gebhart/patrepeval huggingface dataset:
Acoustic and elastic multiple scattering and radiation from cylindrical structures (2014)

Multiple scattering (MS) and radiation of waves by a system of scatterers is of great theoretical and practical importance and is required in a wide variety of physical contexts such as the implementation of ``invisibility" cloaks, the effective parameter characterization, and the fabrication of dynamically tunable structures, etc. The dissertation develops fast, rapidly convergent iterative techniques to expedite the solution of MS problems. The formulation of MS problems reduces to a system of linear algebraic equations using Graf's theorem and separation of variables. The iterative techniques are developed using Neumann expansion and Block Toeplitz structure of the linear system; they are very general, and suitable for parallel computations and a large number of MS problems, i.e. acoustic, elastic, electromagnetic, etc., and used for the first time to solve MS problems. The theory is implemented in Matlab and FORTRAN, and the theoretical predictions are compared to computations obtained by COMSOL. To formulate the MS problem, the transition matrix is obtained by analyzing an acoustic and an elastic single scattering of incident waves by elastic isotropic and anisotropic solids. The mathematical model of wave scattering from multilayered cylindrical and spherical structures is developed by means of an exact solution of dynamic 3D elasticity theory. The recursive impedance matrix algorithm is derived for radially heterogeneous anisotropic solids. An explicit method for finding the impedance in piecewise uniform, transverse-isotropic material is proposed; the solution is compared to elasticity theory solutions involving Buchwald potentials. Furthermore, active exterior cloaking devices are modeled for acoustic and elastic media using multipole sources. A cloaking device can render an object invisible to some incident waves as seen by some external observer. The active cloak is generated by a discrete set of multipole sources that destructively interfere with an incident wave to produce zero total field over a finite spatial region. The approach precisely determines the necessary source amplitudes and enables a cloaked region to be determined using Graf's theorem. To apply the approach, the infinite series of multipole expansions are truncated, and the accuracy of cloaking is studied by modifying the truncation parameter.
Epimerase (Msed_0639) and Mutase (Msed_0638 and Msed_2055) Convert ( S )-Methylmalonyl-Coenzyme A (CoA) to Succinyl-CoA in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Cycle (2012)

Crenarchaeotal genomes encode the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle for carbon dioxide fixation. Of the 13 enzymes putatively comprising the cycle, several of them, including methylmalonyl-coenzyme A (CoA) epimerase (MCE) and methylmalonyl-CoA mutase (MCM), which convert (S)-methylmalonyl-CoA to succinyl-CoA, have not been confirmed and characterized biochemically. In the genome of Metallosphaera sedula (optimal temperature [T(opt)], 73°C), the gene encoding MCE (Msed_0639) is adjacent to that encoding the catalytic subunit of MCM-α (Msed_0638), while the gene for the coenzyme B(12)-binding subunit of MCM (MCM-β) is located remotely (Msed_2055). The expression of all three genes was significantly upregulated under autotrophic compared to heterotrophic growth conditions, implying a role in CO(2) fixation. Recombinant forms of MCE and MCM were produced in Escherichia coli; soluble, active MCM was produced only if MCM-α and MCM-β were coexpressed. MCE is a homodimer and MCM is a heterotetramer (α(2)β(2)) with specific activities of 218 and 2.2 μmol/min/mg, respectively, at 75°C. The heterotetrameric MCM differs from the homo- or heterodimeric orthologs in other organisms. MCE was activated by divalent cations (Ni(2+), Co(2+), and Mg(2+)), and the predicted metal binding/active sites were identified through sequence alignments with less-thermophilic MCEs. The conserved coenzyme B(12)-binding motif (DXHXXG-SXL-GG) was identified in M. sedula MCM-β. The two enzymes together catalyzed the two-step conversion of (S)-methylmalonyl-CoA to succinyl-CoA, consistent with their proposed role in the 3-HP/4-HB cycle. Based on the highly conserved occurrence of single copies of MCE and MCM in Sulfolobaceae genomes, the M. sedula enzymes are likely to be representatives of these enzymes in the 3-HP/4-HB cycle in crenarchaeal thermoacidophiles.
Synthesis, cloning and expression in Escherichia coli of artificial genes coding for biologically active elongated precursors of the vasoactive intestinal polypeptide (1988)

