gebhart/patrepeval huggingface dataset:
On Transductive Regression (2007)

In many modern large-scale learning applications, the amount of unlabeled data far exceeds that of labeled data. A common instance of this problem is the transductive setting where the unlabeled test points are known to the learning algorithm. This paper presents a study of regression problems in that setting. It presents explicit VC-dimension error bounds for transductive regression that hold for all bounded loss functions and coincide with the tight classification bounds of Vapnik when applied to classification. It also presents a new transductive regression algorithm inspired by our bound that admits a primal and kernelized closed-form solution and deals efficiently with large amounts of unlabeled data. The algorithm exploits the position of unlabeled points to locally estimate their labels and then uses a global optimization to ensure robust predictions. Our study also includes the results of experiments with several publicly available regression data sets with up to 20,000 unlabeled examples. The comparison with other transductive regression algorithms shows that it performs well and that it can scale to large data sets.
Quantity of dengue virus required to infect rhesus monkeys (1985)

As part of a dengue vaccine study, it was necessary to determine how much virus was required to infect rhesus monkeys. Serial dilutions of dengue 2 and 4 viruses were inoculated subcutaneously into groups of five monkeys and seroconversions determined on days 30 and 60 post-inoculation. The viruses were also titrated simultaneously in LLC-MK2 cells and mosquitoes. It was calculated that 9.5 mosquito infectious doses 50 (MID50) of dengue 2 virus and 22 MID50 of dengue 4 virus were required to infect 50% of the monkeys. The data suggest that 100 MID50 of dengue virus should be used as a challenge dose for monkeys previously immunized with dengue vaccine.
Recombinant Receptor-Binding Domains of Multiple Middle East Respiratory Syndrome Coronaviruses (MERS-CoVs) Induce Cross-Neutralizing Antibodies against Divergent Human and Camel MERS-CoVs and Antibody Escape Mutants (2016)

MERS-CoV was first identified in June 2012 and has since spread in humans and camels. Mutations in its spike (S) protein receptor-binding domain (RBD), a key vaccine target, have been identified, raising concerns over the efficacy of RBD-based MERS vaccines against circulating human and camel MERS-CoV strains. Here, we constructed five vaccine candidates, designated 2012-RBD, 2013-RBD, 2014-RBD, 2015-RBD, and Camel-RBD, containing single or multiple mutations in the RBD of representative human and camel MERS-CoV strains during the 2012-2015 outbreaks. These RBD-based vaccine candidates maintained good functionality, antigenicity, and immunogenicity, and they induced strong cross-neutralizing antibodies against infection by divergent pseudotyped and live MERS-CoV strains, as well as antibody escape MERS-CoV mutants. This study provides impetus for further development of a safe, highly effective, and broad-spectrum RBD-based subunit vaccine to prevent MERS-CoV infection.
Effects of Input Data on the Performance of a Neural Network in Distinguishing Normal and Glaucomatous Visual Fields (2005)

The choice of type of data input had important effects on the performance of the neural networks in glaucoma diagnosis. Refined input data, based on Pattern Deviations, resulted in higher sensitivity and specificity than did raw threshold values. Neural networks may have high potential in the production of useful clinical tools for the classification of visual field tests.
Iron(II) Complexes Containing Unsymmetrical P–N–P′ Pincer Ligands for the Catalytic Asymmetric Hydrogenation of Ketones and Imines (2014)

