gebhart/patrepeval huggingface dataset:
Input Warping for Bayesian Optimization of Non-stationary Functions (2014)

Bayesian optimization has proven to be a highly effective methodology for the global optimization of unknown, expensive and multimodal functions. The ability to accurately model distributions over functions is critical to the effectiveness of Bayesian optimization. Although Gaussian processes provide a flexible prior over functions which can be queried efficiently, there are various classes of functions that remain difficult to model. One of the most frequently occurring of these is the class of non-stationary functions. The optimization of the hyperparameters of machine learning algorithms is a problem domain in which parameters are often manually transformed a priori, for example by optimizing in "log-space," to mitigate the effects of spatially-varying length scale. We develop a methodology for automatically learning a wide family of bijective transformations or warpings of the input space using the Beta cumulative distribution function. We further extend the warping framework to multi-task Bayesian optimization so that multiple tasks can be warped into a jointly stationary space. On a set of challenging benchmark optimization tasks, we observe that the inclusion of warping greatly improves on the state-of-the-art, producing better results faster and more reliably.
Genomic instability and alterations inApc,Mcc andDcc in Hong Kong patients with colorectal carcinoma (1999)

Our aim was to reveal the significance of tumor-suppressor genes and genomic instability in 99 Hong Kong Chinese colorectal carcinoma (CRC) patients by PCR-LOH analysis and PCR-PTT assay. The frequencies of allelic loss of Apc, Mcc and Dcc and of APC truncation were 31.3% (15/48), 11.6% (5/43), 44.4% (20/45) and 46/93 (49.5%), respectively. The frequency of Apc LOH was similar to, the Mcc LOH was lower than, and the Dcc LOH was higher than that reported for Caucasians and Japanese. In Hong Kong CRC patients, the replication error-positive (RER(+)) phenotype occurred with a frequency of 10% (10/99), which was similar to other results using microsatellite markers where RER(+) frequencies ranged from 11% to 28%. The rates of genetic alteration in RER(+) tumors were lower in tumors harboring p53, Mcc and Dcc alterations; similar in Apc; and higher in Ki-ras tumors compared with RER(-) tumors, though these differences did not achieve statistical significance. None of the biomarkers examined were predictive of survival independently, but strong trends confirming earlier observations of associations between RER(+) phenotypes with proximal tumor location and poorly differentiated tumor status were noted. The RER(+) phenotype was correlated significantly to the less aggressive Duke's stage B and improved prognosis. Additionally, tumors with RER(+) phenotypes were positively correlated with young age and sex. Our results support the observation that a subset of younger male CRC patients in Hong Kong may develop CRC via the RER pathway and show differences in RER status and sex. A significantly higher percentage of older Hong Kong Chinese CRC patients had APC truncations. Int. J. Cancer (Pred. Oncol.) 84:404-409, 1999.
Analysis of mammalian cell genetic regulation in situ by using retrovirus-derived "portable exons" carrying the Escherichia coli lacZ gene. (1989)

Self-inactivating derivatives of Moloney murine leukemia retrovirus containing the Escherichia coli lacZ gene were used to detect and study the regulation of transcription initiated at chromosomally located promoters in mouse fibroblasts. The introduction of splice acceptor sites in all three translational reading frames relative to lacZ and the inclusion of an in-frame ATG translation start codon in one construct allowed synthesis of beta-galactosidase fusion proteins upon insertion of retrovirus vectors containing lacZ into introns 3' to either protein-coding or noncoding exons. Selection of lacZ-expressing cells by fluorescence-activated cell sorting and the analysis of beta-galactosidase production after serum deprivation has yielded lines in which lacZ was fused to genes induced by growth arrest in the G0 state.
Re-tiling polygonal surfaces (1992)

article Free Access Share on Re-tiling polygonal surfaces Author: Greg Turk Department of Computer Science, University of North Carolina at Chapel Hill Department of Computer Science, University of North Carolina at Chapel HillView Profile Authors Info & Claims ACM SIGGRAPH Computer GraphicsVolume 26Issue 2July 1992 pp 55–64https://doi.org/10.1145/142920.134008Online:01 July 1992Publication History 540citation1,815DownloadsMetricsTotal Citations540Total Downloads1,815Last 12 Months73Last 6 weeks18 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 AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Fluvastatin Enhances the Inhibitory Effects of a Selective Angiotensin II Type 1 Receptor Blocker, Valsartan, on Vascular Neointimal Formation (2003)

