gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Syntheses of 1,3‐Disubstituted Dithieno(3,4‐b:3′,2′‐d)pyridines via Halogen‐Metal Exchange of 1,3‐Dibromodithieno(3,4‐b:3′,2′‐d)pyridine. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Full-Wave Model of Frequency-Dispersive Media With Debye Dispersion Relation by Circuit-Oriented FEM (2009)

Dispersive materials play an important role in a wide variety of applications (e.g., waveguides, antenna structures, integrated circuits, bioelectromagnetic applications). In this paper, a full-wave finite-element method (FEM-SPICE) technique for modeling dispersive materials is proposed. A finite-element formulation employing Whitney elements capable of analyzing electromagnetic geometries with dispersive media is described, and a Norton equivalent network is developed for each element. The overall network can be analyzed using a circuit simulator based on SPICE, and is suitable for both frequency- and time-domain analysis. This approach exploits the flexibility of finite-element mesh generation and computational efficiency of modern circuit simulators. Simple test configurations are analyzed to validate the proposed formulation.
Crystal structure of an engineered cro monomer bound nonspecifically to DNA: Possible implications for nonspecific binding by the wild‐type protein (1998)

The structure has been determined at 3.0 A resolution of a complex of engineered monomeric Cro repressor with a seven-base pair DNA fragment. Although the sequence of the DNA corresponds to the consensus half-operator that is recognized by each subunit of the wild-type Cro dimer, the complex that is formed in the crystals by the isolated monomer appears to correspond to a sequence-independent mode of association. The overall orientation of the protein relative to the DNA is markedly different from that observed for Cro dimer bound to a consensus operator. The recognition helix is rotated 48 degrees further out of the major groove, while the turn region of the helix-turn-helix remains in contact with the DNA backbone. All of the direct base-specific interactions seen in the wild-type Cro-operator complex are lost. Virtually all of the ionic interactions with the DNA backbone, however, are maintained, as is the subset of contacts between the DNA backbone and a channel on the protein surface. Overall, 25% less surface area is buried at the protein DNA interface than for half of the wild-type Cro-operator complex, and the contacts are more ionic in character due to a reduction of hydrogen bonding and van der Waals interactions. Based on this crystal structure, model building was used to develop a possible model for the sequence-nonspecific interaction of the wild-type Cro dimer with DNA. In the sequence-specific complex, the DNA is bent, the protein dimer undergoes a large hinge-bending motion relative to the uncomplexed form, and the complex is twofold symmetric. In contrast, in the proposed nonspecific complex the DNA is straight, the protein retains a conformation similar to the apo form, and the complex lacks twofold symmetry. The model is consistent with thermodynamic, chemical, and mutagenic studies, and suggests that hinge bending of the Cro dimer may be critical in permitting the transition from the binding of protein at generic sites on the DNA to binding at high affinity operator sites.
Numerical solutions for jump-diffusions with regime switching (2005)

This paper is devoted to numerical solutions for a class of jump-diffusions with regime switching. After briefly reviewing the notion of jump-diffusions with regime switching, finite-difference procedures are constructed. Under simple conditions, it is proved that the algorithm converges to the desired limit by means of a martingale problem formulation. Numerical experiments are carried out to demonstrate the performance of the algorithm.
Evolution From Single to Hybrid Nanogenerator: A Contemporary Review on Multimode Energy Harvesting for Self-Powered Electronics (2018)

Energy harvesting devices have strong potential to not only meet growing global energy demand but also support a wide range of self-powered electronics applications. Solar cells, electrochemical cells, piezoelectric/triboelectric/pyroelectric nanogenerators, and magnetoelectric energy harvesters are enabling technologies for converting solar, chemical, mechanical, thermal, and magnetic energy to electricity. Merging these harvesters to form hybrid energy cells can help optimize operation of self-powered systems, providing multimode energy harvesting capability that can leverage several energy sources either simultaneously or individually. Energy produced from these hybrid energy cells even can be stored in Li-ion batteries to power various personal electronics, sensors, and next generation technology for the Internet of Things. Ultimately, hybridization provides another degree of freedom in terms of more effective energy utility. This review presents the evolution of the hybrid energy cell concept and development, explores the fabrication approaches taken, and provides insights on the limitations of existing devices, steps toward performance optimization, and the enormous potential for these technologies to benefit myriad applications. Hybrid energy cells show higher output performance by providing better charging characteristics than individual energy harvester unit.
Effect of colloidal silica addition on the formation of porous spherical .ALPHA.-calcium orthophosphate agglomerates by spray pyrolysis technique (2009)

