gebhart/patrepeval huggingface dataset:
Preferential Geometry and Reactivity of Neutral Iridium(III) and Rhodium(III) Complexes Bearing a Flexible Heterochelate PN Ligand (PN =o-Ph2PC6H4CH2OCH2C5H4N-2) (2006)

Reactions of [IrCl(coe)2]2 (coe = cyclooctene) with 1 equiv of the PN ligand (PN = o-Ph2PC6H4CH2OCH2C5H4N-2) in the presence of several phosphines or pyridine (1 equiv) at room temperature afforded a neutral iridium(III) hydride complex, (PCN-κ3P,C,N)Ir(H)(Cl)(L) (PCN = Ph2PC6H4CHOCH2C5H4N) [L = PPh3 (1a), PCy3 (1b), PBu3 (1c), PMePh2 (1d), Py (1e)] in good isolated yield. The PCN ligand is coordinated in a meridional manner, which was confirmed by spectral analyses and X-ray analysis of 1a. The related rhodium(III) hydride complex (PCN-κ3P,C,N)Rh(H)(Cl)(L) (PCN = Ph2PC6H4CHOCH2C5H4N) [L = PPh3 (4a), PCy3 (4b)] was also prepared from the reactions of [RhCl(coe)2]2 with 1 equiv of the PN ligand in the presence of 1 equiv of PPh3 or PCy3. The structure of 4a and 4b was determined by spectral analyses and X-ray analysis of 4a. In contrast to the iridium complexes, the PCN ligand in the rhodium(III) complexes coordinated to the metal center in a facial manner. A ligand exchange reaction of the PPh3 iridium(III) complex 1a with PCy3 did not proceed well (20% conversion), while a similar reaction of the PPh3 rhodium(III) complex 4a with PCy3 afforded the PCy3 complex 4b quantitatively. We examined the ligand exchange reactions of the iridium(III) and rhodium(III) complexes with various phosphines to explain the different reactivities. Using Tolman's parameter, we demonstrated that the ligand exchange reaction in the iridium(III) complexes bearing the meridional-coordinated PCN ligand is controlled by the steric factor of the phosphines and the ligand exchange reaction in the rhodium(III) complexes bearing the facial-coordinated PCN ligand is controlled by their electronic factors. The meridional coordination of the PCN ligand makes the environment around the iridium center sensitive to the steric nature due to the steric repulsion between the diphenyl group in the PCN ligand and the phosphines. The facial coordination of the PCN ligand decreases their repulsion, and reactivity of the metal center depends on the basicity of the phosphines.
Vintage Seismic Data with Current Prospecting and Imaging Technologies: a Case Study of Reprocessing from Offshore Mexico (2019)

Summary Vintage seismic data from the late 1990&apos;s and early 2000&apos;s have been neglected recently as it was considered too old since most of the value had been extracted with processing technology without too much success. This paper documents our recent experience that before investing in a new acquisition, it is important to check if the vintage seismic data can provide new insights with the latest in time processing and imaging technology. A case study in shallow waters offshore Mexico, illustrates how conventional marine streamer data can still be quite valuable when carefully reprocessed with the technology available today.
Genetic analysis of interactions between the somitic muscle, cartilage and tendon cell lineages during mouse development (2005)

Proper formation of the musculoskeletal system requires the coordinated development of the muscle, cartilage and tendon lineages arising from the somitic mesoderm. During early somite development, muscle and cartilage emerge from two distinct compartments, the myotome and sclerotome, in response to signals secreted from surrounding tissues. As the somite matures, the tendon lineage is established within the dorsolateral sclerotome, adjacent to and beneath the myotome. We examine interactions between the three lineages by observing tendon development in mouse mutants with genetically disrupted muscle or cartilage development. Through analysis of embryos carrying null mutations in Myf5 and Myod1, hence lacking both muscle progenitors and differentiated muscle, we identify an essential role for the specified myotome in axial tendon development, and suggest that absence of tendon formation in Myf5/Myod1 mutants results from loss of the myotomal FGF proteins, which depend upon Myf5 and Myod1 for their expression, and are required, in turn, for induction of the tendon progenitor markers. Our analysis of Sox5/Sox6 double mutants, in which the chondroprogenitors are unable to differentiate into cartilage, reveals that the two cell fates arising from the sclerotome, axial tendon and cartilage are alternative lineages, and that cartilage differentiation is required to actively repress tendon development in the dorsolateral sclerotome.
PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze (2018)

