gebhart/patrepeval huggingface dataset:
Unified optimization framework for L2, L1, and/or L0 constrained image reconstruction (2017)

In this paper, we propose a unified optimization framework for L2, L1, and/or L0 constrained image reconstruction. First, we generalize cost functions for image reconstruction, which consist of a fidelity term with L2 norm and constraint terms with L2, L1, and/or L0 norms. This generalized cost function covers many types of existing cost functions for image reconstruction. Then, we show that this generalized cost function can be optimized by the alternating direction method of multipliers (ADMM). The ADMM is a well-known iterative optimization approach for convex problems. Experimental results demonstrate that the proposed unified optimization framework is applicable to a wide range of applications.
Find that photo! (2006)

article Share on Find that photo!: interface strategies to annotate, browse, and share Authors: Ben Shneiderman View Profile , Benjamin B. Bederson View Profile , Steven M. Drucker View Profile Authors Info & Claims Communications of the ACMVolume 49Issue 4April 2006 pp 69–71https://doi.org/10.1145/1121949.1121985Published:01 April 2006Publication History 29citation2,428DownloadsMetricsTotal Citations29Total Downloads2,428Last 12 Months38Last 6 weeks4 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 Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
A new immunoglobulin variant: gamma3 heavy chain disease protein CHI. (1976)

Protein CHI is a defective human gamma3 heavy chain immunoglobulin with a deletion encompassing a portion of the variable and constant regions. Joining of the two pieces takes place at the beginning of an extra fragment (Fh) in the constant region where repetitive sequences are found, apparently as the result of gene duplications and/or unequal crossover between gamma genes. It is postulated that a 45 nucleotide fragment is the repetitive unit coding for the extra fragment.
Error-Bounded and Feature Preserving Surface Remeshing with Minimal Angle Improvement (2016)

Surface remeshing is a key component in many geometry processing applications. The typical goal consists in finding a mesh that is (1) geometrically faithful to the original geometry, (2) as coarse as possible to obtain a low-complexity representation and (3) free of bad elements that would hamper the desired application (e.g., the minimum interior angle is above an application-dependent threshold). Our algorithm is designed to address all three optimization goals simultaneously by targeting prescribed bounds on approximation error , minimal interior angle and maximum mesh complexity (number of vertices). The approximation error bound is a hard constraint, while the other two criteria are modeled as optimization goals to guarantee feasibility. Our optimization framework applies carefully prioritized local operators in order to greedily search for the coarsest mesh with minimal interior angle above and approximation error bounded by . Fast runtime is enabled by a local approximation error estimation, while implicit feature preservation is obtained by specifically designed vertex relocation operators. Experiments show that for reasonable angle bounds ( ) our approach delivers high-quality meshes with implicitly preserved features (no tagging required) and better balances between geometric fidelity, mesh complexity and element quality than the state-of-the-art.
The genetic association between personality and major depression or bipolar disorder. A polygenic score analysis using genome-wide association data (2011)

The relationship between major depressive disorder (MDD) and bipolar disorder (BD) remains controversial. Previous research has reported differences and similarities in risk factors for MDD and BD, such as predisposing personality traits. For example, high neuroticism is related to both disorders, whereas openness to experience is specific for BD. This study examined the genetic association between personality and MDD and BD by applying polygenic scores for neuroticism, extraversion, openness to experience, agreeableness and conscientiousness to both disorders. Polygenic scores reflect the weighted sum of multiple single-nucleotide polymorphism alleles associated with the trait for an individual and were based on a meta-analysis of genome-wide association studies for personality traits including 13,835 subjects. Polygenic scores were tested for MDD in the combined Genetic Association Information Network (GAIN-MDD) and MDD2000+ samples (N=8921) and for BD in the combined Systematic Treatment Enhancement Program for Bipolar Disorder and Wellcome Trust Case-Control Consortium samples (N=6329) using logistic regression analyses. At the phenotypic level, personality dimensions were associated with MDD and BD. Polygenic neuroticism scores were significantly positively associated with MDD, whereas polygenic extraversion scores were significantly positively associated with BD. The explained variance of MDD and BD, ∼0.1%, was highly comparable to the variance explained by the polygenic personality scores in the corresponding personality traits themselves (between 0.1 and 0.4%). This indicates that the proportions of variance explained in mood disorders are at the upper limit of what could have been expected. This study suggests shared genetic risk factors for neuroticism and MDD on the one hand and for extraversion and BD on the other.
Identification of host response signatures of infection. (2013)

