gebhart/patrepeval huggingface dataset:
Microbial Conversion of Glycerol to 1,3-Propanediol by an Engineered Strain of Escherichia coli (2009)

In an effort to improve industrial production of 1,3-propanediol (1,3-PD), we engineered a novel polycistronic operon under the control of the temperature-sensitive lambda phage P(L)P(R) promoter regulated by the cIts857 repressor and expressed it in Escherichia coli K-12 ER2925. The genes for the production of 1,3-PD in Clostridium butyricum, dhaB1 and dhaB2, which encode the vitamin B(12)-independent glycerol dehydratase DhaB1 and its activating factor, DhaB2, respectively, were tandemly arrayed with the E. coli yqhD gene, which encodes the 1,3-propanediol oxidoreductase isoenzyme YqhD, an NADP-dependent dehydrogenase that can directly convert glycerol to 1,3-PD. The microbial conversion of 1,3-PD from glycerol by this recombinant E. coli strain was studied in a two-stage fermentation process. During the first stage, a novel high-cell-density fermentation step, there was significant cell growth and the majority of the metabolites produced were organic acids, mainly acetate. During the second stage, glycerol from the fresh medium was rapidly converted to 1,3-PD following a temperature shift from 30 degrees C to 42 degrees C. The by-products were mainly pyruvate and acetate. During this two-stage process, the overall 1,3-PD yield and productivity reached 104.4 g/liter and 2.61 g/liter/h, respectively, and the conversion rate of glycerol to 1,3-PD reached 90.2% (g/g). To our knowledge, this is the highest reported yield and productivity efficiency of 1,3-PD with glycerol as the sole source of carbon. Furthermore, the overall fermentation time was only 40 h, shorter than that of any other reports.
The NADPH-cytochrome P450 Reductase Gene from Gibberella fujikuroi Is Essential for Gibberellin Biosynthesis (2004)

The fungus Gibberella fujikuroi is used for the commercial production of gibberellins (GAs), which it produces in very large quantities. Four of the seven GA biosynthetic genes in this species encode cytochrome P450 monooxygenases, which function in association with NADPH-cytochrome P450 reductases (CPRs) that mediate the transfer of electrons from NADPH to the P450 monooxygenases. Only one cpr gene (cpr-Gf) was found in G. fujikuroi and cloned by a PCR approach. The encoded protein contains the conserved CPR functional domains, including the FAD, FMN, and NADPH binding motifs. cpr-Gf disruption mutants were viable but showed a reduced growth rate. Furthermore, disruption resulted in total loss of GA(3), GA(4), and GA(7) production, but low levels of non-hydroxylated C(20)-GAs (GA(15) and GA(24)) were still detected. In addition, the knock-out mutants were much more sensitive to benzoate than the wild type due to loss of activity of another P450 monooxygenase, the detoxifying enzyme, benzoate p-hydroxylase. The UV-induced mutant of G. fujikuroi, SG138, which was shown to be blocked at most of the GA biosynthetic steps catalyzed by P450 monooxygenases, displayed the same phenotype. Sequence analysis of the mutant cpr allele in SG138 revealed a nonsense mutation at amino acid position 627. The mutant was complemented with the cpr-Gf and the Aspergillus niger cprA genes, both genes fully restoring the ability to produce GAs. Northern blot analysis revealed co-regulated expression of the cpr-Gf gene and the GA biosynthetic genes P450-1, P450-2, P450-4 under GA production conditions (nitrogen starvation). In addition, expression of cpr-Gf is induced by benzoate. These results indicate that CPR-Gf is the main but not the only electron donor for several P450 monooxygenases from primary and secondary metabolism.
DART (2005)

We present a new tool, named DART, for automatically testing software that combines three main techniques: (1) automated extraction of the interface of a program with its external environment using static source-code parsing; (2) automatic generation of a test driver for this interface that performs random testing to simulate the most general environment the program can operate in; and (3) dynamic analysis of how the program behaves under random testing and automatic generation of new test inputs to direct systematically the execution along alternative program paths. Together, these three techniques constitute Directed Automated Random Testing , or DART for short. The main strength of DART is thus that testing can be performed completely automatically on any program that compiles -- there is no need to write any test driver or harness code. During testing, DART detects standard errors such as program crashes, assertion violations, and non-termination. Preliminary experiments to unit test several examples of C programs are very encouraging.
Immunoassay with Electrochemical Detection (1987)