The effect of colloidal silica (SiO2; CS) addition on the formation of porous spherical α-calcium orthophosphate (α-Ca3(PO4)2; α-TCP) agglomerates has been examined. The starting powder was prepared by the spray pyrolysis of calcium phosphate (Ca/P ratio = 1.50) solution containing 0.9 mol·dm-3 Ca(NO3)2, 0.6 mol·dm-3 (NH4)2HPO4, CS (mean particle size; 14, 24 and 39 nm) and concentrated HNO3 at 600°C, using an air-liquid nozzle; the amounts of CS in the spray-pyrolyzed powder were adjusted to be 0.1-0.4 mass%. The heat-treatment of spray-pyrolyzed power with 0.4 mass% of CS addition at 1200°C for 10 min showed that the transformation from β- to α-TCP was restricted as the diameter of CS decreased from 24 to 14 nm. The heat-treatment of spray-pyrolyzed powder containing 0.1 mass% of CS (mean diameter: 24 nm) at 1200°C for 10 min resulted in not only the complete transformation of β- to α-TCP but also preservation of original spherical framework. The immersion of porous spherical α-TCP agglomerates in simulated body fluid (SBF) brought about the rapid formation of hydroxyapatite, due to higher specific surface area (17.0 m2·g-1) compared to that of commercial powder (10.9 m2·g-1). The hardened body with the porosity of 66.3% could be fabricated by mixing the calcium-phosphate paste with 50 mass% of the present porous α-TCP agglomerates, using the malaxation liquid. Immersion of this hardened body in SBF at 37.0°C resulted in the formation of hydroxyapatite within three days.
Laparoscopic Biopsies in Pancreas Transplantation (2017)

As there is no precise laboratory test or imaging study for detection of pancreas allograft rejection, there is increasing interest in obtaining pancreas tissue for diagnosis. Pancreas allograft biopsies are most commonly performed percutaneously, transcystoscopically, or endoscopically, yet pancreas transplant surgeons often lack the skills to perform these types of biopsies. We have performed 160 laparoscopic pancreas biopsies in 95 patients. There were 146 simultaneous kidney-pancreas biopsies and 14 pancreas-only biopsies due to pancreas alone, kidney loss, or extraperitoneal kidney. Biopsies were performed for graft dysfunction (89) or per protocol (71). In 13 cases, an additional laparoscopic procedure was performed at the same operation. The pancreas diagnostic tissue yield was 91.2%; however, the pancreas could not be visualized in eight cases (5%) and in 6 cases the tissue sample was nondiagnostic (3.8%). The kidney tissue yield was 98.6%. There were four patients with intraoperative complications requiring laparotomy (2.5%) with two additional postoperative complications. Half of all these complications were kidney related. There were no episodes of pancreatic enzyme leak and there were no graft losses related to the procedure. We conclude that laparoscopic kidney and pancreas allograft biopsies can be safely performed with very high tissue yields.
Structures of Hepatitis B Virus Cores Presenting a Model Epitope and Their Complexes with Antibodies (2012)

The core shell of hepatitis B virus is a potent immune stimulator, giving a strong neutralizing immune response to foreign epitopes inserted at the immunodominant region, located at the tips of spikes on the exterior of the shell. Here, we analyze structures of core shells with a model epitope inserted at two alternative positions in the immunodominant region. Recombinantly expressed core protein assembles into T=3 and T=4 icosahedral shells, and atomic coordinates are available for the T=4 shell. Since the modified protein assembles predominantly into T=3 shells, a quasi-atomic model of the native T=3 shell was made. The spikes in this T=3 structure resemble those in T=4 shells crystallized from expressed protein. However, the spikes in the modified shells exhibit an altered conformation, similar to the DNA containing shells in virions. Both constructs allow full access of antibodies to the foreign epitope, DPAFR from the preS1 region of hepatitis B virus surface antigen. However, one induces a 10-fold weaker immune response when injected into mice. In this construct, the epitope is less constrained by the flanking linker regions and is positioned so that the symmetry of the shell causes pairs of epitopes to come close enough to interfere with one another. In the other construct, the epitope mimics the native epitope conformation and position. The interaction of native core shells with an antibody specific to the immunodominant epitope is compared to the constructs with an antibody against the foreign epitope. Our findings have implications for the design of vaccines based on virus-like particles.
Enteroendocrine cells express functional Toll-like receptors (2007)