Synthetic genes coding for elongated precursors of the vasoactive intestinal polypeptide (VIP) were synthesized and cloned in a highly efficient Escherichia coli expression vector. The synthetic genes code for VIP with its methionine (at position 17) replaced by leucine and elongated at the C-terminus by Gly (vasoactive intestinal polypeptide-Gly, i.e. VIPa) or by Gly-Lys-Arg (vasoactive intestinal polypeptide-Gly-Lys-Arg, i.e. VIPb). The synthetic genes fused to the N-terminal part of the E. coli beta-galactosidase gene were expressed to yield high amounts of fusion proteins reaching upon induction at least 60% of the total cellular protein. The fusion proteins of 314 and 316 amino acids carrying in their C-terminal portion either the 29 or 31 amino acids long VIP precursor polypeptide were shown to be immunoreactive with VIP antisera and were further purified and cleaved by CNBr. The resulting purified peptide precursors (VIPa and VIPb) were recognized by VIP receptors in rat liver plasma membranes and by antibodies to porcine VIP in a radioimmunoassay. Both precursors activated adenylate cyclase in rat liver membranes and stimulated pancreatic secretion in the cat. The affinity and potency of the cloned precursors is close to that of VIP purified from porcine intestine, suggesting that the elongated VIP precursors may act even without being converted into the C-terminal amide form of the peptide. The elongated VIP precursors expressed in E. coli may provide a cheap, large-scale source of experimental material for studies on VIP actions.
MgO-based Intermediate-temperature CO2 Adsorbents (2018)

Carbon dioxide (CO2) capture using solid adsorbents at intermediate temperatures has been recognized as a promising technology, enjoying a high level of utilization in integrated gasification combined cycles (IGCC)-related processes. Solid adsorbents have attracted interest as they can capture CO2 at higher temperatures and can be disposed of with minimal environmental precautions. Among the various solid adsorbents studied, layered double hydroxides (LDHs) and magnesium oxides (MgO) have been found to be particularly suitable for CO2 adsorption in the temperature range of 200−400 °C. In recent years, significant advances have been achieved with MgO-based CO2 adsorbents, most notably through the introduction of molten salts. Therefore, we consider it essential to present a timely update on MgO materials for CO2 capture applications. In this chapter, we summarize the great progress made in this short period as well as some important results that have been published in the literature. Finally, the technology in action for current applications and a forecast for future research are briefly discussed.
cDNA Sequence and Chromosomal Localization of Human Enterokinase, the Proteolytic Activator of Trypsinogen (1995)

Enterokinase is a serine protease of the duodenal brush border membrane that cleaves trypsinogen and produces active trypsin, thereby leading to the activation of many pancreatic digestive enzymes. Overlapping cDNA clones that encode the complete human enterokinase amino acid sequence were isolated from a human intestine cDNA library. Starting from the first ATG codon, the composite 3696 nt cDNA sequence contains an open reading frame of 3057 nt that encodes a 784 amino acid heavy chain followed by a 235 amino acid light chain; the two chains are linked by at least one disulfide bond. The heavy chain contains a potential N-terminal myristoylation site, a potential signal anchor sequence near the amino terminus, and six structural motifs that are found in otherwise unrelated proteins. These domains resemble motifs of the LDL receptor (two copies), complement component Clr (two copies), the metalloprotease meprin (one copy), and the macrophage scavenger receptor (one copy). The enterokinase light chain is homologous to the trypsin-like serine proteinases. These structural features are conserved among human, bovine, and porcine enterokinase. By Northern blotting, a 4.4 kb enterokinase mRNA was detected only in small intestine. The enterokinase gene was localized to human chromosome 21q21 by fluorescence in situ hybridization.
A maturation protein is essential for production of active forms of Lactococcus lactis SK11 serine proteinase located in or secreted from the cell envelope (1989)

The complete nucleotide sequence of a gene located immediately upstream of the Lactococcus lactis subsp. cremoris SK11 prtP gene encoding the cell envelope-attached proteinase was determined. This gene, designated prtM, was found to be transcribed from the same promotor region as was the proteinase gene but in the opposite direction. The prtM gene directed the expression in Escherichia coli of a protein with a size similar to the expected value of 33 kilodaltons, as deduced from the nucleotide sequence data. The derived amino acid sequence of the PrtM protein indicated the presence of a consensus lipoprotein signal sequence at the N terminus, which suggested that PrtM is a lipoprotein. Plasmids containing the prtM gene, the prtP gene, or both were constructed. Expression studies of L. lactis clones containing these plasmids showed that the prtM gene encodes a trans-acting activity involved in the maturation of cell envelope-located and -secreted forms of the SK11 proteinase.
Block copolymer micelle nanolithography on non-conductive substrates (2004)