These results suggest that the cholesterol-independent inhibition of AT1 receptor-mediated VSMC proliferation by statins may contribute to the beneficial effects of statins combined with an ARB on vascular diseases.
Stringent repression and homogeneous de‐repression by tetracycline of a modified CaMV 35S promoter in intact transgenic tobacco plants (1992)

Summary A cauliflower mosaic virus (CaMV) 35S promoter derivative, which is tightly repressed by the Tn 10 encoded Tet repressor in a transient expression system as well as in transgenic plants has been constructed. After treatment of transgenic plants with tetracycline (Tc) the activity of the reporter enzyme β‐glucuronidase (GUS) increased up to 500‐fold in tissue culture as well as under greenhouse conditions. Efficient derepression was achieved by Tc uptake through the roots as well as by Tc treatment of leaves of intact plants. As Tc is not very stable in the plants, this system can also be used for a transient expression of a transgene. This system provides a unique tool for regenerating transgenic plants carrying a repressed transgene and for efficiently de‐repressing its activity by a specific inducer at any time point of further development.
Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area (1991)

Protein folding and the transfer of hydrocarbons from a dilute aqueous solution to the pure liquid phase are thermodynamically similar in that both processes remove nonpolar surface from water and both are accompanied by anomalously large negative heat capacity changes. On the basis of a limited set of published surface areas, we previously proposed that heat capacity changes (delta C degrees p) for the transfer of hydrocarbons from water to the pure liquid phase and for the folding of globular proteins exhibit the same proportionality to the reduction in water-accessible nonpolar surface area (delta Anp) [Spolar, R.S., Ha, J.H., & Record, M.T., Jr. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 8382-8385]. The consequence of this proposal is that the experimental delta C degrees p for protein folding can be used to obtain estimates of delta Anp and of the contribution to the stability of the folded state from removal of a nonpolar surface from water. In this paper, a rigorous molecular surface area algorithm [Richmond, T.J. (1984) J. Mol. Biol. 178, 63-89] is applied to obtain self-consistent values of the water-accessible nonpolar surface areas of the native and completely denatured states of the entire set of globular proteins for which both crystal structures and delta C degrees p of folding have been determined and for the set of liquid and liquefiable hydrocarbons for which delta C degrees p of transfer are known. Both processes (hydrocarbon transfer and protein folding) exhibit the same direct proportionality between delta C degrees p and delta Anp. We conclude that the large negative heat capacity changes observed in protein folding and other self-assembly processes involving proteins provide a quantitative measure of the reduction in the water-accessible nonpolar surface area and of the contribution of the hydrophobic effect to the stability of the native state and to protein assembly.
Tissue Engineered Bone Formation Using Chitosan/Tricalcium Phosphate Sponges (2000)

These results suggest that the chitosan/TCP sponge is a feasible tool as a scaffolding material to grow osteoblast in a three-dimensional structure for transplantation into a site for bone regeneration.
What is expected of the SA Forestry Journal in future? : editorial (2005)

Extracted from text ... 
Editorial 
What is expected of the SA Forestry Journal in 
In an editorial on Journal achievements, in SAFJ No 
200 (March 2004), I posed the question in closing What 
of the future? and expressed the hope that our Journal 
would more aggressively promote the SAIF mission 
and assist forestry practitioners achieve and 
maintain excellence in the practice of forestry. 
We have now moved on a year and your Editorial 
team has given attention to the nature and future of the 
Journal. In this edition an editorial notice welcomes a 
great new Editorial Advisory Board and expresses 
disappointment that ..
Filamentous Phage Active on the Gram-Positive BacteriumPropionibacterium freudenreichii (2002)