After their treatment with LiAlH4 and then alcohol, new iron dicarbonyl complexes mer-trans-[Fe(Br)(CO)2(P-CH═N-P')][BF4] (where P-CH═N-P' = R2PCH2CH═NCH2CH2PPh2 and R = Cy or iPr or P-CH═N-P' = (S,S)- Cy2PCH2CH═NCH(Me)CH(Ph)PPh2) are catalysts for the hydrogenation of ketones in THF solvent with added KOtBu at 50 °C and 5 atm H2. Complexes with R = Ph are not active. With the enantiopure complex, alcohols are produced with an enantiomeric excess of up to 85% (S) at TOF up to 2000 h(-1), TON of up to 5000, for a range of ketones. An activated imine is hydrogenated to the amine in 90% ee at a TOF 20 h(-1)and TON 99. This is a significant advance in asymmetric pressure hydrogenation using iron. The complexes are prepared in two steps: (1) a one-pot reaction of phosphonium dimers ([cyclo-(PR2CH2CH(OH)(-))2][Br]2), KOtBu, FeBr2, and Ph2PCH2CH2NH2 (or (S,S)-Ph2PCH(Ph)CH(Me)NH2 for the enantiopure complex) in THF under a CO atmosphere to produce the complexes cis- and trans-[Fe(Br)2(CO)(P-CH═N-P')]; (2) the reaction of these with AgBF4 under CO(g) to afford the dicarbonyl complexes in high yield (50-90%). NMR and DFT studies of the process of precatalyst activation show that the dicarbonyl complexes are converted first to hydride-aluminum hydride complexes where the imine of the P-CH═N-P' ligand is reduced to an amide [P-CH2N-P'](-) with aluminum hydrides still bound to the nitrogen. These hydride species react with alcohol to give monohydride amine iron compounds FeH(OR')(CO)(P-CH2NH-P'), R' = Me, CMe2Et as well as the iron(0) complex Fe(CO)2(P-CH2NH-P') under certain conditions.
Tolerogenic dendritic cells and their potential applications (2011)

Dendritic cells (DCs) play a pivotal role in regulating the balance between immunity and tolerance of the immune system. Recent advancements in DC biology and techniques for manipulating the function of these cells have shown their immense therapeutic potential for treating a variety of immune disorders. Theoretically, antigen-specific tolerogenic DCs can be generated in vitro and delivered to patients to correct the dysfunctional immune responses that attack their own tissues or over-react to innocuous foreign antigens. However, DCs are a heterogeneous population of cells with differences in cell surface makers, differentiation pathways and functions. Studies are needed to examine which subset of DCs can be used for what type of applications. Furthermore, most of the information on tolerogenic DCs has been obtained from animal models and translational studies are needed to examine how a DC therapeutic strategy can be implemented clinically to modulate immunity.
Magnetic ordering of DNA liquid crystals (1986)

Sonicated calf thymus DNA with an average length of approximately 100 base pairs has been found to form a cholesteric liquid crystal at a concentration of approximately 250 mg of DNA/mL of solution. Immediately after preparation, small ordered domains of a few micrometers are formed, resulting in an opaque solution. This liquid crystal can readily be oriented in the magnetic field of an NMR magnet, resulting in a clear birefringent phase. The DNA molecules align with their helix axes perpendicular to the field so that the cholesteric pitch axis was parallel with the field. A pitch length of approximately 2.5 microns for the cholesteric phase was determined both from optical measurements (optical light rotation) and from NMR measurements (solvent diffusion). The observation that DNA molecules can be magnetically oriented opens up new possibilities for studying the structure and dynamics of the aligned DNA molecules.
Comprehensive Proteomic Analysis of Human Endometrial Fluid Aspirate (2009)

The endometrial fluid is a noninvasive sample which contains numerous secreted proteins representative of endometrial function and reflects the state of the endometrium. In this study, we describe, for the first time, a comprehensive catalogue of proteins of the endometrial fluid during the secretory phase of the menstrual cycle. To achieve this objective, three different but complementary strategies were used: First, in-solution digestion followed by reverse phase high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS); second, protein separation by denaturing one-dimensional electrophoresis (SDS-PAGE) followed by HPLC-MS/MS analysis. Finally, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) followed by MALDI-TOF/TOF analysis. The combination of the three strategies led to the successful identification of 803 different proteins in the International Protein Index (IPI) human database (v3.48). An extensive description of the endometrial fluid proteome will help provide the basis for a better understanding of a number of diseases and processes, including endometriosis, endometrial cancer and embryo implantation. We believe that the thorough catalogue of proteins presented here can serve as a valuable reference for the study of embryo implantation and for future biomarker discovery involved in pathologic alterations of endometrial function.
Cysteine-Containing Fusion Tag for Site-Specific Conjugation of Therapeutic and Imaging Agents to Targeting Proteins (2008)