Rhinovirus (RV) infections are major triggers of acute exacerbations of severe respiratory diseases such as pre-school wheeze, asthma and chronic obstructive pulmonary disease (COPD). The occurrence of numerous RV types is a major challenge for the identification of the culprit virus types and for the improvement of virus type-specific treatment strategies. Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. Importantly, we identify RV-A and RV-C species as giving rise to most severe respiratory symptoms. Thus, we have generated a chip for the serological identification of RV-induced respiratory illness which should be useful for the rational development of preventive and therapeutic strategies targeting the most important RV types.
Higher-order narrowing with definitional trees (1999)

Functional logic languages with a sound and complete operational semantics are mainly based on an inference rule called narrowing. Narrowing extends functional evaluation by goal solving capabilities, as in logic programming. Due to the huge search space of simple narrowing, steadily improved narrowing strategies have been developed in the past. Needed narrowing is currently the best narrowing strategy for first-order functional logic programs due to its optimality properties wrt the length of derivations and the number of computed solutions. In this paper, we extend the needed narrowing strategy to higher-order functions and λ-terms as data structures. By the use of definitional trees, our strategy computes only independent solutions. Thus, it is the first calculus for higher-order functional logic programming which provides for such an optimality result. Since we allow higher-order logical variables denoting λ-terms, applications go beyond current functional and logic programming languages. We show soundness and completeness of our strategy with respect to LNT reductions, a particular form of higher-order reductions defined via definitional trees. A general completeness result is only provided for terminating rewrite systems due to the lack of an overall theory of higher-order reduction which is outside the scope of this paper.
Robust indoor scene recognition based on 3D laser scanning and Bearing Angle image (2011)

Robust scene recognition serves as an essential task for robots to work within a complex dynamic environment. Considering vision device's limited adaptability in the dark environment, a 3D-laser-based scene recognition approach that extracts and matches SIFT features from Bearing Angle images is proposed, which makes it possible to make full use of both global metric information and local scale-invariant features. This approach can not only cope with irregular disturbances of dynamic objects, but also tackle obvious changes of observation location robustly in a semi-structured environment. An large-scale indoor environment with more than 30 offices is selected as the real-world scenes to test the performance of the proposed approach.
Video summarization using reinforcement learning in eigenspace (2000)

We propose video summarization using reinforcement learning. The importance score of each frame in a video is calculated from the user's actions in handling similar previous frames; if such frames were watched rather than skipped, a high score is assigned. To calculate the score, instead of using raw feature vectors extracted from images, we use feature vectors projected on eigenspace: as a result, we can deal with the features comprehensively. We also give an algorithm that uses the reinforcement learning method to create a personalized video summary. The summarization algorithm is applied to a soccer video to confirm its effectiveness.
Photoluminescence of a Dense Quasi‐2D Electron‐Hole System in a Modulation‐Doped Heterostructure with Strained InGaAs QW (1990)

Abstract The photoluminescence of dense homogeneous quasi‐2D electron‐hole (e‐h) system in the strained InGaAs QW is investigated for the modulation‐doped n‐AlGaAs‐InGaAs‐GaAs heterostructure under excitation density up to 10 5 W/cm 2 and magnetic field H ≦ 8.3 T. The many body effects are found to become well pronounced in the emission spectra when the concentration of the photoexcited e‐h pairs exceeds the electronic density due to modulation doping (10 12 cm −3 ). There are found and investigated i) the band gap renormalization, ii) the effective mass renormalization, and iii) the change of the damping of one‐particle states in the dense e‐h system.
Circulating tumor cells (CTC) in metastatic hepatocellular carcinoma (HCC): Comparison to control patients with nonmalignant liver diseases (NMLD) and exploratory characterization by next generation sequencing (NGS). (2013)

