gebhart/patrepeval huggingface dataset:
Towards New Oligomesogenic Phosphonic Acids as Stabilizers of Nanoparticles Colloids in Nematic Liquid Crystals (2015)

Several synthetic strategies for the construction of linear and branched oligomesogenic phosphonic acids are examined, which differ in the method of building the key bimesogen unit. An efficient synthetic approach to the most promising compounds employs regioselective Kumada cross-coupling between [11-(4′-pentylbiphenyl-4-yl)undecyl]magnesium bromide and 4-(11-bromoundecyl)-4′-iodobiphenyl as the key step. Preliminary studies on the ability of the new ligands to stabilize nanoparticles colloids in nematic liquid crystals are undertaken for the example of quantum dots.
Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections (1997)

Pathogenic microbes have evolved highly sophisticated mechanisms for colonizing host tissues and evading or deflecting assault by the immune response. The ability of these microbes to avoid clearance prolongs infection, thereby promoting their long-term survival within individual hosts and, through transmission, between hosts. Many pathogens are capable of extensive antigenic changes in the face of the multiple constitutive and dynamic components of host immune defenses. As a result, highly diverse populations that have widely different virulence properties can arise from a single infecting organism (clone). In this review, we consider the molecular and genetic features of antigenic variation and corresponding host-parasite interactions of different pathogenic bacterial, fungal, and protozoan microorganisms. The host and microbial molecules involved in these interactions often determine the adhesive, invasive, and antigenic properties of the infecting organisms and can dramatically affect the virulence and pathobiology of individual infections. Pathogens capable of such antigenic variation exhibit mechanisms of rapid mutability in confined chromosomal regions containing specialized genes designated contingency genes. The mechanisms of hypermutability of contingency genes are common to a variety of bacterial and eukaryotic pathogens and include promoter alterations, reading-frame shifts, gene conversion events, genomic rearrangements, and point mutations.
Sodium‐glucose cotransporter 2 inhibition does not reduce hepatic steatosis in overweight, insulin‐resistant patients without type 2 diabetes (2019)

SGLT2 inhibition for 12 weeks does not improve hepatic steatosis in patients without T2D. Additional studies in patients with established T2D or impairments of fasting or postprandial glucose homeostasis are needed to determine whether SGLT2 inhibition represents a viable therapeutic strategy for NAFLD. (http://clinicaltrials.gov Number NCT02696941).
End-to-end detection-segmentation network with ROI convolution (2018)

We propose an end-to-end neural network that improves the segmentation accuracy of fully convolutional networks by incorporating a localization unit. This network performs object localization first, which is then used as a cue to guide the training of the segmentation network. We test the proposed method on a segmentation task of small objects on a clinical dataset of ultrasound images. We show that by jointly learning for detection and segmentation, the proposed network is able to improve the segmentation accuracy compared to only learning for segmentation.
Capacitive Gas Sensor of Mixed Oxide CoO ‐ In2 O 3 to Selectively Detect Nitrogen Monoxide (1996)

Selective detection of nitric oxide, NO, based on the capacitance change of a mixed‐oxide capacitor was investigated. Since the capacitance of an oxide mixture consisting of two kinds of semiconductive oxides depends on the NO concentration, the NO concentration can be estimated from the capacitance of these mixed‐oxide capacitors. In particular, the capacitance of the physical mixture of CoO and was highly sensitive and selective to NO. Although the sensitivity to NO was decreased, the period for recovery was extremely shortened by increasing the operating temperature. In considering the sensitivity and response characteristics, the optimum operating temperature of seems to exist around 500 K. Whereas the sensitivity to NO diluted with was higher than that in air, the sensitivity to NO was almost independent of the oxygen partial pressure over a wide range. Furthermore, the capacitance of increased with increasing concentration of NO in the range from 1 to 1000 ppm. The sensitivity of to , CO, and was far smaller than that to NO. Consequently, a mixed oxide of is one of the promising materials for the detection of NO in exhaust gases.
Two-Dimensional Self-Limiting Wet Oxidation of Silicon Nanowires: Experiments and Modeling (2013)

In this paper, a CMOS compatible silicon nanowire (Si NW) fabrication method on bulk silicon substrate is carried out using the self-limiting oxidation (SLO) to accurately control its size and cross-sectional shape. A predictive model for the 2-D SLO of Si NWs is presented. In this model, both the reduced reaction rate and diffusivity result in the oxidation rate degradation. The orientation dependence and the deformation of silicon core and oxide shell are further discussed here. The modeling results show good agreement with the experimental data within a wide range of oxidation temperatures, oxidation time, and various initial silicon core sizes. This model provides useful process design guidelines for Si nanostructures, especially in controlling the final diameter and cross-sectional shape of Si NWs from the top-down approach.
Genomic Analysis and Antimicrobial Components of M7, an Aspergillus terreus Strain Derived from the South China Sea (2022)