Targeted delivery of therapeutic and imaging agents requires conjugation of a corresponding payload to a targeting peptide or protein. The ideal procedure should yield a uniform preparation of functionally active conjugates and be translatable for development of clinical products. We describe here our experience with site-specific protein modification via a novel cysteine-containing fusion tag (Cys-tag), which is a 15-amino-acid (aa) N-terminal fragment of human ribonuclease I with the R4C substitution. Several Cys-tagged proteins and peptides with different numbers of native cysteines were expressed and refolded into functionally active conformation, indicating that the tag does not interfere with the formation of internal disulfide bonds. We also describe standardized procedures for site-specific conjugation of very different payloads, such as functionalized lipids and liposomes, radionuclide chelators and radionuclides, fluorescent dyes, drug-derivatized dendrimers, scaffold proteins, biotin, and polyethyleneglycol to Cys-tagged peptides and proteins, as well as present examples of functional activity of targeted conjugates in vitro and in vivo. We expect that Cys-tag would provide new opportunities for development of targeted therapeutic and imaging agents for research and clinical use.
Acyl carrier protein: structure–function relationships in a conserved multifunctional protein family (2007)

Acyl carrier protein (ACP) is a universal and highly conserved carrier of acyl intermediates during fatty acid synthesis. In yeast and mammals, ACP exists as a separate domain within a large multifunctional fatty acid synthase polyprotein (type I FAS), whereas it is a small monomeric protein in bacteria and plastids (type II FAS). Bacterial ACPs are also acyl donors for synthesis of a variety of products, including endotoxin and acylated homoserine lactones involved in quorum sensing; the distinct and essential nature of these processes in growth and pathogenesis make ACP-dependent enzymes attractive antimicrobial drug targets. Additionally, ACP homologues are key components in the production of secondary metabolites such as polyketides and nonribosomal peptides. Many ACPs exhibit characteristic structural features of natively unfolded proteins in vitro, with a dynamic and flexible conformation dominated by 3 parallel alpha helices that enclose the thioester-linked acyl group attached to a phosphopantetheine prosthetic group. ACP conformation may also be influenced by divalent cations and interaction with partner enzymes through its "recognition" helix II, properties that are key to its ability to alternately sequester acyl groups and deliver them to the active sites of ACP-dependent enzymes. This review highlights recent progress in defining how the structural features of ACP are related to its multiple carrier roles in fatty acid metabolism.
Comparison of DNA Enzyme Immunoassay and Line Probe Assays (Inno-LiPA HCV I and II) for Hepatitis C Virus Genotyping (1998)

Two methods for genotyping hepatitis C virus (DNA enzyme immunoassay [DEIA] and line probe assay [Inno-LiPA HCV I and II]) were compared on 120 samples and of these 87% were assigned to the same subtype by both assays. There were 15 subtyping discrepancies which involved 5% of type 1 isolates and 90% of type 2 isolates. Amplified products from the core and 5' untranslated regions (UTR) were sequenced to resolve conflicts. Type 1 discordant samples had a guanosine at position -99 in the 5' UTR, a characteristic of genotype 1b, and a core region typical of subtype 1a. The eight isolates classified as 2a/2c by LiPA and as subtype 2c by DEIA belonged to type 2.
Primary Structure of CD52 (1995)

The CD52 antigen was extracted from human spleens with organic solvents and purified by immunoaffinity and reverse-phase chromatography. The latter step resolved two CD52 species, called CD52-I and CD52-II. Both species were found to contain similar N-linked oligosaccharides and glycosylphosphatidylinositol (GPI) anchor glycans. The N-linked oligosaccharides were characterized by methylation linkage analysis and, following exhaustive neuraminidase and endo-beta-galactosidase digestion, by the reagent array analysis method. The results showed that the single CD52 N-glycosylation site is occupied by large sialylated, polylactosamine-containing, core-fucosylated tetraantennary oligosaccharides. The locations of the phosphoryl substituents on the GPI anchor glycan were determined using a new and sensitive method based upon partial acid hydrolysis of the GPI glycan. The difference between CD52-I and CD52-II was in the phosphatidylinositol (PI) moieties of the GPI anchors. The phosphatidylinositol-specific phospholipase C-sensitive CD52-I contained exclusively distearoyl-PI, while the PI-phospholipase C-resistant CD52-II contained predominantly a palmitoylated stearoyl-arachidonoyl-PI, as judged by electrospray ionization mass spectrometry. Tandem mass spectrometric studies indicated that the palmitoyl residue of the CD52-II anchor is attached to the 2-position of the myo-inositol ring. Both the CD52-I and CD52-II PI structures are unusual for GPI anchors and the possible significance of this is discussed. The alkali-lability of the CD52 epitope recognized by the Campath-1H monoclonal antibody was studied. The data suggest that the alkali-labile hydroxyester-linked fatty acids of the GPI anchor are necessary for antibody binding.
Pulse microwave effects on nerve vitality. (1982)