This chapter contains sections titled: Introduction Enzyme Label Catalyzing Production of Electroactive Product Nonenzymatic Electroactive Labels Conclusions
Three‐Dimensional Assessment of Cam Engagement in Femoroacetabular Impingement (2010)

Typically, during internal rotation in 90° of flexion, the centromedial portion of the cam lesion was found to abut against the anterosuperior quadrant of the acetabular cartilage. During abduction and flexion, this appeared to be the lateral and medial portions of the cam lesion, respectively. All motions causing cam intrusion appeared to focus on the same cartilage area of the acetabulum in its anterosuperior quadrant.
Production of targeted aromatics by using Diels–Alder classes of reactions with furans and olefins over ZSM-5 (2012)

In this paper we study the co-feeding of olefins (ethylene and propylene) with a series of furanic compounds (furan, 2-methylfuran, furfural, and furfuryl alcohol) over ZSM-5 catalyst in a continuous flow fixed-bed reactor at a temperature range of 450–600 °C. We show the importance of Diels–Alder cycloaddition reactions when olefins are co-fed with furanics over ZSM-5. Co-feeding propylene with furan (C4 diene) increased the toluene aromatic selectivity from 22% to 59%. Similarly, co-feeding propylene with 2-methylfuran (C5 diene) increased the xylenes aromatic selectivity from 9% to 27%. Co-feeding of ethylene with furans did not change the aromatics selectivity. The increase of toluene selectivity was also observed in the co-feeding of propylene with furfural and fufuryl alcohol. Furfural and furfuryl alcohol both underwent decarbonylation reactions to produce CO and furan. The reaction conditions that maximize Diels–Alder products were a propylene to 2MF molar ratio of 1 at 450 °C. Increasing the temperature to 600 °C increased the selectivity of benzene, toluene and CO. Decreasing the temperature to 300 °C increased the coke yield and decreased the xylene yield. The xylene selectivity went through a maximum at a propylene to 2-methylfuran molar ratio of 1 : 1.
Microbial siderophore-mediated transport (2002)

Microbial iron chelates, called siderophores, are synthesized by bacteria and fungi in response to low iron availability in the environment. The present review summarizes structural details of siderophore ligands with respect to their transport properties. This presentation is largely centred on the occurrence and function of siderophores in the various bacterial and fungal genera.
Analysis of Factor XIII Substrate Specificity Using Recombinant Human Factor XIII and Tissue Transglutaminase Chimeras (1997)

Human factor XIII (FXIII) and tissue transglutaminase (tTG) are homologous proteins. FXIII requires thrombin for activation and cross-links the gamma chains of fibrin(ogen) more efficiently than the Aalpha chains. On the other hand, tTG is thrombin-independent and forms predominantly Aalpha and Aalpha-gamma chain complexes. Previous work from this laboratory demonstrated that amino acid residues within exon 7 of FXIII were important for catalysis (Hettasch, J. M., and Greenberg, C. S. (1994) J. Biol. Chem. 269, 28309-28313). To determine to what extent the primary amino acid sequence within exon 7 defines substrate specificity, exon 7 of FXIII was replaced with the corresponding exon of tTG using gene splicing by overlap extension. Other work from this laboratory (Achyuthan, K. E., Slaughter, T. F., Santiago, M. A., Enghild, J. J., and Greenberg, C. S. (1993) J. Biol. Chem. 268, 21284-21292) using synthetic peptides identified two other domains that might play a role in substrate recognition (located in exons 3 and 5). Therefore, recombinant chimeras of FXIII/tTG were also created in which these two exons were exchanged. FXIII, tTG, and chimeras 3, 5, and 7 were expressed in Escherichia coli, purified, and the nature of the fibrin cross-linking pattern of these five proteins was determined by immunoblot analysis. FXIII preferentially formed the gamma-gamma dimer, whereas tTG formed Aalpha-gamma complexes. Chimera 7 formed Aalpha-gamma complexes that resembled the cross-linking pattern of tTG. This finding demonstrates that the primary amino acid sequence of exon 7 of tTG confers some of the specificity for the Aalpha and Aalpha-gamma cross-link pattern characteristic of tTG. Chimera 5 exhibited reduced cross-linking activity (50% of FXIII activity) but still retained preference for formation of the gamma-gamma dimer, whereas chimera 3 was not active. In conclusion, exchanging the primary amino acid sequence of the active site exon of human FXIII with that of human tTG modifies the enzyme such that the fibrin cross-linking pattern more closely resembles that of tTG (Aalpha and Aalpha-gamma complexes) instead of FXIII (gamma-gamma dimers).
Autophagy Is Activated for Cell Survival after Endoplasmic ReticulumStress (2006)