As a typical filamentous fungus, <i>Aspergillus</i> species are highly adaptive to diverse ecological habitats, represented by their occurrence in both terrestrial and marine environments; this could plausibly be ascribed to their preeminent biological diversity and metabolic variability. In this context, marine-derived <i>Aspergillus</i> fungi have recently attracted great interest as a promising potential source of biologically active compounds. The present study depicts the genomic and chemical profiles of M7, a strain of <i>Aspergillus terreus</i> isolated from mussels in the South China Sea; the crude extracts of its soybean fermentation exhibit potent growth-inhibitory properties against <i>A. baumannii</i> and <i>P. aeruginosa</i>. Subsequently, functional genomics analysis based on sequences implied a considerable biosynthetic potential of the strain, which is substantiated by the 75 biosynthetic gene clusters (BGCs) identified via genome mining; the majority (49 BGCs) were functionally unknown. Representatively, the putative biosynthetic pathways of terramide A and terramide B, the bacteriostatic products obtained through chemical separation and characterized from the fermentation, could not be allocated to any known BGC, highlighting the metabolic potency and diversity of this strain. Meanwhile, based on a comprehensive analysis of fermentation conditions, we confirmed that the presence of environmental iron was inversely correlated with antimicrobial characteristics of the strain M7, presumably due to the interference in the biosynthetic pathway or bioactive mechanisms of the antimicrobial components, e.g., terramide A and B. Our observations provide genomic and biochemical insight into the metabolic and ecological novelties of this strain, underpinning the diversity of biosynthetic flexibility and adaptive strategies of marine <i>Aspergillus</i> fungi.
Role of the unfolded protein response in tumor cell characteristics and cancer outcome (2016)

The contribution of the UPR to the characteristics of malignant tumors is complex and dependent on both intrinsic (e.g. oncogene addiction) and extrinsic (e.g. hypoxia) contexts. Through adaptation to severe microenvironmental conditions, UPR branches are generally a survival strategy for cancer cells, which are able to cope with this challenging context. We address the question of whether the activation status of the UPR is related to tumor properties and discuss the role of the UPR in the clinical context.
The potential role of two LEAFY orthologs in the chasmogamous/cleistogamous mixed breeding system ofViola pubescens(Violaceae)1 (2017)

Many plants, including most species in Viola, produce both open, outcrossing chasmogamous and closed, self-pollinating cleistogamous flowers. The chasmogamous/cleistogamous mixed breeding system is considered an evolutionarily successful reproductive strategy, but the underlying molecular basis remains largely unknown. The LEAFY (LFY) gene in Arabidopsis is responsible for the initiation of floral meristems and the regulation of flower development; therefore, we sought to identify LFY orthologs in Viola pubescens Aiton with the goal of understanding possible differences in the regulatory genetics of flower development and the molecular genetics underlying chasmogamous/cleistogamous mixed breeding systems. A genomic library of V. pubescens was constructed to identify LFY orthologs, and reverse transcription polymerase chain reaction was employed to study gene expression in both flower types. In addition, overexpression studies of the orthologs were carried out in Arabidopsis to explore their role in the breeding system of Viola. Two LFY orthologs, VpLFY1 and VpLFY2, were isolated from a genomic library of V. pubescens. Both genes were expressed in both flower types, especially in young floral buds. However, over-expression of VpLFY2, but not VpLFY1, caused precocious flowering in Arabidopsis, indicating a potentially unique role of each ortholog. The results suggest that VpLFY1 and VpLFY2 function together in flower development of V. pubescens. The different effects caused by VpLFY1 and VpLFY2 in Arabidopsis indicate that the two orthologs may have unique, gene-specific properties that might contribute to the flower type in violets.
CD34 marks angiogenic tip cells in human vascular endothelial cell cultures (2012)

The functional shift of quiescent endothelial cells into tip cells that migrate and stalk cells that proliferate is a key event during sprouting angiogenesis. We previously showed that the sialomucin CD34 is expressed in a small subset of cultured endothelial cells and that these cells extend filopodia: a hallmark of tip cells in vivo. In the present study, we characterized endothelial cells expressing CD34 in endothelial monolayers in vitro. We found that CD34-positive human umbilical vein endothelial cells show low proliferation activity and increased mRNA expression of all known tip cell markers, as compared to CD34-negative cells. Genome-wide mRNA profiling analysis of CD34-positive endothelial cells demonstrated enrichment for biological functions related to angiogenesis and migration, whereas CD34-negative cells were enriched for functions related to proliferation. In addition, we found an increase or decrease of CD34-positive cells in vitro upon exposure to stimuli that enhance or limit the number of tip cells in vivo, respectively. Our findings suggest cells with virtually all known properties of tip cells are present in vascular endothelial cell cultures and that they can be isolated based on expression of CD34. This novel strategy may open alternative avenues for future studies of molecular processes and functions in tip cells in angiogenesis.
Potent nonopioid antinociceptive activity of telocinobufagin in models of acute pain in mice (2019)