Intestinal epithelial cells (IECs) provide a physical and immunological barrier against enteric microbial flora. Toll-like receptors (TLRs), through interactions with conserved microbial patterns, activate inflammatory gene expression in cells of the innate immune system. Previous studies of the expression and function of TLRs in IECs have reported varying results. Therefore, TLR expression was characterized in human and murine intestinal sections, and TLR function was tested in an IEC line. TLR1, TLR2, and TLR4 are coexpressed on a subpopulation of human and murine IECs that reside predominantly in the intestinal crypt and belong to the enteroendocrine lineage. An enteroendocrine cell (EEC) line demonstrated a similar expression pattern of TLRs as primary cells. The murine EEC line STC-1 was activated with specific TLR ligands: LPS or synthetic bacterial lipoprotein. In STC-1 cells stimulated with bacterial ligands, NF-kappaB and MAPK activation was demonstrated. Furthermore, the expression of TNF and macrophage inhibitory protein-2 were induced. Additionally, bacterial ligands induced the expression of the anti-inflammatory gene transforming growth factor-beta. LPS triggered a calcium flux in STC-1 cells, resulting in a rapid increase in CCK secretion. Finally, conditioned media from STC-1 cells inhibited the production of nitric oxide and IL-12 p40 by activated macrophages. In conclusion, human and murine IECs that express TLRs belong to the enteroendocrine lineage. Using a murine EEC model, a broad range of functional effects of TLR activation was demonstrated. This study suggests a potential role for EECs in innate immune responses.
Optimized expression of (S)‐carbonyl reductase in Pichia pastoris for efficient production of (S)‐1‐phenyl‐1, 2‐ethanediol (2013)

The recombinant (S)-carbonyl reductase (SCR) in Escherichia coli catalyzed the reduction of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol (PED) with low efficiency. In this work, its 6× histidine fusion gene his6 -scr was cloned in Pichia pastoris under the control of the AOX1 methanol inducible promoter. The heterologous protein SCR was expressed through a Mut(s) phenotype. Under the optimal conditions: pH 7.0, initial OD600 2.5, methanol daily addition concentration 1.0% and induction duration 4-5 days, the recombinant protein SCR was produced at the highest level. The enzyme activity in the cell-free exacts of P. pastoris was 0.38, which was over twofold than that of the recombinant E. coli-SCR. The enzyme was purified to homogeneity with a specific activity of 3.41 U mg(-1) , and it catalyzed the biotransformation of (S)-PED with a high optical purity of 96.9% in a high yield of 89.7% at optimum pH of 7.0. The developed effective system of P. pastoris-SCR will facilitate the preparation of pure chiral alcohol in industry.
0D to 1D Switching of Hybrid Polyoxometalate Assemblies at the Nanoscale by Using Molecular Control (2013)

Watered down: Polyoxometalate (POM) hybrids based on [C<sub>16</sub> H<sub>36</sub> N]<sub>4</sub> [SiW<sub>11</sub> O<sub>40</sub> (SiCH<sub>2</sub> CH<sub>2</sub> CH<sub>2</sub> NH<sub>2</sub> ⋅HCl)<sub>2</sub> ] covalently functionalized with different lengths of alkyl chains (n=0, 5, or 10) terminated with azobenzene moieties have been successfully prepared. The assembly behavior of these POMs can be affected by hydrophobic and π-π interactions by finely tuning the lengths of the alkyl chains in different ratios of CH<sub>3</sub> CN/H<sub>2</sub> O.
Transcutaneous angioplasty of experimental aortic coarctation. (1982)

