gebhart/patrepeval huggingface dataset:
Control of Amino Acid Permease Sorting in the Late Secretory Pathway of <i>Saccharomyces cerevisiae</i> by <i>SEC13, LST4, LST7</i> and <i>LST78</i> (1997)

The SEC13 gene was originally identified by temperature-sensitive mutations that block all protein transport from the ER to the Golgi. We have found that at a permissive temperature for growth, the sec13-1 mutation selectively blocks transport of the nitrogen-regulated amino acid permease, Gap1p, from the Golgi to the plasma membrane, but does not affect the activity of constitutive permeases such as Hip1p, Can1p, or Lyp1p. Different alleles of SEC13 exhibit different relative effects on protein transport from the ER to the Golgi, or on Gap1p activity, indicating distinct requirements for SEC13 function at two different steps in the secretory pathway. Three new genes, LST4, LST7, and LST8, were identified that are also required for amino acid permease transport from the Golgi to the cell surface. Mutations in LST4 and LST7 reduce the activity of the nitrogen-regulated permeases Gap1p and Put4p, whereas mutations in LST8 impair the activities of a broader set of amino acid permeases. The LST8 gene encodes a protein composed of WD-repeats and has a close human homologue. The LST7 gene encodes a novel protein. Together, these data indicate that SEC13, LST4, LST7, and LST8 function in the regulated delivery of Gap1p to the cell surface, perhaps as components of a post-Golgi secretory-vesicle coat.
Evidence for <i>in vivo</i> but not <i>in vitro</i> expression of a <i>Borrelia burgdorferi</i> outer surface protein F (OspF) homologue (1995)

Protein export signals from the low-passage 297 strain of Borrelia burgdorferi were cloned as fusions with an Escherichia coli alkaline phosphatase (PhoA) reporter lacking a signal sequence. One PhoA+ clone (BbK2.10-PhoA) was derived from a borrelial lipoprotein. Although the polypeptide encoded by the full-length bbk2.10 gene had 76% similarity and 56% identity to outer surface protein F (OspF) from B. burgdorferi strain N40, antibodies directed against recombinant forms of the two proteins revealed that they were not cross-reactive. The nucleotide sequences of bbk2.10 and ospF from the N40 and 297 strains, respectively, were determined to confirm that the N40 and 297 strains each contained both genes. Southern blot analysis revealed that bbk2.10 is a single-copy gene and that the B. burgdorferi strain 297 and N40 genomes appeared to contain one other gene more closely related to ospF than bbk2.10. It was particularly noteworthy that ospF, but not bbk2.10, was expressed in vitro while B. burgdorferi-infected mice generated antibodies reactive with both lipoproteins. To help confirm that the BbK2.10-reactive antibodies produced by the B. burgdorferi-infected mice were specific for that protein, a second gene, bbk2.11, which hybridized with the ospF probe was cloned; the corresponding polypeptide reacted strongly with OspF antisera but failed to react with BbK2.10-specific antisera. Taken together, these data demonstrate that BbK2.10, BbK2.11, and OspF comprise a B. burgdorferi lipoprotein family and that at least one member (BbK2.10) appears to be expressed only during infection.
Multiplexed Surrogate Analysis of Glycotransferase Activity in Whole Biospecimens (2013)