The results suggest that TCB may represent a novel potential nonopioid therapeutic analgesic for treatment of acute pains.
Development of surface profile measurement method for ellipsoidal x-ray mirrors using phase retrieval (2012)

An ellipsoidal mirror is a promising type of X-ray mirror, because it can focus X-rays to nanometer size with a very large aperture and no chromatic aberration. However, ideal ellipsoidal mirrors have not yet been realized by any manufacturing method. This is partly because there is no evaluation method for its surface figure profile. In this paper, we propose and develop a method for measuring surface figure profile of ellipsoidal mirrors using phase retrieval. An optical design for soft X-ray focusing, the employed phase retrieval method and an experimental optical system specialized for wavefront measurement using a He-Ne laser are reported.
Using Design of Experiments To Assess Escherichia coli Fermentation Robustness (2005)

OCTOBER 2005 A s initial bench-scale processes progress to full-scale commercial manufacturing, it is important to identify critical parameters and assess their robustness. If manufacturing deviations occur, researchers with process robustness data in hand have critical information with which to evaluate the effects of those deviations. With this in mind, we recently conducted a statistical study to assess fermentation process robustness in the manufacture of an active pharmaceutical ingredient. Design of experiments (DOE) is a structured and efficient methodology for planning experiments such that statistically valid relationships between factors affecting a process and its outputs can be established. DOE was a key element in our study because it is ideally suited to establishing critical parameters and their acceptable ranges. To begin the study, we first scaled down an Escherichia coli fed-batch fermentation process that was already in full-scale operation producing a recombinant protein in the form of inclusion bodies. Next, using historical data that was thus available, we identified parameters that were likely to affect process performance. Finally, we performed statistically designed experiments to assess the impact of those process parameters. As a result, we were able to establish a data set to support broader parameter ranges for routine manufacturing.
A polymer‐based systemic hemostat for managing uncontrolled bleeding (2023)

Uncontrolled bleeding is a life-threatening emergency that requires immediate intervention. Currently available on-site bleeding interventions largely rely on the use of tourniquets, pressure dressing, and other topical hemostatic agents, which can only treat bleeding injuries that are known, accessible, and potentially compressible. Synthetic hemostats that are stable at room temperature, easy to carry, field-usable, and able to stop internal bleeding at multiple or unknown sources, are still lacking. We recently developed a hemostatic agent via polymer peptide interfusion (HAPPI), which can selectively bind to activated platelets and injury sites after intravascular administration. Here we report that HAPPI is highly effective in treating multiple lethal traumatic bleeding conditions in normal as well as hemophilia models via either systemic administration or topical application. In a rat liver traumatic model, intravenous injection of HAPPI resulted in a significant decrease in blood loss and a four-fold reduction in mortality rate within 2 h after injury. When applied topically on liver punch biopsy wounds in heparinized rats, HAPPI achieved a 73% of reduction in blood loss and a five-fold increase in survival rate. HAPPI also exhibited hemostatic efficacy in hemophilia A mice by reducing blood loss. Further, HAPPI worked synergistically with rFVIIa to induce immediate hemostasis and 95% reduction in total blood loss compared to the saline-treated group in hemophelia mice models. These results demonstrate that HAPPI is a promising field-usable hemostatic agent for a broad range of different hemorrhagic conditions.
ChemInform Abstract: 2‐BENZYLIDENE(3)FERROCENOPHANE‐1,3‐DIONES AND THEIR SPECTRAL PROPERTIES (1980)

Abstract Die Titelverbindungen (III) werden durch Kondensation der Aldehyde (II) mit dem [3]Ferrocenophandion (I) mit Triethylamin als Katalysator synthetisiert.
Optimizing laser coupling, matter heating, and particle acceleration from solids using multiplexed ultraintense lasers (2022)