A new lithographic technique has been developed and applied to cell adhesion studies and electro-optical material development. Attachment of 6 nm Au particles, in periodic and non-periodic pattern, onto non-conductive substrates has been achieved. This was performed via a combination of diblock copolymer self-assembly and electron beam lithographic techniques. To optimize e-beam resolution on non-conductive materials, an additional carbon layer was thread-coated onto the substrates. This carbon coating and the diblock copolymer used in the self-assembly step were simultaneously removed by a final hydrogen plasma treatment to reveal Au nanodot patterns of unprecedented pattern quality. These optically transparent substrates (glass cover slips) were bio-functionalized via the Au-dot patterns to yield a platform for unique cell adhesion studies. The same Au-dot patterning technique was applied to sapphire substrates, which were subsequently employed to nucleate electro-optically active ZnO nanopost growth.
Cyclic Alternating Pattern Sequences in Non-Apneic Snorers with and without Nasal Dilation (1996)

A study was conducted to polysomnographically evaluate the effects of external nasal dilation on sleep quality in mild snorers by examining the amount of sleep fragmentation and cyclic alternating pattern sequences (CAPS) rates. A two-night, open-label, one-way crossover polysomnographic evaluation, with and without use of an external nasal dilator, was done at the Tri-State Sleep Disorders Center in Cincinnati, Ohio. Nine snorers, polysomnographically determined to be free of clinically significant levels of obstructive sleep apnea, were studied. CAPS rates with nasal dilation were 28.4% as compared to 37.9% without nasal dilation (p < 0.05). We conclude that external nasal dilation reduces arousal instability in snorers without obstructive sleep apnea.
Sufentanil pharmacokinetics in young adult and elderly surgical patients. (1994)

Sufentanil 3 microgram kg-1 was administered as an intravenous (i.v.) bolus to 12 elderly patients, aged 65-87 years and 12 young adults, 17-43 years of age, all ASA class I-II, scheduled for orthopaedic surgery. Plasma sufentanil concentrations were measured by a specific radioimmunoassay. Plasma concentration time-curves for the young adult and the elderly groups were superimposible. Pharmacokinetic parameters were calculated from the derived compartmental models. Elimination half-lives, clearance and total volumes of distribution were calculated with non-compartment methods. The major pharmacokinetic parameters, elimination half-life, clearance and volume of distribution did not differ between both groups. The age-related differences in the action of sufentanil cannot be explained by its pharmacokinetic properties.
Gender-specific differences in expression in human lymphoblastoid cell lines (2007)

Women and men have different risks for certain diseases and they often respond differently to treatment. These differences could be due to the sex-specific differences in the expression of genes related to primary disease susceptibility or pharmacodynamic targets. To evaluate the sex-specific pattern of gene expression, we compared gene expression levels using a publicly available microarray dataset of 233 (115 women and 118 men) lymphoblastoid cell lines. From the 4799 probes meeting a specified minimal level of expression, 10 genes (P<0.005, permutation adjusted false discovery rate less than 50%) located on autosomal chromosomes were identified using a permutation-based approach. These genes were found to be over-represented in certain gene ontology terms of biological process (cell adhesion, apoptosis, transcription and signal transduction), and molecular function (structural molecule activity, zinc ion binding, transcription factor activity and protein binding). A Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that two known pathways are over-represented: adherens junction and cytokine-cytokine receptor interaction.
Potential role of HER2‐overexpressing exosomes in countering trastuzumab‐based therapy (2011)