Isolated sciatic nerves of frogs were exposed to 2.45-GHz pulse-microwave radiation in a waveguide exposure system at an average specific absorption rate (SAR) of 10 mW/g. In previous studies using continuous-wave (cw) microwave radiation at an SAR of 10 mW/g, survival time of the irradiated nerve when stimulated to fire at a high rate (50 twin pulses per sec) was shorteded significantly. This investigation was performed to determine if pulse-microwave radiation produced the same of different effects on the vitality of frog sciatic nerves as continuous-wave microwave radiation. Three sets of experiments were carried out using 10-..mu..sec-wide pulses at 50 pps, with an average SAR of 10 mW/g: (1) asynchronous pulsing wherein the mw pulse was delivered at varying times in the firing cycle; (2) synchronous pulsing during the peak of the nerve action potential; and (3) synchronous pulsing during the quiescent period between nerve firings. In all three cases a significant decrease in the survival time of the exposed nerves, as compared to their unexposed mates, was seen. However, the magnitude of this effect was essentially the same in all three cases and was also comparable with the ffect seen earlier using cw (of equivalent SAR).
Towards therapeutic vaccines for colorectal carcinoma: a review of clinical trials (2005)

Colorectal carcinoma is a leading cause of cancer-related mortality. Despite the introduction of new cytotoxic drugs, improved surgical and radiotherapeutic techniques, a large proportion of colorectal carcinomas remain incurable. New targeted therapeutic strategies, including immunotherapy, are being explored as complementary treatments. Recent advances in immunology and molecular biology have opened new avenues for the clinical testing of rationally designed vaccination strategies against cancer. The present report reviews the results of therapeutic vaccine trials in colorectal carcinoma, published mainly in the past 6 years. Tumor-associated antigens (self-antigens) have been targeted by therapeutic vaccination in more than 2000 colorectal carcinoma patients. The results demonstrate that tumor antigen-specific immune responses are reproducibly induced; that is, tolerance can be reversed, without the induction of serious adverse events or autoimmune disorders. No long-term autoimmune side effects have been observed after a minimum follow-up of 4 years in over 700 patients. Over 1300 colorectal carcinoma patients with minimal residual disease have been enrolled in randomized controlled Phase II/III trials using autologous tumor cell vaccines. A significantly improved overall survival was noted for Stages I-IV colorectal carcinoma patients utilizing Newcastle-disease virus as an adjuvant. Autologous tumor cells mixed with bacillus Calmette-Guerin (BCG) were of significant clinical benefit for patients with Stage II colon cancer. Results of randomized controlled trials targeting Ep-CAM have shown clinical benefit in subgroups of patients. Several new generation vaccines have demonstrated excellent safety profile and immunogenicity. Some studies have also demonstrated a statistically significant correlation between the induced immune response and prolonged overall survival, which should be confirmed in enlarged trials. Although it is unlikely that active specific immunotherapy will provide a standard complementary therapeutic approach for colorectal carcinoma in the near future, the results so far are encouraging. Randomized controlled vaccine trials targeting molecularly defined tumor antigens are warranted, particularly in colon carcinoma with minimal residual disease.
Drug's Link to Genes Reveals Estrogen's Many Sides (1996)

The hormone estrogen is both a villain and a savior, thought to contribute to the development of breast and uterine cancers but also to protect women against heart attacks and osteoporosis. Now a study of an estrogenlike drug, reported on page 1222 , may help explain the hormone's contradictory personality and open the way to designing drugs that block only its unwanted effects—or mimic only its beneficial ones. The drug, called raloxifene, sends its signals to the genes by different pathways depending on the tissue it is acting on. The natural hormone may owe its many guises to a similar variety of pathways.
Effect of Placement Techniques on the Marginal Adaptation of Class V Composite Restorations (2005)