Biological weapons of mass destruction and emerging infectious diseases represent a serious and growing threat to our national security. Effective response to a bioattack or disease outbreak critically depends upon efficient and reliable distinguishing between infected vs healthy individuals, to enable rational use of scarce, invasive, and/or costly countermeasures (diagnostics, therapies, quarantine). Screening based on direct detection of the causative pathogen can be problematic, because culture- and probe-based assays are confounded by unanticipated pathogens (e.g., deeply diverged, engineered), and readily-accessible specimens (e.g., blood) often contain little or no pathogen, particularly at pre-symptomatic stages of disease. Thus, in addition to the pathogen itself, one would like to detect infection-specific host response signatures in the specimen, preferably ones comprised of nucleic acids (NA), which can be recovered and amplified from tiny specimens (e.g., fingerstick draws). Proof-of-concept studies have not been definitive, however, largely due to use of sub-optimal sample preparation and detection technologies. For purposes of pathogen detection, Sandia has developed novel molecular biology methods that enable selective isolation of NA unique to, or shared between, complex samples, followed by identification and quantitation via Second Generation Sequencing (SGS). The central hypothesis of the current study is that variations on this approach will support efficient identification and verification of NA-based host response signatures of infectious disease. To test this hypothesis, we re-engineered Sandia's sophisticated sample preparation pipelines, and developed new SGS data analysis tools and strategies, in order to pioneer use of SGS for identification of host NA correlating with infection. Proof-of-concept studies were carried out using specimens drawn from pathogen-infected non-human primates (NHP). This work provides a strong foundation for large-scale, highly-efficient efforts to identify and verify infection-specific host NA signatures in human populations.
A Two-Phase Expansion Protocol Combining Interleukin (IL)-15 and IL-21 Improves Natural Killer Cell Proliferation and Cytotoxicity against Rhabdomyosarcoma (2017)

Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy in children. Despite intensive research in recent decades the prognosis for patients with metastatic or relapsed diseases has hardly improved. New therapeutic concepts in anti-tumor therapy aim to modulate the patient's immune system to increase its aggressiveness or targeted effects toward tumor cells. Besides surgery, radiotherapy and chemotherapy, immune activation by direct application of cytokines, antibodies or adoptive cell therapy are promising approaches. In the last years, adoptive transfer of natural killer (NK) cells came into the focus of translational medicine, because of their high cytotoxic potential against transformed malignant cells. A main challenge of NK cell therapy is that it requires a high amount of functional NK cells. Therefore, <i>ex vivo</i> NK cell expansion protocols are currently being developed. Many culturing strategies are based on the addition of feeder or accessory cells, which need to be removed prior to the clinical application of the final NK cell product. In this study, we addressed feeder cell-free expansion methods using common γ-chain cytokines, especially IL-15 and IL-21. Our results demonstrated high potential of IL-15 for NK cell expansion, while IL-21 triggered NK cell maturation and functionality. Hence, we established a two-phase expansion protocol with IL-15 to induce an early NK cell expansion, followed by short exposure to IL-21 that boosted the cytotoxic activity of NK cells against RMS cells. Further functional analyses revealed enhanced degranulation and secretion of pro-inflammatory cytokines such as interferon-γ and tumor necrosis factor-α. In a proof of concept <i>in vivo</i> study, we also observed a therapeutic effect of adoptively transferred IL-15 expanded and IL-21 boosted NK cells in combination with image guided high precision radiation therapy using a luciferase-transduced RMS xenograft model. In summary, this two-phased feeder cell-free <i>ex vivo</i> culturing protocol combined efficient expansion and high cytolytic functionality of NK cells for treatment of radiation-resistant RMS.
The gymnochromes: novel marine brominated phenanthroperylenequinone pigments from the stalked crinoid Gymnocrinus richeri (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe gymnochromes: novel marine brominated phenanthroperylenequinone pigments from the stalked crinoid Gymnocrinus richeriFrancesco De Riccardis, Maria Iorizzi, Luigi Minale, Raffaele Riccio, Bertrand Richer de Forges, and Cecile DebitusCite this: J. Org. Chem. 1991, 56, 24, 6781–6787Publication Date (Print):November 1, 1991Publication History Published online1 May 2002Published inissue 1 November 1991https://pubs.acs.org/doi/10.1021/jo00024a016https://doi.org/10.1021/jo00024a016research-articleACS PublicationsRequest reuse permissionsArticle Views249Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Enhancement of cell-mediated immunity against HIV-1 induced by coinnoculation of plasmid-encoded HIV-1 antigen with plasmid expressing IL-12 (1997)