207 Background: Noninvasive biomarkers are urgently needed to improve diagnosis, prognosis, and molecular characterization in HCC. Detection of CTC by EpCAM-enrichment methods is associated with poor outcomes in other tumors. Approximately 35% of HCC are EpCAM+. We hypothesized that CTC are detectable in a subset of metastatic HCC but not in NMLD and that CTC DNA might serve as a source of tumor DNA for biomarker detection and discovery. Methods: Whole blood was obtained from (1) patients with metastatic HCC and (2) NMLD controls. CTC were enumerated using CellSearch by blinded investigators. If &gt; 10 CTC/7.5 mL, immunomagnetic enrichment for EpCAM followed by fluorescence-activated cell sorting (FACS) was also performed to collect highly purified CTC for whole genome amplification (WGA) by GenomePlex WGA4 kit. NGS using 46-gene AmpliSeq Cancer Panel (Ion Torrent) was performed on DNA from CTC, formalin-fixed paraffin embedded tumor (FFPE), and peripheral blood mononuclear cells (PBMC) if available. Results: 20 HCC and 10 NMLD were enrolled. FFPE was available in 7 HCC. In HCC cohort, median alpha-fetoprotein (AFP) was 492 ng/mL (range: 3.8-587,134) and vascular invasion (VI) was present in 13/20 (65%). CTC ≥ 3/7.5 mL were detected in 6/20 (30%, 95% CI: 0.08, 0.52) HCC and 0/9 (95% CI: 0, 0) eligible NMLD (p=0.07). One NMLD had CTC &gt; 3/7.5 mL but was found to have HCC on surveillance ultrasound and excluded. CTC ≥ 3/7.5 mL were associated with AFP ≥ 400 (p=0.01) and VI (p=0.05) by Fisher’s exact test. NGS identified mutations listed in COSMIC in the majority including TP53 and CTNNB1. Variants appeared more frequent in CTC than FFPE in this small sample. Coverage was significantly lower in CTC than FFPE (coverage 20x mean 50% vs 93%, p &lt; 0.02 by unpaired t-test). Conclusions: CTC are a promising biomarker in metastatic HCC and merit further study, including non-EpCAM methods. CTC were associated with AFP and VI. NGS of CTC WGA DNA is feasible and identified characteristic mutations but was limited by coverage bias. Updated NGS findings including 5 cases with paired CTC, FFPE, and/or PBMC will be presented.
Does C++ Work for Embedded Systems? (1999)

C++ has now become a major player in desktop system development, but attempting to apply it embedded systems often proves to be frustrating. C++ hides detail which can make it very difficult for programmer attempting to understand what is happening in a C++ program, particularly when attempting to understand performance issues. Various criteria can be applied for selecting which parts embedded systems might be suitable for C++ and for using it effectively.
Pattern reasoning: Logical reasoning of neural networks (2001)

This paper presents pattern reasoning, which is logical reasoning on patterns. Pattern reasoning can be a partial solution to the knowledge acquisition problem. Knowledge acquisition tried to acquire linguistic rules from patterns. On the contrary, we try to modify logics in order to reason with patterns. Patterns are represented as functions, which are approximated by artificial neural networks. Therefore, the logical reasoning of neural networks is studied. Neural networks can be used for inference by a few nonclassical logics because neural networks are multilinear functions (in the discrete domain) and the multilinear function space is the model of a few nonclassical logics such as intermediate logic LC, Lukasiewicz logic, and product logic. Due to space limitations, only intermediate logic LC is briefly explained. © 2001 Scripta Technica, Syst Comp Jpn, 32(2): 1–10, 2001
Author Correction: Developmental exposure of California mice to endocrine disrupting chemicals and potential effects on the microbiome-gut-brain axis at adulthood (2020)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
SYNTHESIS OF NUCLEOSIDE PHOSPHOTRIESTERS CONTAINING AMIDATE OR THIOATE FUNCTIONS (1981)

Abstract Phosphorylation of properly protected nucleosides with aryl or alkyl phosphorodichloridates, in the presence of 1-hydroxybenzotriazole, gives phosphorylated intermediates which react smoothly with different amine or thiol functions to afford the corresponding amidate or thioate phosphotriester derivatives.
Synthesis and Antiallergic Activity of Novel Azaazulene Derivatives. (1994)