We present the first description of a single-stranded DNA filamentous phage able to replicate in a gram-positive bacterium. Phage B5 infects Propionibacterium freudenreichii and has a genome consisting of 5,806 bases coding for 10 putative open reading frames. The organization of the genome is very similar to the organization of the genomes of filamentous phages active on gram-negative bacteria. The putative coat protein exhibits homology with the coat proteins of phages PH75 and Pf3 active on Thermus thermophilus and Pseudomonas aeruginosa, respectively. B5 is, therefore, evolutionarily related to the filamentous phages active on gram-negative bacteria.
Treatment of chronic hepatitis C: A systematic review (2002)

This systematic review addressed 3 issues regarding current treatments for chronic hepatitis C: (1) efficacy and safety in treatment-naive patients; (2) efficacy and safety in selected subgroups of patients; and (3) effects on long-term clinical outcomes. Electronic databases were searched for articles from January 1996 to March 2002. Additional articles were identified by searching references in pertinent articles and recent journals and by questioning experts. Articles were eligible for review if they reported original human data from a study that used virological, histological, or clinical outcome measures. For data collection, paired reviewers assessed the quality of each study and abstracted data. This systematic review found that the combination of high-dose peginterferon and ribavirin was more efficacious than standard interferon and ribavirin in persons infected with hepatitis C virus (HCV) genotype 1 (sustained virologic response [SVR] rate: 42% vs. 33%) and that ranges of SVR rates were higher with peginterferon than standard interferon monotherapy in naïve patients (10% to 39% vs. 3% to 19%). Reports were consistent in showing treatment with interferon and ribavirin was more efficacious than interferon monotherapy in treatment-naive persons and previous nonresponders and relapsers. Studies were moderately consistent in showing that treatment decreases the risk for hepatocellular carcinoma (HCC). The evidence on treatment in important subgroups was limited by a lack of randomized controlled trials. Thus, the combination of peginterferon and ribavirin was the most efficacious treatment in patients with HCV genotype 1. Long-term outcomes were improved in patients with hepatitis C who achieved an SVR with treatment.
Regulatable Arabinose-Inducible Gene Expression System with Consistent Control in All Cells of a Culture (2000)

The arabinose-inducible promoter P(BAD) is subject to all-or-none induction, in which intermediate concentrations of arabinose give rise to subpopulations of cells that are fully induced and uninduced. To construct a host-vector expression system with regulatable control in a homogeneous population of cells, the araE gene of Escherichia coli was cloned into an RSF1010-derived plasmid under control of the isopropyl-beta-D-thiogalactopyranoside-inducible P(tac) and P(taclac) promoters. This gene encodes the low-affinity, high-capacity arabinose transport protein and is controlled natively by an arabinose-inducible promoter. To detect the effect of arabinose-independent araE expression on population homogeneity and cell-specific expression, the gfpuv gene was placed under control of the arabinose-inducible araBAD promoter (P(BAD)) on the pMB1-derived plasmid pBAD24. The transporter and reporter plasmids were transformed into E. coli strains with native arabinose transport systems and strains deficient in one or both of the arabinose transport systems (araE and/or araFGH). The effects of the arabinose concentration and arabinose-independent transport control on population homogeneity were investigated in these strains using flow cytometry. The araE, and araE araFGH mutant strains harboring the transporter and reporter plasmids were uniformly induced across the population at all inducer concentrations, and the level of gene expression in individual cells varied with arabinose concentration. In contrast, the parent strain, which expressed the native araE and araFGH genes and harbored the transporter and reporter plasmids, exhibited all-or-none behavior. This work demonstrates the importance of including a transport gene that is controlled independently of the inducer to achieve regulatable and consistent induction in all cells of the culture.
"The Old Adorns the New": Reading the Book of Mormon in Light of the Bible (2000)