Realizing the full potential of ultrahigh-intensity lasers for particle and radiation generation will require multi-beam arrangements due to technology limitations. Here, we investigate how to optimize their coupling with solid targets. Experimentally, we show that overlapping two intense lasers in a mirror-like configuration onto a solid with a large preplasma can greatly improve the generation of hot electrons at the target front and ion acceleration at the target backside. The underlying mechanisms are analyzed through multidimensional particle-in-cell simulations, revealing that the self-induced magnetic fields driven by the two laser beams at the target front are susceptible to reconnection, which is one possible mechanism to boost electron energization. In addition, the resistive magnetic field generated during the transport of the hot electrons in the target bulk tends to improve their collimation. Our simulations also indicate that such effects can be further enhanced by overlapping more than two laser beams.
Bootstrapping from Game Tree Search (2009)

In this paper we introduce a new algorithm for updating the parameters of a heuristic evaluation function, by updating the heuristic towards the values computed by an alpha-beta search. Our algorithm differs from previous approaches to learning from search, such as Samuel's checkers player and the TD-Leaf algorithm, in two key ways. First, we update all nodes in the search tree, rather than a single node. Second, we use the outcome of a deep search, instead of the outcome of a subsequent search, as the training signal for the evaluation function. We implemented our algorithm in a chess program Meep, using a linear heuristic function. After initialising its weight vector to small random values, Meep was able to learn high quality weights from self-play alone. When tested online against human opponents, Meep played at a master level, the best performance of any chess program with a heuristic learned entirely from self-play.
Noninvasive Coronary Angiography by Retrospectively ECG-Gated Multislice Spiral CT (2000)

The coronary arteries could be visualized over long segments (left main, 9+/-4 mm; left anterior descending, 112+/-34 mm; left circumflex, 80+/-29 mm; right coronary artery, 116+/-33 mm). On average, 78+/-16% of these distances were visualized free of motion artifacts. The mean contrast-to-noise ratio was 9.3+/-3.3. Coronary artery diameters in multislice spiral CT showed close correlation to quantitative coronary angiography (CT, 3.3+/-1.0 mm; angiography, 3. 2+/-0.9 mm; mean difference, 0.38 mm; r=0.86). Contrast-enhanced multislice spiral CT permits visualization of the coronary artery lumen. Further studies are necessary to determine whether image quality is sufficient to reliably detect coronary artery stenoses.
Tuning Orbital Symmetry of Iridium Nitrenoid Enables Catalytic Diastereo- and Enantioselective Alkene Difunctionalizations (2021)

Among the central themes in synthetic chemistry is the establishment of novel strategies that usher in the development of more efficient and mild reactions and also expand the chemical space for asymmetric catalysis. Herein, we present an approach to revitalize the Cp*Ir(κ<sup>2</sup>-LX) system as a catalyst toward alkene difunctionalizations via a nitrenoid-mediated pathway. A key strategy is tuning the orbital symmetry of the key Ir nitrenoid intermediates by ligand modification to impart the desired catalytic activity with the suppression of catalyst deactivation. On the basis of a frontier molecular orbital (FMO) analysis, we systematically engineered a new catalyst system capable of a stepwise nitrenoid transfer to allow for nucleophile incorporation. Using the catalytic protocol, a range of difunctionalized lactams can be produced in a diastereoselective manner with various nucleophiles. Mechanistic investigations revealed that the ligand plays a crucial role in both nitrenoid-delivery and stereoselectivity-determining steps. The current mechanistic platform also enabled the development of new asymmetric methods for introducing two-point chirality in (oxy-alkyl)lactam products with excellent enantioselectivity.
Monitoring vibrational wave packet dynamics via direct femtosecond pump-probe measurements (2007)

Femtosecond pump-probe measurements are shown to reveal the evolution of excited vibrational wave packets in CS2 through the probe transmission modulation. Frequency-resolved acquisition allows for selective monitoring of different subsets of the Raman transitions excited.
Minimizing the monitoring cost in network management (2003)

Many rapidly-changing environments need to be monitored to ensure that they stay within acceptable parameters. The monitoring consists of measuring properties of the environment, and of inferring an aggregate predicate from these measurements. In many cases it is too complex, or too expensive to conduct explicit monitoring at all times. In these cases, information (integrity constraints) on the evolution of this environment can often allow us to use past measurements to infer the future behavior, thus reducing the monitoring cost. We provide a formal description of the problem of monitoring rapidly-changing data, which we call the monitoring problem. We then classify this problem in terms of the integrity constraints that govern the evolution of the environment, and propose different algorithms for each of these classes. For the most restricted case, we can find a greedy algorithm which is optimal, while for the more general cases we use competitive analysis and show that optimal worst- and average-case cost measurement algorithms exist. We then present heuristics for low-cost low-complexity measurement algorithms. We believe that the results of this paper can serve as a framework for further studies.
Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution (2001)

The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.