Various azaazulene derivatives were synthesized and their antiallergic activity was examined. The structure-activity relationship among various derivatives modified by introducing substituents at the 1-,2-, or 3-position of the azaazulene ring was investigated. The inhibitory activities on allergic histamine release of the compounds bearing a 5-tetrazolyl group at the 3-position were more potent than those of the corresponding compounds with other groups (CN, COOH, and CHO). The compounds substituted with amino, azide and carboxymethylamino groups at the 2-position showed strong inhibitory activity. The compounds with various phenylalkyl groups at the 1-position showed a greater activity than those with other substituents. Among the compounds with substituents at the 1-,2-, or 3-position of the azaazulene ring, 1-benzyl-7-isopropyl-3-(5-tetrazolyl)-1-azaazulen-2-one (18f) and 1-(4-fluorobenzyl)-7-isopropyl-3-(5-tetrazolyl)-1-azaazulen- 2-one (19c) had the most potent inhibitory activities on histamine release from mast cells and on passive cutaneous anaphylaxis (PCA) in rats after oral administration (ED50 = 0.56 and 0.58 mg/kg, respectively).
Magnesium-Containing Nanostructured Hybrid Scaffolds for Enhanced Dentin Regeneration (2014)

Dental caries is one of the most prevalent chronic diseases in the United States, affecting 92% of adults aged 20-64 years. Scaffold-based tissue engineering represents a promising strategy to replace damaged dental structures and restore their biological functions. Current single-component scaffolding materials used for dental tissue regeneration, however, cannot provide the proper microenvironment for dental stem/progenitor cell adhesion, proliferation, and differentiation; new biomimetic hybrid scaffolds are needed to promote better dental tissue formation. In this work, we developed a biomimetic approach to prepare three-dimensional (3D) nanofibrous gelatin/magnesium phosphate (NF-gelatin/MgP) hybrid scaffolds. These scaffolds not only mimic the nanostructured architecture and the chemical composition of natural dentin matrices but also constantly present favorable chemical signals (Mg ions) to dental pulp stem cells (DPSCs), thus providing a desirable microenvironment to facilitate DPSC proliferation, differentiation, and biomineralization. Synthesized hybrid NF-gelatin/MgP possesses natural extracellular matrix (ECM)-like architecture, high porosity, high pore interconnectivity, well-defined pore size, and controlled Mg ion release from the scaffold. Adding MgP into NF-gelatin also increased the mechanical strength of the hybrid scaffold. The sustained release of Mg ions from the NF-gelatin/MgP (MgP=10% wt/wt) scaffold significantly enhanced the proliferation, differentiation, and biomineralization of human DPSCs in vitro. The alkaline phosphatase (ALP) activity and the gene expressions for odontogenic differentiation (collagen I [Col I], ALP, osteocalcin [OCN], dentin sialophosphoprotein [DSPP], and dentin matrix protein 1 [DMP1]) were all significantly higher (p<0.05) in the NF-gelatin/MgP group than in the NF-gelatin group. Those results were further confirmed by hematoxylin and eosin (H&E) and von Kossa staining, as shown by greater ECM secretion and mineral deposition in the hybrid scaffold. Consistent with the in vitro study, the DPSCs/NF-gelatin/MgP constructs produced greater ECM deposition, hard tissue formation, and expression of marker proteins (DSPP, DMP1, Col I) for odontogenic differentiation than did the DPSCs/NF-gelatin after 5 weeks of ectopic implantation in rude mice. The controlled release of metallic ions from biomimetic nanostructured hybrid scaffolds, therefore, is a promising approach to enhancing the biological capability of the scaffolds for dental tissue regeneration.
The FKB2 gene of Saccharomyces cerevisiae, encoding the immunosuppressant-binding protein FKBP-13, is regulated in response to accumulation of unfolded proteins in the endoplasmic reticulum. (1993)