Previous investigations have demonstrated that CTL may play an important role in suppressing the disease progression of HIV infection. In this study, we inoculated mice with IL-12 expression plasmid together with plasmid-encoding HIV-1 envelope to enhance CTL activity by activating a Th1-type response. The results of delayed-type hypersensitivity using the footpad swelling response and of CTL activity clearly showed that HIV-1-specific cell-mediated immunity was enhanced by inoculation of the IL-12 expression plasmid. Quantitation of cytokine in the sera of IL-12-inoculated mice revealed that IFN-gamma significantly increased. The enhanced cell-mediated immunity responses were abrogated by combined administration of the IL-12 expression plasmid and neutralizing anti-IFN-gamma Ab. Together, these results suggest that enhanced virus-specific cell-mediated immunity occurred via an endogenously produced IFN-gamma by inoculation of IL-12 expression plasmid.
Supplementary Figure 2 from Tasisulam Sodium, an Antitumor Agent That Inhibits Mitotic Progression and Induces Vascular Normalization (2023)

&lt;p&gt;PDF file - 1.3MB&lt;/p&gt;
Intrazeolite Topotaxy (1992)

The self‐assembly of semiconductor quantum dots or wires within the cavity of a zeolite or molecular‐sieve host to form qunatum supralattices has great potential in the development and study of organized systems with value in, for example, quantum electronics, nonlinear optics, optical data storage, and chemoselective sening. The organization of inorganic, organometallic, and metal‐carbonyl moieties on the internal surfaces of the hosts (e.g. see figure) is thebasis of the work and the chemsitry and its applications are reviewed. magnified image
Reverse Phase Protein Microarrays for Clinical Applications (2011)

Phosphorylated proteins represent one of the most important constituents of the proteome and are under intense analysis by the biotechnology and pharmaceutical industry because of their central role for cellular signal transduction. Indeed, alterations in cellular signaling and control mechanisms that modulate signal transduction, functionally underpin most human cancers today. Beyond their central role as the causative components of tumorigenesis, these proteins have become an important research focus for discovery of predictive and prognostic biomarkers. Consequently, these pathway constituents comprise a powerful biomarker subclass whereby the same analyte that provides prediction and/or prognosis is also the drug target itself: a theranostic marker. Reverse phase protein microarrays have been developed to generate a functional patient-specific circuit "map" of the cell signaling networks based directly on cellular analysis of a biopsy specimen. This patient-specific circuit diagram provides key information that identifies critical nodes within aberrantly activated signaling that may serve as drug targets for individualized or combinatorial therapy. The protein arrays provide a portrait of the activated signaling network by the quantitative analysis of the phosphorylated, or activated, state of cell signaling proteins. Based on the growing realization that each patient's tumor is different at the molecular level, the ability to measure and profile the ongoing phosphoprotein biomarker repertoire provides a new opportunity to personalize therapy based on the patient-specific alterations.
Mesosecrin: a secreted glycoprotein produced in abundance by human mesothelial, endothelial, and kidney epithelial cells in culture. (1987)