No differences on marginal adaptation were observed when restoring conservative Class V cavities using incremental or bulk placement techniques.
Weighing Naked Proteins: Practical, High-Accuracy Mass Measurement of Peptides and Proteins (1992)

Two new technologies have made the study of proteins by mass spectrometry straight-forward. Proteins with molecular masses of up to more than 100 kilodaltons can be analyzed at picomole sensitivities to give simple mass spectra corresponding to the intact molecule. This development has allowed unprecedented accuracy in the determination of the molecular weights of proteins. A number of "case studies" are used to present the revolutionary impact that these powerful new ways of looking at proteins are having on biological research.
A capacitive‐coupled ground resistivity system for engineering and environmental applications: Results of two Canadian field tests (1994)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1994A capacitive‐coupled ground resistivity system for engineering and environmental applications: Results of two Canadian field testsAuthors: Marten DoumaVladimir M. TimofeevAndrew W. RogozinskiJames A. HunterMarten DoumaGeological Survey of Canada, Vladimir M. TimofeevAll‐Russian Research Institute for Hydrogeology and Engineering Geology, Andrew W. RogozinskiAndrotex, Ltd., and James A. HunterGeological Survey of Canadahttps://doi.org/10.1190/1.1932158 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1932158FiguresReferencesRelatedDetailsCited by2D INVERSION OF DIPOLE-DIPOLE AXIAL ARRAY WITH LINEAR CAPACITIVE ELECTRODES FOR ENGINEERING TASKS4 September 2019 | Engineering survey, Vol. 13, No. 2 SEG Technical Program Expanded Abstracts 1994ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1994 Pages: 1679 publication data© 1994 Copyright © 1994 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 10 Feb 2005 CITATION INFORMATION Marten Douma, Vladimir M. Timofeev, Andrew W. Rogozinski, and James A. Hunter, (1994), "A capacitive‐coupled ground resistivity system for engineering and environmental applications: Results of two Canadian field tests," SEG Technical Program Expanded Abstracts : 559-561. https://doi.org/10.1190/1.1932158 Plain-Language Summary PDF DownloadLoading ...
Effect of Computed Tomography of the Appendix on Treatment of Patients and Use of Hospital Resources (1998)

Routine appendiceal CT performed in patients who present with suspected appendicitis improves patient care and reduces the use of hospital resources.
Comprehensive Quantitative Profiling of Tau and Phosphorylated Tau Peptides in Cerebrospinal Fluid by Mass Spectrometry Provides New Biomarker Candidates (2016)

Aberrant tau phosphorylation is a hallmark in Alzheimer's disease (AD), believed to promote formation of paired helical filaments, the main constituent of neurofibrillary tangles in the brain. While cerebrospinal fluid (CSF) levels of total tau and tau phosphorylated at threonine residue 181 (pThr181) are established core biomarkers for AD, the value of alternative phosphorylation sites, which may have more direct relevance to pathology, for early diagnosis is not yet known, largely due to their low levels in CSF and lack of standardized detection methods. To overcome sensitivity limitations for analysis of phosphorylated tau in CSF, we have applied an innovative mass spectrometry (MS) workflow, TMTcalibratortrademark, to enrich and enhance the detection of phosphoproteome components of AD brain tissue in CSF, and enable the quantitation of these analytes. We aimed to identify which tau species present in the AD brain are also detectable in CSF and which, if any, are differentially regulated with disease. Over 75% coverage of full-length (2N4R) tau was detected in the CSF with 47 phosphopeptides covering 31 different phosphorylation sites. Of these, 11 phosphopeptides were upregulated by at least 40%, along with an overall increase in tau levels in the CSF of AD patients relative to controls. Use of the TMTcalibratortrademark workflow dramatically improved our ability to detect tau-derived peptides that are directly related to human AD pathology. Further validation of regulated tau peptides as early biomarkers of AD is warranted and is currently being undertaken.