The FKB2 gene of Saccharomyces cerevisiae encodes a homolog of mammalian FKBP-13, an FK506/rapamycin-binding protein that localizes to the lumen of the endoplasmic reticulum (ER). We have found that FKB2 mRNA levels increase in response to the accumulation of unfolded precursor proteins in the ER. FKB2 mRNA levels are elevated in cells blocked in N-glycosylation--i.e., in wild-type cells treated with tunicamycin and in the sec53-6 mutant grown at the nonpermissive temperature. Mutations that block other steps in secretion have no effect on FKB2 mRNA levels, indicating that increases in FKB2 mRNA are not the consequence of a general block in secretion. The increase in FKB2 mRNA in response to unfolded proteins in the ER is mediated through a 21-bp unfolded-protein response (UPR) element located in the 5' noncoding region of FKB2. UPR elements present in other ER chaperone genes, such as yeast KAR2 (BiP), mammalian GRP78 (BiP), and GRP94, function in an analogous manner to that in FKB2. As with KAR2, FKB2 mRNA levels are also elevated by heat shock. The similarities in the regulation of FKB2 and other ER chaperone genes suggest that FKBP-13 may play a role in protein trafficking in the ER.
Lung CD200 Receptor Activation Abrogates Airway Hyperresponsiveness in Experimental Asthma (2015)

In allergic asthma, homeostatic pathways are dysregulated, which leads to an immune response toward normally innocuous antigens. The CD200-CD200 receptor pathway is a central regulator of inflammation, and CD200 expression was recently found to be down-regulated in circulating leukocytes of patients with asthma. Given the antiinflammatory properties of CD200, we investigated whether local delivery of recombinant CD200 (rCD200) could reinstate lung homeostasis in an experimental model of asthma. Brown Norway rats were sensitized with ovalbumin (OVA) and alum. rCD200 was intratracheally administered 24 hours before OVA challenge, and airway responsiveness to methacholine was measured 24 hours after the allergen challenge. Inflammation was also assessed by measuring cell recruitment and cytokine levels in bronchoalveolar lavages, as well as lung and draining lymph node accumulation of dendritic cells (DCs) and T cells. In sensitized rats, rCD200 abolished airway hyperresponsiveness, whereas the sham treatment had no effect. In addition, rCD200 strongly reduced OVA-induced lung accumulation of myeloid DCs, CD4(+) T cells, and T helper type 2 cells. This was associated with a strong reduction of OVA-induced IL-13 level and with an increase of IL-10 in supernatants of bronchoalveolar lavages. Lung eosinophilia and draining lymph node accumulation of myeloid DCs and T cells were not affected by rCD200. Overall, these data reveal that rCD200 can inhibit airway hyperresponsiveness in a model of asthma by a multistep mechanism associated with local alterations of the T cell response and the cytokine milieu.
Broylerlerde Rasyona Çinko ‹lavesinin Elektrokardiyogram Üzerine Etkisi (2001)

This study was carried out to evaluate the effects of ration supplemented with zinc on the electrocardiograms of 60 broiler chicks. The chicks were divided into four groups, one control and three experimental groups (II, III, IV). Zinc was given to the experimental groups at doses of 125, 500, 1000 mk/kg respectively, in their ration for 60 days. The electrocardiogram recordings were performed on chicks on the 60 th day of the experiment. Leads I, II, III, aVR, aVL and aVF were recorded in the electrocardiographs of the chicks. All electrocardiograms exhibited P, R, S and T waves but P wave generally interfered with the T wave. No Q waves were observed. All the waves in lead I were very low or almost isoelectric. The R and S waves in leads II and III were of about equal amplitude. The T waves in leads I, II, III and aVF were positive but in leads aVR and aVF they were negative. The heart rates of the groups were found to be 363, 362, 400 and 410 per minute respectively, but the differences among the groups were not statistically significant. In the groups, the mean electrical axis of heart was found to be between -60 0
Synthetically Programmable Nanoparticle Superlattices Using a Hollow Three-Dimensional Spacer Approach* (2020)

This chapter reports an example of entropy-driven crystallization behavior in DNA-nanoparticle superlattice assembly, marking a divergence from the well-established enthalpic driving force of maximizing nearest-neighbor hybridization connections. The field of DNA-mediated nanoparticle crystallization has led to a breadth of superlattice symmetries, both with and without atomic counterparts, giving rise to the term “programmable atom equivalent” (PAE) to describe an individual building block. An important feature of the PAE assembly process that has enabled the predictability and exquisite control over superlattice design is that most observed crystal phases operate under the following guiding principle: “The thermodynamic product is one that maximizes the number of nearest-neighbor connections”. The chapter demonstrates that under specific sets of conditions, contributions beyond the enthalpically centered “maximization of nearest-neighbor interactions” in DNA-directed crystallization of nanoparticles become significant.