A dilatable form of juxtaductal aortic coarctation was surgically created in 29 newborn lambs. Of the 17 long-term survivors, four lambs served as controls and 13 underwent transcutaneous balloon dilation angioplasty with either polyvinylchloride or polyethylene catheters after 7--10 weeks of recovery. During growth before dilation, there was little change in the systolic gradient across the coarctation (36.6-35.3 mm Hg) despite an increase in animal weight from 3.8 to 19.3 kg. This systolic gradient remained constant in undilated lambs throughout a 6-month follow-up. Dilation produced an immediate 65% increase in the diameter of the coarctation and a 68% decrease in the systolic gradient across the coarctation site. Successful dilation required very high (6--8 atmospheres) dilating pressures. This gradient relief persisted throughout a follow-up of up to 1 year. Although no late sequelae could be attributed to the angioplasty, one lamb suffered an anterior aortic tear (associated with a difficult postdilation wire passage across the dilation site), which resulted in fatal intrathoracic hemorrhage. Cross pathologic inspection demonstrated intimal and medial tears in successfully dilated lambs in the first 3 days after dilation; on late pathologic examination, the intima appeared completely healed, without evidence of aneurysm or accelerated atheroma formation, within 2 months. These results, in conjunction with previous human in vitro studies, support the hypothesis that human aortic coarctation may be a dilatable lesion, although the safe limits and optimal protocols for dilating human coarctations are not known.
Physiological cytosolic Ca2+ transients evoke concurrent mitochondrial depolarizations. (1994)

Calcium, a ubiquitous second messenger, stimulates the activity of several mitochondrial dehydrogenases. This has led to the suggestion that the same messenger that signals cell activation could also activate mitochondrial electron/proton transport, thereby meeting demands for increased cellular energy. To test this in live cells, quantitative three-dimensional microscopy and ratio imaging were used to measure membrane potential of individual mitochondria and cytosolic calcium distribution. Mitochondria reversibly depolarized as cytosolic calcium rose and then fell following physiological stimulation. Thus, the dominant response of the mitochondrion to a rise in cytosolic [Ca2+] is to draw on the electrochemical potential, possibly to accelerate processes directly involved in ATP synthesis and calcium homeostasis.
Immune cell extracellular vesicles and their mitochondrial content decline with ageing (2020)

Abstract Background Although the mechanisms of action are not fully understood, extracellular vesicles (EVs) have emerged as key indicators and effectors of immune function. Characterizing circulating EVs associated with stem and immune cells across the lifespan of healthy individuals could aid an understanding of immunosenescence, a process of age-related decline of cells in both adaptive and innate immune systems. Results Using high resolution multicolor flow cytometry, we identified three major subsets of EVs of varying sizes in healthy control (HC) plasma. Multiple plasma EVs associated with immune cells declined with ageing in HCs. In addition, we observed age-associated declines of respiring mitochondria cargo in EVs of several types of immune cells, suggesting that these parent cells may experience a decline in mitophagy or a mitochondrial dysfunction-induced immunosenescence. By contrast, the number of CD34 + hematopoietic stem cell-associated EVs were high and carried respiring mitochondria, which did not decline with age. Conclusion As demonstrated here, multicolor flow cytometry simultaneously measures plasma EV size, surface markers and cargo that reflect biological processes of specific cell types. The distinct surface markers and cytokine cargo of plasma EVs suggest that they may carry different bio-messages and originate by different biogenesis pathways.
Offshore & Onshore contracts (2005)

We study the buyer-seller relationship in a supply chain from the perspective of quality. In particular, we examine situations where quality levels of the product can be observed, yet, conformance cannot be enforced unless the buyer engages in costly, legally-binding activity, which we call audit. We assume that the cost of audit is borne by the buyer. We examine three types of remedies that can be taken in case an audit confirms the existence of quality problems, namely â Full Rebate", â Compensate" and â Repair" contracts. Under the Full Rebate regime, the seller rebates the buyer the purchase price of defective units. Under the Compensate regime (Expectation Damages), the buyer is compensated for his loss of profit due to defects. Finally, under the Repair regime (Specific Performance), the seller is made to repair all the defective units at his own expense. We examine the effects of these contracts on the performance of the supply-chain, and point out the implications for offshore and onshore supply networks, respectively. Our results indicate conditions where the buyer is not motivated to â squeeze" all the profits out of the supply chain, even in a setting of complete information, and even if the relationship is short-term. We extend the analysis to examine supply-chains which include more than one seller or buyer. Also, as part of the analysis, we study a problem, which we call the â Crime and Punishment" problem that is interesting in its own right.
Bacillus subtilis YngB contributes to wall teichoic acid glucosylation and glycolipid formation during anaerobic growth (2021)