Human mesothelial cells, endothelial cells, and type II kidney epithelial cells growing in culture devote approximately 3% of their total protein synthesis to the production of an Mr approximately 46-kD, pI 7.1, secreted glycoprotein (designated Sp46). Fibroblasts make about 1/10th as much Sp46 as these cell types, and their synthesis is dependent upon hydrocortisone. Keratinocytes, urothelial cells, conjunctival epithelial cells, and mammary epithelial cells do not make detectable amounts of Sp46. Mesothelial cells secrete Sp46 onto the substratum, and from there it is subsequently released into the medium. Immunofluorescence analysis using specific antisera discloses that Sp46 is deposited beneath cells as a fine coating on the substratum. In sparse cultures, Sp46 is detected in trails behind motile cells. In contrast, secreted fibronectin coalesces into fibers, most of which remain in contact with and on top of the cells; thus Sp46 does not preferentially bind to fibronectin. About 6 kD of the mass of human Sp46 is N-linked oligosaccharide, which is terminally sialated before secretion. Sp46 has a low glycine content, indicating that it is not a collagenlike protein. Its NH2-terminal sequence over the first 40 amino acids does not resemble any protein for which sequence information is available. Sp46 appears to be a novel extracellular glycoprotein, high-level constitutive expression of which is restricted to mesoderm-derived epithelial and endothelial cells. We therefore propose for it the name "mesosecrin."
Structural Basis for High-Affinity Peptide Inhibition of Human Pin1 (2007)

Human Pin1 is a key regulator of cell-cycle progression and plays growth-promoting roles in human cancers. High-affinity inhibitors of Pin1 may provide a unique opportunity for disrupting oncogenic pathways. Here we report two high-resolution X-ray crystal structures of human Pin1 bound to non-natural peptide inhibitors. The structures of the bound high-affinity peptides identify a type-I beta-turn conformation for Pin1 prolyl peptide isomerase domain-peptide binding and an extensive molecular interface for high-affinity recognition. Moreover, these structures suggest chemical elements that may further improve the affinity and pharmacological properties of future peptide-based Pin inhibitors. Finally, an intramolecular hydrogen bond observed in both peptide complexes mimics the cyclic conformation of FK506 and rapamycin. Both FK506 and rapamycin are clinically important inhibitors of other peptidyl-prolyl cis-trans isomerases. This comparative discovery suggests that a cyclic peptide polyketide bridge, like that found in FK506 and rapamycin or a similar linkage, may significantly improve the binding affinity of structure-based Pin1 inhibitors.
Pellet Bed Reactor for nuclear thermal propelled vehicles (1991)

The Pellet Bed Reactor (PeBR) concept is capable of operating at a high power density of up to 3.0 kWt/cm3 and an exit hydrogen gas temperature of 3000 K. The nominal reactor thermal power is 1500 MW and the reactor core is 0.80 m in diameter and 1.3 m high. The nominal PeBR engine generates a thrust of approximately 315 kN at a Specific Impulse (Isp) of 1000 s for a mission duration to Mars of 250 days requiring a total firing time of 170 minutes. Because of its low diameter‐to‐height ratio, PeBR has enough surface area for passive removal of the decay heat from the reactor core. In addition, the reactor is equipped with two independent shutdown mechanisms; 8‐D4C safety rods and 26 BeO/B4C control drums; each system is capable of operating and scraming the reactor safely. The core k‐effective at Beginning of‐Life (BOL) is about 1.07 and in case of water immersion the reactor core is subcritical (k‐effective of 0.93). Due to the absence of core internal support structures, the PeBR can be fueled and refueled in orbit using the vacuum of space. These unique features of the PeBR provide for safety during launch, simplicity of handling, deployment, and end‐of‐life disposal, and vehicle extended lifetime.
Low‐refractive‐index materials: A new class of optical thin‐film materials (2007)