Exosomes are endosome-derived nanovesicles actively released into the extracellular environment and biological fluids, both under physiological and pathological conditions, by different cell types. We characterized exosomes constitutively secreted by HER2-overexpressing breast carcinoma cell lines and analyzed in vitro and in vivo their potential role in interfering with the therapeutic activity of the humanized antibody Trastuzumab and the dual tyrosine kinase inhibitor (TKI) Lapatinib anti-HER2 biodrugs. We show that exosomes released by the HER2-overexpressing tumor cell lines SKBR3 and BT474 express a full-length HER2 molecule that is also activated, although to a lesser extent than in the originating cells. Release of these exosomes was significantly modulated by the growth factors EGF and heregulin, two of the known HER2 receptor-activating ligands and naturally present in the surrounding tumor microenvironment. Exosomes secreted either in HER2-positive tumor cell-conditioned supernatants or in breast cancer patients' serum bound to Trastuzumab. Functional assays revealed that both xenogeneic and autologous HER2-positive nanovesicles, but not HER2-negative ones, inhibited Trastuzumab activity on SKBR3 cell proliferation. By contrast, Lapatinib activity on SKBR3 cell proliferation was unaffected by the presence of autologous exosomes. Together, these findings point to the role of HER2-positive exosomes in modulating sensitivity to Trastuzumab, and, consequently, to HER2-driven tumor aggressiveness.
Effects of the farnesyl transferase inhibitor R115777 (Zarnestra) on mammary carcinogenesis: prevention, therapy, and role of HaRas mutations (2006)

The ability of the farnesyl transferase inhibitor R115777 to act as a cancer therapeutic/preventive agent and to modulate proliferation/apoptosis markers was determined in the methylnitrosourea-induced model of mammary carcinogenesis. Female Sprague-Dawley rats were given methylnitrosourea at 50 days of age. In the prevention study, R115777 (5, 16, or 50 mg/kg body weight/d), beginning 5 days after methylnitrosourea treatment, decreased the formation of mammary cancers by 6%, 42%, and 75%, respectively. Approximately 50% of the mammary cancers that developed had HaRas mutations. Only 1 of 15 tumors that grew out in the presence of R115777 (16 or 50 mg/kg body weight/d) had a HaRas mutation. In the therapeutic study, a surgical biopsy of a mammary cancer was done to determine HaRas status, and growth of the cancer was then followed during treatment of the rat with R115777. Virtually every cancer with a HaRas mutation underwent complete regression within 3 weeks, whereas tumors without a HaRas mutation had variable responses to the inhibitor. Both of these studies implied a high sensitivity of tumors with HaRas mutations to the effects of R115777. In order to understand the preferential susceptibility of tumors with HaRas mutations, rats with a palpable cancer were treated with R115777 for a period of 36 or 96 hours prior to sacrifice, and the proliferation and apoptosis levels in the cancers were determined. The proliferative index was significantly (>85%) decreased in all mammary cancers with HaRas mutations, whereas variable responses were observed in cancers without HaRas mutations. Apoptosis was also measured and a 5-fold increase was observed in HaRas mutant tumors, again with varying responses in the HaRas wild-type cancers. Thus, R115777 was active in the prevention and therapy of these chemically induced mammary cancers, but was strikingly more effective in cancers with HaRas mutations.
Arabidopsis ent-Kaurene Oxidase Catalyzes Three Steps of Gibberellin Biosynthesis (1999)

The Arabidopsis GA3 cDNA was expressed in yeast (Saccharomyces cerevisiae) and the ability of the transformed yeast cells to metabolize ent-kaurene was tested. We show by full-scan gas chromatography-mass spectrometry that the transformed cells produce ent-kaurenoic acid, and demonstrate that the single enzyme GA3 (ent-kaurene oxidase) catalyzes the three steps of gibberellin biosynthesis from ent-kaurene to ent-kaurenoic acid.
Structure-function analysis of the triphosphatase component of vaccinia virus mRNA capping enzyme (1997)

The N-terminal 60 kDa (amino acids 1 to 545) of the D1 subunit of vaccinia virus mRNA capping enzyme is an autonomous bifunctional domain with triphosphatase and guanylyltransferase activities. We previously described two alanine cluster mutations, R77 to A (R77A)-K79A and E192A-E194A, which selectively inactivated the triphosphatase component. Here, we characterize the activities of 11 single alanine mutants-E37A, E39A, Q60A, E61A, T67A, T69A, K75A, R77A, K79A, E192A, and E194A-and a quadruple mutant in which four residues (R77, K79, E192, and E194) were replaced by alanine. We report that Glu-37, Glu-39, Arg-77, Glu-192, and Glu-194 are essential for gamma-phosphate cleavage. The five essential residues are conserved in the capping enzymes of Shope fibroma virus, molluscum contagiosum virus, and African swine fever virus. Probing the structure of D1(1-545) by limited V8 proteolysis suggested a bipartite subdomain structure. The essential residue Glu-192 is the principal site of V8 cleavage. Secondary cleavage by V8 occurs at the essential residue Glu-39. The triphosphatase-defective quadruple mutant transferred GMP to the triphosphate end of poly(A) to form a tetraphosphate cap structure, GppppA. We report that GppppA-capped RNA is a poor substrate for cap methylation by the vaccinia virus and Saccharomyces cerevisiae RNA (guanine-7) methyltransferases. The transcription termination factor activity of the D1-D12 capping enzyme heterodimer was not affected by mutations that abrogated ATPase activity. Thus, the capping enzyme is not responsible for the requirement for ATP hydrolysis during transcription termination.
Homologous Expression of the Lipase and ABC Transporter Gene Cluster, tliDEFA , Enhances Lipase Secretion in Pseudomonas spp (2001)