Dysregulated glycotransferase enzymes in cancer cells produce aberrant glycans--some of which can help facilitate metastases. Within a cell, individual glycotransferases promiscuously help to construct dozens of unique glycan structures, making it difficult to comprehensively track their activity in biospecimens--especially where they are absent or inactive. Here, we describe an approach to deconstruct glycans in whole biospecimens then analytically pool together resulting monosaccharide-and-linkage-specific degradation products ("glycan nodes") that directly represent the activities of specific glycotransferases. To implement this concept, a reproducible, relative quantitation-based glycan methylation analysis methodology was developed that simultaneously captures information from N-, O-, and lipid linked glycans and is compatible with whole biofluids and homogenized tissues; in total, over 30 different glycan nodes are detectable per gas chromatography-mass spectrometry (GC-MS) run. Numerous nonliver organ cancers are known to induce the production of abnormally glycosylated serum proteins. Thus, following analytical validation, in blood plasma, the technique was applied to a group of 59 lung cancer patient plasma samples and age/gender/smoking-status-matched non-neoplastic controls from the Lung Cancer in Central and Eastern Europe (CEE) study to gauge the clinical utility of the approach toward the detection of lung cancer. Ten smoking-independent glycan node ratios were found that detect lung cancer with individual receiver operating characteristic (ROC) c-statistics ranging from 0.76 to 0.88. Two glycan nodes provided novel evidence for altered ST6Gal-I and GnT-IV glycotransferase activities in lung cancer patients. In summary, a conceptually novel approach to the analysis of glycans in unfractionated human biospecimens has been developed that, upon clinical validation for specific applications, may provide diagnostic and/or predictive information in glycan-altering diseases.
Invited communication. Adhesion between living tissue and plastics. I. Adhesion of epoxy and polyurethane resins to dentin and enamel (1969)

Abstract In previous papers, 3,4 we have discussed the synthesis of epoxy resins suitable for dental and orthopedic adhesives. In this paper we have outlined our research on two other critical aspects: surface preparation and test methods.
Ultraviolet Plasmonic Chirality from Colloidal Aluminum Nanoparticles Exhibiting Charge‐Selective Protein Detection (2015)

Chiral aluminum nanoparticles, dispersed in water, are prepared, which provide strong ultraviolet plasmonic circular dichroism, high-energy superchiral near-fields, and charge-selective protein detection.
The MYB46 Transcription Factor Is a Direct Target of SND1 and Regulates Secondary Wall Biosynthesis in <i>Arabidopsis</i> (2007)

We demonstrate that the Arabidopsis thaliana MYB46 transcription factor is a direct target of SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1), which is a key transcriptional activator regulating the developmental program of secondary wall biosynthesis. The MYB46 gene is expressed predominantly in fibers and vessels in stems, and its encoded protein is targeted to the nucleus and can activate transcription. MYB46 gene expression was shown to be regulated by SND1, and transactivation analysis demonstrated that SND1 as well as its close homologs were able to activate the MYB46 promoter. Electrophoretic mobility shift assays and chromatin immunoprecipitation experiments revealed that SND1 binds to the MYB46 promoter. Dominant repression of MYB46 caused a drastic reduction in the secondary wall thickening of fibers and vessels. Overexpression of MYB46 resulted in an activation of the biosynthetic pathways of cellulose, xylan, and lignin and concomitantly led to ectopic deposition of secondary walls in cells that are normally nonsclerenchymatous. In addition, the expression of two secondary wall-associated transcription factors, MYB85 and KNAT7, was highly upregulated by MYB46 overexpression. These results demonstrate that MYB46 is a direct target of SND1 and is another key player in the transcriptional network involved in the regulation of secondary wall biosynthesis in Arabidopsis.
Gas‐Phase Nucleophilic Aromatic Substitution between Piperazine and Halobenzyl Cations: Reactivity of the Methylene Arenium Form of Benzyl Cations (2011)

Methylene arenium involved in SNAr: The gas-phase nucleophilic aromatic substitution reactions of halobenzyl cations with piperazine through a cationic σ complex were studied using ESI mass spectrometry. This study demonstrates that the methylene arenium form of halobenzyl cations exhibits nucleophilic substitution reactivity at the phenyl ring (see scheme).
The effect of different carbon and nitrogen sources on the activity of glutamine synthetase and glutamate dehydrogenase in lupine embryonic axes (1981)

Embryos of yellow lupine ( Lupinus luteus L. cv. Jantar), deprived of cotyledons, were incubated for 72 h in media containing various combinations of saccharose, ammonia, nitrate, glutamine and asparagine. Induction of glutamine synthetase (GS) was observed in embryos in media containing saccharose while the activity of this enzyme was inhibited by glutamine, asparagine and ammonia in the absence of sugar. The above mentioned nutritional factors had an opposite effect on the activity of glutamate dehydrogenase (GDH). Changes in glutamate dehydrogenase activity were preceded by reverse changes in the activity of glutamine synthetase. The possibility of GDH repression by GS in lupine embryos is discussed.
[Vascularization and resorption of different supporting tissues by the greater omentum in the formation of compound microvascular transplants]. (1985)