Abstract The refractive index, a most fundamental quantity in optics and optoelectronics, determines many figures of merit of optical components such as reflectors, filters, and resonators. Here we present a new class of optical thin‐film materials that have a very low refractive index. Specular films of high optical quality with refractive indices as low as 1.05 are demonstrated. A single pair DBR incorporating low‐ n material is demonstrated to have enhanced reflectivity, showing the great potential of low‐refractive‐index films for many photonic device applications. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Chinese hamster ovary cell mutants affecting cholesterol metabolism (1997)

The approach of somatic cell and molecular genetics for the study of intracellular regulation of cholesterol metabolism has blossomed in recent years. This review lists all the Chinese hamster ovary cell mutants involved in cholesterol metabolism. In addition, it summarizes the characteristics of mutants involved in three different processes: (1) sequential cleavage of the membrane-bound sterol regulatory element-binding proteins; (2) cholesterol esterification; and (3) intracellular cholesterol transport from the lysosome/endosome.
Favism in a Portuguese Family Due to a Deficient Glucose-6-Phosphate Dehydrogenase Variant of ‘Canton’ or ‘Canton-Like’ Type (1976)

In a Portuguese boy with favism G-6PD deficiency was found. Deficiency was due to a G-6PD variant close or identical to Canton-type G-6PD. The muted protein had a lowered catalytic activity and furthermore, was unstable. The post-translational modifications undergone by this deficient G-6PD variant are described.
ChemInform Abstract: SYN AND ANTI STEREOCHEMISTRY IN ELIMINATION REACTIONS PRODUCING ACYCLIC CONJUGATED THIOESTERS (1983)

Abstract Die basenkatalysierte 1,2‐Eliminierung des Thio =sters (I), der ein geeignetes Modell als Substif t von Enoyl‐COA‐Hydratase (eines die syn‐Eliminierung katalysierenden Enzyms) da stellt, liefert unter der Bedingung (A) das nichtdeuterierte (IIa), und das deuterierte Produkt (IIb) im Verhältnis 57:43; d. h. nach Berücksichtigung des Isotopeneffektes erfolgt mithin zu 86% anti‐Eliminierung [→(IIa)] und zu 14% syn‐Eliminierung [→(lIb)].
Optimizing patient derived mesenchymal stem cells as virus carriers for a Phase I clinical trial in ovarian cancer (2013)

These studies confirmed the feasibility of using patient derived MSC as carriers for oncolytic MV therapy. We propose an approach where MSC from ovarian cancer patients will be expanded, frozen and validated to ensure compliance with the release criteria. On the treatment day, the cells will be thawed, washed, mixed with virus, briefly centrifuged and incubated for 2 hours with virus prior to infusion of the virus/MSC cocktail into patients.
Fast-responding chemiluminescent ozone analyzer for respiratory applications (1989)

With the eventual goal of measuring ozone (O3 ) uptake distribution in human lungs, we developed a fast-responding chemiluminescent O3 analyzer. As the instrument will be used to sample gases respired by human subjects, it is necessary that the reacting species be nontoxic. We chose to test ten alternative alkenes known to be biologically inert. For each of the alkene reactants, we measured the effect of reacting species flow, reaction cell pressure, and ozone inlet fraction. At fixed ozone fraction, the analyzer output reaches a well-defined maximum value at an optimum reaction cell pressure and the signal reaches a plateau value at a critical reacting flow. Operating at the optimum pressure and critical alkene flow, the ozone calibration curve is nonlinear for seven of the alkenes. It appears, however, that the calibration curve can be made linear by operating at a pressure above the optimum value. Comparison of analyzer performance among the ten alkenes indicates that the most effective reacting species is 2-methyl-2-butene. Using this vapor, the analyzer exhibited a linear calibration curve with a resolution of 20 ppb O3 and a 90% step response of 200 ms at a sampling flow of 3 mℓ/s and a reaction cell pressure of 107 Torr. By increasing sampling rate, it may be possible to improve dynamic response further.