Book Review| January 01 2000 "The Old Adorns the New": Reading the Book of Mormon in Light of the Bible From Jerusalem to Zarahemla: Literary and Historical Studies of the Book of Mormon, S. Kent Brown. David Rolph Seely David Rolph Seely Search for other works by this author on: This Site Google FARMS Review of Books (2000) 12 (2000) (2): 39–43. https://doi.org/10.2307/44797067 Cite Icon Cite Share Icon Share Facebook Twitter LinkedIn MailTo Permissions Search Site Citation David Rolph Seely; "The Old Adorns the New": Reading the Book of Mormon in Light of the Bible. FARMS Review of Books 1 January 2000; 12 (2000) (2): 39–43. doi: https://doi.org/10.2307/44797067 Download citation file: Zotero Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All Scholarly Publishing CollectiveUniversity of Illinois PressMormon Studies Review Search Advanced Search The text of this article is only available as a PDF. © 2000 Foundation for Ancient Research and Mormon Studies at Brigham Young University2000 Article PDF first page preview Close Modal You do not currently have access to this content.
Polyubiquitin-regulated DsRed marker for transgenic insects. (2001)

Genetic transformation of most insect systems requires dominant-acting markers that do not depend on reverting a mutant phenotype in a host strain, andfor this purpose GFP has proven to be useful in several insect orders. However, detection of multiple transgenes and reporters for gene expression requires the development of new visible markers that can be unambiguously detected when co-expressed with GFP The DsRed fluorescentprotein has spectral characteristics that are most distinct from GFP and GFP variants, and we have explored the use of DsRed as a selectable marker for piggyBac transformation in Drosophila melanogaster and its use as a reporter when co-expressed with GFP. Transformants marked with polyubiquitin-regulated DsRed1 were detected throughout development at a relatively high frequency, and they exhibited brighter fluorescence than transformants marked with EGFP. The use of a Texas Red filter set eliminated detection of EGFP fluorescence and autofluorescence, and DsRed expressedfrom a reporter construct could be unambiguously detected when co-expressed with EGFP DsRed should prove to be a highly efficient marker system for the selection of transformant insects and as a reporter in gene expression studies.
Reduction of voltage-length product for Y-branch digital optical switch (1993)

A structure which shows a nearly constant mode coupling peak for a wide guide asynchronism range is described. The device exhibits low drive voltage and crosstalk
High-efficiency gene transfer into skeletal muscle mediated by electric pulses (1999)

Gene delivery to skeletal muscle is a promising strategy for the treatment of muscle disorders and for the systemic secretion of therapeutic proteins. However, present DNA delivery technologies have to be improved with regard to both the level of expression and interindividual variability. We report very efficient plasmid DNA transfer in muscle fibers by using square-wave electric pulses of low field strength (less than 300 V/cm) and of long duration (more than 1 ms). Contrary to the electropermeabilization-induced uptake of small molecules into muscle fibers, plasmid DNA has to be present in the tissue during the electric pulses, suggesting a direct effect of the electric field on DNA during electrotransfer. This i.m. electrotransfer method increases reporter and therapeutic gene expression by several orders of magnitude in various muscles in mouse, rat, rabbit, and monkey. Moreover, i.m. electrotransfer strongly decreases variability. Stability of expression was observed for at least 9 months. With a pCMV-FGF1 plasmid coding for fibroblast growth factor 1, this protein was immunodetected in the majority of muscle fibers subjected to the electric pulses. DNA electrotransfer in muscle may have broad applications in gene therapy and in physiological, pharmacological, and developmental studies.
Analysis of the absorbance spectra of skin lesions as a helpful tool for detection of major pathophysiological changes (2004)

Background/aims: Although reflectance spectrophotometry is often applied to measurement of skin color, raw data of reflectance spectra of normal and lesional skin are difficult to analyze. The purpose of this pilot study was to determine whether measurement of spectral difference in absorbance (SDA) between various skin lesions and normal skin adjacent to them could yield useful information for clinics in dermatology. Methods: We studied spectral reflectance of a total of 173 various skin lesions. After converting obtained reflectance into apparent absorbance A (=log 10 (1/reflectance)), we examined the profile of SDA, that is, A lesion − A normal skin in the range of 400–700 nm, and compared them with the absorbance spectra of melanin and hemoglobin. Results: SDA of epidermal pigmentary disorders was similar to the absorption spectrum of melanin in vitro , but the cases with intradermal melanin deposition showed a different pattern, reflecting the scattering effect of the dermis. SDA of erythematous lesions was similar to the spectra of either oxygenated or reduced hemoglobin, and varied according to the oxygenated level of cutaneous blood. SDA of lesions with a combination of factors appeared as a simple summation of spectra corresponding to each of the factors. Conclusion: Our method may offer easy and quick detection of major pathophysiological changes in skin lesions.
Chemical Dissection of Protein Translocation through the Anthrax Toxin Pore (2011)