In former investigations the author described the use of omentum majus in building microsurgical compound island flaps employing supporting tissue. Now different kinds of hard tissue, such as autogenous bone and cartilage, allogenous bone and cartilage (preserved by Cialit-solution), Teflon-Fluorocarbon Polymer (Proplast) and tri-calcium phosphate were presented in omentum-sandwich flaps in a histological investigation. We paid special attention to resorption and vascularisation of hard tissue. Allogenous cartilage grafts or artificial materials like Proplast were the most suitable to put into a compound omental island flap. There was good vascularisation with no resorption, especially with Proplast.
Gamma-Retroviral Vector Design for the Co-Expression of Artificial microRNAs and Therapeutic Proteins (2014)

To generate γ-retroviral vectors for stable conjoint expression of artificial microRNAs (amiR) and therapeutic genes in primary human lymphocytes, and to identify the design parameters that are key for successful vector generation. Gamma-retroviral vectors were designed to co-express both amiRs and a linked reporter gene, truncated CD34 (tCD34). Artificial miRs based on microRNAs miR-16, miR-142, miR-146b, miR-150, miR155, and miR-223 were inserted into sites within the intron of the vector and tested for tCD34 expression by flow cytometry (FACS). Different constructs were assembled with amiRs targeted to knockdown expression of suppressor of cytokine signaling 1 (SOCS1) or programmed cell death 1 (PDCD1, PD-1). Three of the six amiRs maintained tCD34 expression. Expansion of primary human T cells transduced with these amiR vectors, as well as transgene expression, were equivalent to control engineered T cells over a 40-day period. Knockdown of SOCS1 RNA and PD-1 expression by FACS was shown to vary between constructs, dependent on either the specific short interfering RNA sequence used in the amiR, or the microRNA backbone and location in the vector intron. Gamma-retroviral vectors that both efficiently knockdown endogenous gene expression and maintain linked transgene production can be produced, but empirical vector evaluations were best suited for optimal construct analysis.
Is the higher incidence of ischemic disease in patients with hypertension and diabetes related to intracellular depletion of high energy metabolites? (1994)

To study mechanisms underlying ischemia in hypertension and non-insulin dependent diabetes mellitus (NIDDM), 31P-magnetic resonance spectroscopy was used to evaluate adenosine triphosphate and 2,3 diphosphoglycerate (2,3 DPG) levels in erythrocytes of control (n = 21), hypertensive (n = 22), and NIDDM (n = 10) subjects. Compared to adenosine triphosphate levels in controls (2.22 +/- 0.10 mM), both hypertensive (1.89 +/- 0.10 mM, sig = 0.05 versus normal) and NIDDM subjects (1.57 +/- 0.13 mM, sig = 0.05 versus normal) exhibited lower values. NIDDM subjects also displayed suppressed levels of 2,3 DPG (6.84 +/- 0.48 mM, sig = 0.05 versus normal and EH), compared to hypertensives (8.34 +/- 0.27 mM). These data suggest cellular energy metabolism is disrupted in hypertension and NIDDM. Both conditions may thereby sensitize tissues to ischemic damage, lower adenosine triphosphate levels by decreasing energy reserves, and lower 2,3 DPG levels by inhibiting hemoglobin-oxygen dissociation.
Mutational analysis of <i>slyD</i>, an <i>Escherichia coli</i> gene encoding a protein of the FKBP immunophilin family (1997)

slyD encodes a 196 amino acid polypeptide that is a member of the FKBP family of cis-trans peptidyl-prolyl isomerases (PPlases). slyD mutations affect plaque formation by the phage phiX174 by blocking the action of the phage lysis protein E. Here we describe the selection of a set of spontaneous slyD mutations conferring resistance to the expression of gene E from a plasmid. These mutations occur disproportionately in residues of SlyD that, based on the structure of the prototype mammalian FKBP12, make ligand contacts with immunosuppressing drug molecules or are conserved in other FKBP proteins. A wide variation in the plating efficiency of phiX174 on these E(R) strains is observed, relative to the parental, indicating that these alleles differ widely in residual SlyD activity. Moreover, it is found that slyD mutations cause significant growth rate defects in Escherichia coli B and C backgrounds. Finally, overexpression of slyD causes filamentation of the host. Thus, among the FKBP genes found in organisms across the evolutionary spectrum, slyD is unique in having three distinct drug-independent phenotypes.
Changes in maturation‐promoting activity in the cytoplasm of pig oocytes throughout maturation (1991)