Eukaryotic cells deal with accumulation of unfolded proteins in the endoplasmic reticulum (ER) by the unfolded protein response, involving the induction of molecular chaperones, translational attenuation, and ER-associated degradation, to prevent cell death. Here, we found that the autophagy system is activated as a novel signaling pathway in response to ER stress. Treatment of SK-N-SH neuroblastoma cells with ER stressors markedly induced the formation of autophagosomes, which were recognized at the ultrastructural level. The formation of green fluorescent protein (GFP)-LC3-labeled structures (GFP-LC3 "dots"), representing autophagosomes, was extensively induced in cells exposed to ER stress with conversion from LC3-I to LC3-II. In IRE1-deficient cells or cells treated with c-Jun N-terminal kinase (JNK) inhibitor, the autophagy induced by ER stress was inhibited, indicating that the IRE1-JNK pathway is required for autophagy activation after ER stress. In contrast, PERK-deficient cells and ATF6 knockdown cells showed that autophagy was induced after ER stress in a manner similar to the wild-type cells. Disturbance of autophagy rendered cells vulnerable to ER stress, suggesting that autophagy plays important roles in cell survival after ER stress.
Temperature and stress dependencies of the magnetic and magnetostrictive properties of Fe0.81Ga0.19 (2002)

It was recently reported that the addition of nonmagnetic Ga increased the saturation magnetostriction (λ100) of Fe over tenfold while leaving the rhombohedral magnetostriction (λ111) almost unchanged. To determine the relationship between the magnetostriction and the magnetization we measured the temperature and stress dependence of both the magnetostriction and magnetization from −21 °C to +80 °C under compressive stresses ranging from 14.4 MPa to 87.1 MPa. For this study a single crystal rod of Fe0.81Ga0.19 was quenched from 800 °C into water to insure a nearly random distribution of Ga atoms. Constant temperature tests showed that compressive stresses greater than 14.4 MPa were needed to achieve the maximum magnetostriction. For the case of a 45.3 MPa compressive stress and applied field of 800 Oe, the maximum magnetostriction at 80 °C decreases from its value at −21 °C by 12.9%. This small magnetostrictive decrease is consistent with a correspondingly small 3.6% decrease in magnetization over the same temperature range. This well-behaved temperature response makes this alloy particularly valuable for industrial and military smart actuator, transducer, and active damping applications. The measured value of Young’s modulus is low (∼55±1 GPa) and almost temperature independent. The large magnetostriction over a wide temperature range combined with the nonbrittle nature of the alloy is rare.
Ethylene oxide-mediated reduction of CO2 to CO and ethylene glycol catalysed by ruthenium complexes (1995)

K. Tominaga, Y. Sasaki, T. Watanabe and M. Saito, J. Chem. Soc., Chem. Commun., 1995, 1489 DOI: 10.1039/C39950001489
Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA (2013)

N(6)-methyladenosine (m(6)A) is the most abundant modification in mammalian mRNA and long noncoding RNA (lncRNA). Recent discoveries of two m(6)A demethylases and cell-type and cell-state-dependent m(6)A patterns indicate that m(6)A modifications are highly dynamic and likely play important biological roles for RNA akin to DNA methylation or histone modification. Proposed functions for m(6)A modification include mRNA splicing, export, stability, and immune tolerance; but m(6)A studies have been hindered by the lack of methods for its identification at single nucleotide resolution. Here, we develop a method that accurately determines m(6)A status at any site in mRNA/lncRNA, termed site-specific cleavage and radioactive-labeling followed by ligation-assisted extraction and thin-layer chromatography (SCARLET). The method determines the precise location of the m(6)A residue and its modification fraction, which are crucial parameters in probing the cellular dynamics of m(6)A modification. We applied the method to determine the m(6)A status at several sites in two human lncRNAs and three human mRNAs and found that m(6)A fraction varies between 6% and 80% among these sites. We also found that many m(6)A candidate sites in these RNAs are however not modified. The precise determination of m(6)A status in a long noncoding RNA also enables the identification of an m(6)A-containing RNA structural motif.
Genetic analysis of splenic lymphoma with villous lymphocytes: a Groupe Français d'Hématologie Cellulaire (GFHC) study (1998)