Through the pore: The N-terminal domain of the lethal factor of anthrax toxin was modified to probe protein translocation through the toxin pore. Replacing acidic residues with cysteic acid inhibited translocation, whereas introduction of D-amino acids or an alternating Lys–Glu sequence had no effect. The findings demonstrate independence of translocation from stereospecificity and strict sequence, and dependence on the charge state of acidic residues.
Sequence of a Specifically Encapsidated RNA Fragment Originating from the Tobacco‐Mosaic‐Virus Coat‐Protein Cistron (1975)

When 25-S tobacco mosaic virus (TMV) protein aggregate and TMV RNA, which has been partially digested by T1 RNase, are mixed under conditions suitable for reconstitution, only a few RNA fragments are encapsidated. These fragments were isolated and purified by polyacrylamide gel electrophoresis. The sequence of the three main fragments, the longest of which (fragment 1) was estimated to contain 103 nucleotides, has been determined. The two smaller fragments are portions of the longer chain produced by an additional specific scission. Because of the great affinity of 25-S TMV protein for this nucleotide sequence, it will be referred to as the "specifically encapsidated RNA fragment". The occurrence of a "hidden break" in the sequence has been demonstrated: fragment 1, purified by electrophoresis on a polyacrylamide gel without 8 M urea, gives rise upon further electroporesis in the presence of urea to two new bands corresponding to the two halves of the molecule. A stable hair-pin secondary structure has been derived from the base sequence which can account for the specificity of action of the enzyme. Because of its properties, we have suggested elsewhere that the sequence of fragment 1 might correspond to the disk recognition site for reconstitution, which is known to be located at the 5' end of the intact RNA. But experiments with TMV RNA whose 5'-OH end has been radioactively phosphorylated with polynucleotide kinase show that this is not the case. Analysis of the amino acid coding capacity of the fragment has instead revealed that fragment 1 is a portion of the TMV coat protein cistron.
The Lymphoproliferative Disease of Granular Lymphocytes: Updated Criteria for Diagnosis (1997)

The lymphoproliferative disease of granular lymphocytes (LDGL), also referred to as LGL leukemia, is a heterogeneous disorder, but is clinically, morphologically, and immunologically distinct. Although LDGL has recently been included in the revised classification of lymphomas as an independent clinical entity, no consensus exists on the criteria to establish the diagnosis. The aim of this report was to refine the parameters needed to make the diagnosis of LDGL. We studied 11 patients with chronic granular lymphocytosis selected from among 195 cases observed by our institutions from three different geographic areas (North America, Europe, and Asia). These cases did not meet the current criteria for inclusion in LDGL, since all patients had less than 2,000 GL/microL. However, in each of these patients, we found evidence for expansion of a discrete GL population. Clonal rearrangement of the T-cell receptor (TCR) beta gene was found in peripheral blood mononuclear cells (PBMC) of all nine patients with CD3+ LDGL. Using recently generated monoclonal antibodies (MoAbs) against the TCR V beta gene regions, we identified a unique TCR V beta on GL from each of three patients studied. In two patients with CD3- LDGL, we also identified a restricted pattern of reactivity, by staining with MoAbs against p58 antigen found on normal natural killer (NK) cells. The clinical features of these 11 patients with relatively low absolute number of GL were similar to those reported previously for patients with greater than 2,000 GL/microL. These data demonstrate that newer techniques such as MoAbs against V beta gene regions and p58 molecules and molecular analyses are useful to identify expansions of discrete GL proliferations. Demonstration of an expansion of a restricted GL subset is evidence for the diagnosis of LDGL, even in patients with a relatively low GL count. Our results also contribute to distinguish between the end of normality and the beginning of pathology in the broad spectrum of GL lymphocytoses.