Maturation-promoting factor (MPF) was examined in maturing pig oocytes by electrofusing them with germinal vesicle (GV) oocytes. Oocytes containing high levels of MPF (MI or MII stages) induced the breakdown of the GV introduced by fusion and the formation of the metaphase plate in 1 hr. A similar effect was seen when two or three GV oocytes were fused with a MII oocyte and then incubated for 1 hr in the presence of cycloheximide (a specific protein synthesis inhibitor), indicating that high levels of preformed MPF are present at the metaphase stage. During the maturation in vitro of cumulus-enclosed oocytes, a first sharp rise in MPF was seen between 26 and 29 hr of culture (MI stage); MPF declined after 2 hr (AI-TI stages) and again reached high levels at 35 hr, where it remained for the rest of maturation. Denuded oocytes showed a similar behavior, but MPF appeared 9 hr earlier and the rise, due to the asynchronous maturation of these oocytes, was not as sharp as in cumulus enclosed oocytes. Cycloheximide was used to study protein synthesis requirements for oocyte maturation. Intact GV were observed after 44 hr of culture when cycloheximide was added at 26 hr or earlier, and chromosome decondensation and pronuclear formation were observed when the drug was added at 32 hr. Transcriptional requirements were investigated by treating the oocytes with alpha-amanitin, an RNA polymerase inhibitor. This drug could completely inhibit the maturation of cumulus-enclosed oocytes, but this was a somatic cell-mediated effect since denuded oocytes were insensitive to this treatment.(ABSTRACT TRUNCATED AT 250 WORDS)
DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing (2017)

The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person's lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2-90 years) analysed with Illumina's genome-wide methylation platforms (27K/450K). Applying stepwise regression for variable selection, 23 of these CpG sites were identified that could significantly contribute to age prediction modelling and multiple regression analysis carried out with these markers provided an accurate prediction of age (R<sup>2</sup>=0.92, mean absolute error (MAE)=4.6 years). However, applying machine learning, and more specifically a generalised regression neural network model, the age prediction significantly improved (R<sup>2</sup>=0.96) with a MAE=3.3 years for the training set and 4.4 years for a blind test set of 231 cases. The machine learning approach used 16 CpG sites, located in 16 different genomic regions, with the top 3 predictors of age belonged to the genes NHLRC1, SCGN and CSNK1D. The proposed model was further tested using independent cohorts of 53 monozygotic twins (MAE=7.1 years) and a cohort of 1011 disease state individuals (MAE=7.2 years). Furthermore, we highlighted the age markers' potential applicability in samples other than blood by predicting age with similar accuracy in 265 saliva samples (R<sup>2</sup>=0.96) with a MAE=3.2 years (training set) and 4.0 years (blind test). In an attempt to create a sensitive and accurate age prediction test, a next generation sequencing (NGS)-based method able to quantify the methylation status of the selected 16 CpG sites was developed using the Illumina MiSeq<sup>®</sup> platform. The method was validated using DNA standards of known methylation levels and the age prediction accuracy has been initially assessed in a set of 46 whole blood samples. Although the resulted prediction accuracy using the NGS data was lower compared to the original model (MAE=7.5years), it is expected that future optimization of our strategy to account for technical variation as well as increasing the sample size will improve both the prediction accuracy and reproducibility.
Introduction to optimization (2004)

