that give rise to the liver, pancreas and lungs, but how these two signaling pathways are coordinated in the extracellular space is unknown. Here we identify the transmembrane heparan sulphate proteoglycan Syndecan-4 (Sdc4), as a key regulator of both non-canonical Wnt and BMP signaling in the Xenopus foregut. Foregut-specific Sdc4 depletion results in a disrupted Fibronectin (Fn1) matrix, reduced cell adhesion, and failure to maintain foregut gene expression ultimately leading to foregut organ hypoplasia. Sdc4 is required to maintain robust Wnt/JNK and BMP/Smad1 signaling in the hhex+ foregut progenitors. Pathway analysis suggests that Sdc4 functionally interacts with Fzd7 to promote Wnt/JNK signaling, which maintains foregut identity and cell adhesion. In addition, the Sdc4 ectodomain is required to support Fn1 matrix assembly, which is essential for the robust BMP signaling that promotes foregut gene expression. This work sheds lights on how the extracellular matrix can coordinate different signaling pathways during organogenesis.
Towards healthier libraries: the HLI statistical survey 2011 (2011)

The HLI statistical survey provides evidence on the resources, services and economics of our libraries. Sixteen libraries participated in the 2011 survey. This report uses the data subsets of these sixteen libraries to illustrate averages and trends in specific areas of current Victorian health library practice.
The interaction of protein A and Fc fragment of rabbit immunoglobulin G as probed by complement-fixation and nuclear-magnetic-resonance studies (1977)

Protein-A-Fc-fragment complexes were observed in sedimentation-velocity experiments by ultracentrifugation. The interaction was studied by protein-fluorescence-quenching titrations of the Fc fragment with protein A, allowing the dissociation constant to be determined under a variety of conditions. The first component of the complement pathway, C1, is activated by complexes of protein A with rabbit IgG (immunoglobulin G), and the structural basis for this interaction was studied by using n.m.r. (nuclear magnetic resonance). The four Fc-fragment binding sites on protein A were shown to contain aromatic amino acids, and to be connected by mobile hydrophilic regions. Neither n.m.r. nor proton-relaxation-enhancement studies show evidence of a large conformational change of the Fc fragment on binding protein A, and this suggests that the cross-linking of the Fc fragments may be primarily responsible for the activation of component C1. This is supported by the inability of a univalent tryptic fragment of protein A to activate complement fixation by rabbit IgG.