In order to characterize the genetic diversity in splenic lymphoma with villous lymphocytes (SLVL), we have undertaken cytogenetic and molecular analyses of CCND1 expression and BCL1-IgH PCR rearrangement in 76 cases diagnosed predominantly on morphological criteria. Cytogenetic abnormalities were detected in 19/44 (43%) of cases, including in 16/25 (64%) of cases with an absolute lymphocytosis. Abnormalities included those involving chromosome 14q32 (9/19, 47%), predominantly t(11;14)(q13;q32) (5/19, 26%), chromosome 3 (26%), predominantly 3q, chromosome 17p (26%) and trisomy 12 (3/19, 16%) and were thus suggestive of pathogenetic diversity. CCND1 was expressed in 8/30 (27%) cases, including in all t(11;14) cases, 5/10 (50%) CD5-positive cases and also in 3/20 (15%) CD5-negative cases. Three CCND1-positive SLVL demonstrated immunophenotypic features similar to mantle cell lymphoma (MCL) but the majority differed in their CD5 negativity or CD23 positivity. BCL1-IgH rearrangement was only seen in 1/62 (2%) of cases overall and in none of the t(11;14) cases, which demonstrated FISH breakpoints both centromeric and telomeric to the BCL1/MTC, suggesting that, if genomic clustering exists in t(11;14) SLVL, it differs from MCL. Although CCND1 expressing SLVL more commonly had marked lymphocytosis, they did not demonstrate a more aggressive clinical course than their negative counterparts, demonstrating that the detection of CCND1 expression or of a t(11;14) should not suffice to alter diagnostic classification in the absence of other criteria.
A Genome-Wide Association Study of Type 2 Diabetes in Finns Detects Multiple Susceptibility Variants (2007)

Identifying the genetic variants that increase the risk of type 2 diabetes (T2D) in humans has been a formidable challenge. Adopting a genome-wide association strategy, we genotyped 1161 Finnish T2D cases and 1174 Finnish normal glucose-tolerant (NGT) controls with >315,000 single-nucleotide polymorphisms (SNPs) and imputed genotypes for an additional >2 million autosomal SNPs. We carried out association analysis with these SNPs to identify genetic variants that predispose to T2D, compared our T2D association results with the results of two similar studies, and genotyped 80 SNPs in an additional 1215 Finnish T2D cases and 1258 Finnish NGT controls. We identify T2D-associated variants in an intergenic region of chromosome 11p12, contribute to the identification of T2D-associated variants near the genes IGF2BP2 and CDKAL1 and the region of CDKN2A and CDKN2B, and confirm that variants near TCF7L2, SLC30A8, HHEX, FTO, PPARG, and KCNJ11 are associated with T2D risk. This brings the number of T2D loci now confidently identified to at least 10.
Bacterial binding protein‐dependent permeases: characterization of distinctive signatures for functionally related integral cytoplasmic membrane proteins (1994)

Bacterial binding protein-dependent transport systems belong to the superfamily of ABC transporters, which is widely distributed among living organisms. Their hydrophobic membrane proteins are the least characterized components. The primary structures of 61 integral membrane proteins from 35 uptake systems were compared in order to characterize a short conserved hydrophilic segment, with a consensus EAA---G---------I-LP, located approximately 100 residues from the C-terminus. Secondary structure predictions indicated that this conserved region might be formed by two amphipathic alpha-helices connected by a loop containing the invariant G residue. We classified the conserved motifs and found that membrane proteins from systems transporting structurally related substrates specifically display a greater number of identical residues in the conserved region. We determined a consensus for each class of membrane protein and showed that these can be considered as signatures.
A down-conversion optical link with RF gain (1997)