A modern, up-to-date introduction to optimization theory and methods This authoritative book serves as an introductory text to optimization at the senior undergraduate and beginning graduate levels. With consistently accessible and elementary treatment of all topics, An Introduction to Optimization, Second Edition helps students build a solid working knowledge of the field, including unconstrained optimization, linear programming, and constrained optimization. Supplemented with more than one hundred tables and illustrations, an extensive bibliography, and numerous worked examples to illustrate both theory and algorithms, this book also provides: * A review of the required mathematical background material * A mathematical discussion at a level accessible to MBA and business students * A treatment of both linear and nonlinear programming * An introduction to recent developments, including neural networks, genetic algorithms, and interior-point methods * A chapter on the use of descent algorithms for the training of feedforward neural networks * Exercise problems after every chapter, many new to this edition * MATLAB(r) exercises and examples * Accompanying Instructor's Solutions Manual available on request An Introduction to Optimization, Second Edition helps students prepare for the advanced topics and technological developments that lie ahead. It is also a useful book for researchers and professionals in mathematics, electrical engineering, economics, statistics, and business.
Measurement unit invariant coefficients in multiplicative-logarithmic functions (1995)

It has been demonstrated that the coefficients of the non-multiplicative terms of a multiplicative-logarithmic function are dependent on the units used. In addition, Dickey-Fuller tests on the multiplicative terms are unit sensitive. It is demonstrated that a simple transformation circumvents these problems. It is still true that individual coefficients of logarithmic variables in such functions are meaningless and that the Dickey–Fuller test is disturbingly arbitary. However, the transformation appears to increase the meaningfulness of a technical change trend in a translog cost function.
Sensitivity of PCA for traffic anomaly detection (2007)

Detecting anomalous traffic is a crucial part of managing IP networks. In recent years, network-wide anomaly detection based on Principal Component Analysis (PCA) has emerged as a powerful method for detecting a wide variety of anomalies. We show that tuning PCA to operate effectively in practice is difficult and requires more robust techniques than have been presented thus far. We analyze a week of network-wide traffic measurements from two IP backbones (Abilene and Geant) across three different traffic aggregations (ingress routers, OD flows, and input links), and conduct a detailed inspection of the feature time series for each suspected anomaly. Our study identifies and evaluates four main challenges of using PCA to detect traffic anomalies: (i) the false positive rate is very sensitive to small differences in the number of principal components in the normal subspace, (ii) the effectiveness of PCA is sensitive to the level of aggregation of the traffic measurements, (iii) a large anomaly may in advertently pollute the normal subspace, (iv) correctly identifying which flow triggered the anomaly detector is an inherently challenging problem.
Mixed-initiative planning, replanning and execution: From concept to field testing using AUV fleets (2017)

Mission planning and execution for autonomous vehicles is crucial for their effective and efficient operation during scientific exploration, or search and rescue missions, to mention a few. Automated Planning has shown to be a useful tool for “high level” mission planning, that is, allocating tasks to vehicles while following given constraints (e.g., energy, collision avoidance). In this paper, we focus on making mission planning flexible and robust. That is, a human mission coordinator can modify tasks during the mission execution, so the tasks have to be dynamically reallocated during the process. Moreover, we assume that communication might not be reliable when vehicles are “outside”, i.e., performing the tasks, and thus we enforce vehicles to come back to their safe spots regularly. To address these requirements, we have developed two models, namely “all tasks” and “one round”, and integrated them to the control software. We have evaluated our approach in a field experiment focused on a mine-hunting scenario.
Commutation quality factor of two-state switchable devices (2000)

A unified way to characterize a two-state one-port switchable network is discussed in this paper. A figure-of-merit of the two-state one-port, called the commutation quality factor (CQF), is introduced. It can be applied to different types of switching devices (semiconductor, ferroelectric, superconductor, etc.) and used for a design of two-state components with optimal characteristics. The CQF is defined as the ratio of the input impedances of a lossless reciprocal two-port terminated in the impedance pair Z/sub 1/ and Z/sub 2/, provided the imaginary parts of both input impedances are zero. A simple formula is derived for a calculation of the CQF. The invariance of the CQF with respect to lossless reciprocal transformation is shown. The applicability of the CQF does not depend on the physical nature of the device. The CQF is a working tool for a selection of switching devices while designing electronically controlled microwave components and subsystems. The CQF is recommended to be used for determining the available minimum of insertion loss of a switching microwave component. Thus, the introduced CQF can be used for optimization of the switching microwave component designed.