The ABC transporter TliDEF was found to be an efficient secretory apparatus for extracellular lipase TliA in Pseudomonas fluorescens. For the enhanced secretion of the lipase, we tried to coexpress tliA and tliDEF in various Pseudomonas species. Whereas the coexpression of tliA and tliDEF was required for the lipase secretion in P. fragi, the expression of tliA was sufficient for the lipase secretion in P. fluorescens, P. syringae, and P. putida, indicating the existence of compatible ABC transporter in these species. However, P. fluorescens harboring tliDEFA secreted much more lipase than P. fluorescens harboring only tliA, but the tliDEF was functional only at temperatures below 30 degrees C. The recombinant P. fluorescens overexpressing tliDEFA showed the highest secretion level, 217 U/ml. OD (optical density) (28 microg/ml. OD) of lipase in Luria-Bertani medium under microaerated conditions. With the increase of aeration, the lipase production was decreased and the lipase seemed to be degraded as the cells entered the cell death phase. These results demonstrate that P. fluorescens can be used as a host system for the secretory production of the lipase using the ABC transporter, thus producing lipase in over 14% of the total protein.
Structural Snapshots of an Engineered Cystathionine-γ-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site (2017)

Enzyme therapeutics that can degrade l-methionine (l-Met) are of great interest as numerous malignancies are exquisitely sensitive to l-Met depletion. To exhaust the pool of methionine in human serum, we previously engineered an l-Met-degrading enzyme based on the human cystathionine-γ-lyase scaffold (hCGL-NLV) to circumvent immunogenicity and stability issues observed in the preclinical application of bacterially derived methionine-γ-lyases. To gain further insights into the structure-activity relationships governing the chemistry of the hCGL-NLV lead molecule, we undertook a biophysical characterization campaign that captured crystal structures (2.2 Å) of hCGL-NLV with distinct reaction intermediates, including internal aldimine, substrate-bound, gem-diamine, and external aldimine forms. Curiously, an alternate form of hCGL-NLV that crystallized under higher-salt conditions revealed a locally unfolded active site, correlating with inhibition of activity as a function of ionic strength. Subsequent mutational and kinetic experiments pinpointed that a salt bridge between the phosphate of the essential cofactor pyridoxal 5'-phosphate (PLP) and residue R62 plays an important role in catalyzing β- and γ-eliminations. Our study suggests that solvent ions such as NaCl disrupt electrostatic interactions between R62 and PLP, decreasing catalytic efficiency.
Self-Learned Feature Reconstruction and Offset-Dilated Feature Fusion for Real-Time Semantic Segmentation (2019)

Recent approaches for real-time semantic segmentation usually employ the encoder-decoder architecture as the backbone to generate a high-quality segmentation prediction. There has been a lot of research on designing efficient encoding methods. However, enhancing the performance of components in decoder is also crucial for pixel-level recognition. In this paper, we propose a self-learned feature reconstruction (SFR) method and an offset-dilated feature fusion (ODFF) module to improve the prediction reconstruction capability of the decoder. Concretely, SFR can effectively reconstruct the high-resolution feature maps by recombining feature space, in which the space transformation matrix implicitly contained in a convolution layer can selectively highlight features at each position by leveraging the knowledge of label space in a self-learned way. Moreover, ODFF module can effectively fuse multilevel features with multiscale contextual information by feeding the feature maps into designed parallel offset-dilated convolutions, which enhances the feature representation capability of the decoder. Experiments on Cityscapes and CamVid datasets demonstrate the superior performance of our proposed methods embedded in ESPNet.