A down-conversion optical link with a radio frequency (RF) conversion gain of 33 dB was demonstrated at 450 MHz. The gain was increased to 17 dB using photodetector impedance matching. Limitations due to each link element are examined and down-conversion gain up to the millimeter-wave (mm-wave) frequency band is predicted.
A Dual-Band Rectangular CPW Folded Slot Antenna for GNSS Applications (2014)

In this paper, a dual-band rectangular CPW folded slot antenna is studied for the Global Navigation Satellite Systems (GNSS) applications. The antenna operates for all the bands of the GNSS Systems (L1-L2-L5-E5-E6-G1-G2) and its maximum gain varies between 0.2dB and 2.9dB in the band of 1200-1800MHz.The antenna is simulated with "FEKO 6.3", manufactured and measured with "FeedBack Antenna Lab 52-200".
Deep sclerectomy with collagen implant in patients with glaucoma and high myopia (2001)

Deep sclerectomy with collagen implant provided reasonable control of IOP in patients with glaucoma and high myopia over a long-term follow-up. There were relatively few postoperative complications.
Selective optimization of the Rev-binding element of HIV-1 (1993)

RNA molecules that can bind to the Rev protein of HIV-1 have been isolated from random sequence nucleic acid pools based on a minimal Rev-binding element (RBE) found within the Rev Responsive Element (RRE). While the selected sequences are related to the wild-type element, they also contain substitutions that allow them to bind Rev up to 10-fold better in vitro. A hypothesized homopurine pairing at G48:G71 is generally replaced by A48:A71; the occasional selection of C48:A71 suggests that R71 may be in a syn conformation. These data support the structural model for the RBE originally proposed by Bartel et al. (1). Additional interactions with the Rev protein are promoted by the sequence CUC ... UYGAG, found in one class of high-affinity aptamers, but absent from the wild-type element. Within each class of aptamers different residues and substructures covary with one another to generate optimal Rev-binding surfaces. The interdependencies of different nucleotide substitutions suggest structural models for both the wild-type RBE and the selected high-affinity aptamers.
Characterization of the fusion domain of the human immunodeficiency virus type 1 envelope glycoprotein gp41. (1990)

The human immunodeficiency virus transmembrane glycoprotein gp41 has at its amino terminus a strongly hydrophobic stretch of 28 amino acids flanked by a highly conserved series of polar amino acids. To investigate the role in syncytium formation of the hydrophobic amino terminus of gp41 and the polar border of this hydrophobic region, we introduced eight single-amino acid substitutions and one double-amino acid substitution in the amino-terminal 31 amino acids of gp41. The mutant envelope glycoproteins were expressed from two distinct human immunodeficiency virus type 1 envelope glycoprotein expression vectors; the effects of the mutations on syncytium formation, envelope glycoprotein transport, secretion, and CD4 receptor-binding were analyzed. Results showed that polar substitutions throughout the hydrophobic amino terminus of gp41 greatly reduced or blocked syncytium formation mediated by the human immunodeficiency virus type 1 envelope glycoproteins, as did nonconservative mutations in the polar border of the hydrophobic amino terminus. Mutations at gp41 amino acids 15, 26, and 29 also significantly increased the extent of gp120 secretion into the extracellular medium. None of the mutations detectably affected envelope glycoprotein processing or envelope glycoprotein binding to CD4.
Prospective grading of neoplastic change in rat esophagus epithelium using angle-resolved low-coherence interferometry (2005)

Angle-resolved low-coherence interferometry (a/LCI) is used to obtain quantitative, depth-resolved nuclear morphology measurements. We compare the average diameter and texture of cell nuclei in rat esophagus epithelial tissue to grading criteria established in a previous a/LCI study to prospectively grade neoplastic progression. We exploit the depth resolution of a/LCI to exclusively examine the basal layer of the epithelium, approximately 50 to 100 microm beneath the tissue surface, without the need for exogenous contrast agents, tissue sectioning, or fixation. The results of two studies are presented that compare the performance of two a/LCI modalities. Overall, the combined studies show 91% sensitivity and 97% specificity for detecting dysplasia, using histopathology as the standard. In addition, the studies enable the effects of dietary chemopreventive agents, difluoromethylornithine (DFMO) and curcumin, to be assessed by observing modulation in the incidence of neoplastic change. We demonstrate that a/LCI is highly effective for monitoring neoplastic change and can be applied to assessing the efficacy of chemopreventive agents in the rat esophagus.