UTP-glucose-1-phosphate uridylyltransferases are enzymes that produce UDP-glucose from UTP and glucose-1-phosphate. In Bacillus subtilis 168, UDP-glucose is required for the decoration of wall teichoic acid (WTA) with glucose residues and the formation of glucolipids. The B. subtilis UGPase GtaB is essential for UDP-glucose production under standard aerobic growth conditions, and gtaB mutants display severe growth and morphological defects. However, bioinformatics predictions indicate that two other UTP-glucose-1-phosphate uridylyltransferases are present in B. subtilis. Here, we investigated the function of one of them named YngB. The crystal structure of YngB revealed that the protein has the typical fold and all necessary active site features of a functional UGPase. Furthermore, UGPase activity could be demonstrated in vitro using UTP and glucose-1-phosphate as substrates. Expression of YngB from a synthetic promoter in a B. subtilis gtaB mutant resulted in the reintroduction of glucose residues on WTA and production of glycolipids, demonstrating that the enzyme can function as UGPase in vivo. When WT and mutant B. subtilis strains were grown under anaerobic conditions, YngB-dependent glycolipid production and glucose decorations on WTA could be detected, revealing that YngB is expressed from its native promoter under anaerobic condition. Based on these findings, along with the structure of the operon containing yngB and the transcription factor thought to be required for its expression, we propose that besides WTA, potentially other cell wall components might be decorated with glucose residues during oxygen-limited growth condition.
Re-Estimation of Low Level Gamma Ray Doses Detected by Lithium Fluoride Thermoluminescence Dosemeters (1986)

An experimental method has been described for the re-estimation of low level gamma ray doses detected by standard Harshaw TLD cards, consisting of two extruded ribbon type LiF thermoluminescence dosemeters covered with thin Teflon foils. After the first readout at a temperature plateau of 300 oC for 10 s the dosemeters were exposed to 254 nm UV light for 25 min at a temperature of 110 oC and re-evaluated. A primary gamma ray dose as low as 2 mSv was re-assessed with an accuracy of ±25% from the second evaluation of the glow peak, resulting from the UV induced phototransferred thermoluminescence.
Downregulation of Neurodevelopmental Gene Expression in iPSC-Derived Cerebral Organoids Upon Infection by Human Cytomegalovirus (2021)

Abstract Human cytomegalovirus (HCMV) is a beta herpesvirus that, upon congenital infection, can cause severe birth defects including vision and hearing loss, microcephaly, and seizures. Currently, no approved treatment options exist for in utero infections. We previously demonstrated that HCMV infection decreases calcium signaling responses and alters neuronal differentiation in induced pluripotent stem cell (iPSC) derived neural progenitor cells (NPCs). Here we aimed to determine the impact of infection on the transcriptome in developing human neurons using iPSC-derived 3-dimensional cerebral organoids. We infected iPSC-derived cerebral organoids with HCMV encoding eGFP and sorted cell populations based on GFP signal strength. Significant transcriptional downregulation was observed including in key neurodevelopmental gene pathways in both the GFP (+) and intermediate groups. Interestingly, the GFP (-) group also showed downregulation of the same targets indicating a mismatch between GFP expression and viral infection. Using a modified HCMV virus destabilizing IE 1 and 2 proteins, we still observed significant downregulation of neurodevelopmental gene expression in infected neural progenitor cells. Together, these data indicate that IE viral proteins are not the main drivers of neurodevelopmental gene dysregulation in HCMV infected neural tissues suggesting therapeutically targeting IE gene expression is insufficient to restore neural differentiation and function.
Comparison of Essential Oils from Three Plants for Enhancement of Antimicrobial Activity of Nitrofurantoin against Enterobacteria (2006)

M. spicata and A. graveolens oils exhibited the highest effects. Gas chromatography-mass spectrometry analysis showed that the oils of these two plants contained 40.12 and 20.32% carvone, respectively. Pure carvone and piperitone equally increased the bactericidal activity of nitrofurantoin. Other ingredients of essential oils, including camphor, limonene and menthone, were less effective.