gebhart/patrepeval huggingface dataset:
Attenuation of Virulence in Pathogenic Bacteria Using Synthetic Quorum-Sensing Modulators under Native Conditions on Plant Hosts (2011)

Quorum sensing (QS) is often critical in both pathogenic and mutualistic relationships between bacteria and their eukaryotic hosts. Gram-negative bacteria typically use N-acylated l-homoserine lactone (AHL) signals for QS. We have identified a number of synthetic AHL analogues that are able to strongly modulate QS in culture-based, reporter gene assays. While informative, these assays represent idealized systems, and their relevance to QS under native conditions is often unclear. As one of our goals is to utilize synthetic QS modulators to study bacterial communication under native conditions, identifying robust host-bacteria model systems for their evaluation is crucial. We reasoned that the host-pathogen interaction between Solanum tuberosum (potato) and the Gram-negative pathogen Pectobacterium carotovora would be ideal for such studies as we have identified several potent, synthetic QS modulators for this pathogen, and infection assays in potato are facile. Herein, we report on our development of this host-pathogen system, and another in Phaseolus vulgaris (green bean), as a means for monitoring the ability of abiotic AHLs to modulate QS-regulated virulence in host infection assays. Our assays confirmed that QS modulators previously identified through culture-based assays largely retained their activity profiles when introduced into the plant host. However, inhibition of virulence in wild-type infections was highly dependent on the timing of compound dosing. This study is the first to demonstrate that our AHL analogues are active in wild-type bacteria in their native eukaryotic hosts and provides compelling evidence for the application of these molecules as probes to study QS in a range of organisms and environments.
Binding Site Dynamics and Aromatic–Carbohydrate Interactions in Processive and Non-Processive Family 7 Glycoside Hydrolases (2013)

In nature, processive and non-processive cellulase enzymes deconstruct cellulose to soluble sugars. From structural studies, the consensus is that processive cellulases exhibit tunnels lined with aromatic and polar residues, whereas non-processive cellulases exhibit open clefts with fewer ligand contacts. To gain additional insight into the differences between processive and non-processive cellulases, we examine the glycoside hydrolase family 7 (GH7) cellobiohydrolase, Cel7A, and the endoglucanase, Cel7B, from Trichoderma reesei with molecular simulation. We compare properties related to processivity and compute the binding affinity changes for mutation of four aromatic residues lining the Cel7A active site tunnel and Cel7B cleft to alanine. For the wild-type enzymes, dissimilar behavior is observed at nearly every glucopyranose-binding site from -7 to +2, except in the -2 site, suggesting that the structural differences directly around the catalytic center and at the active site tunnel entrances and exits may all contribute to processivity in GH7s. Interestingly, the -2 site is similar in both enzymes, likely due to the significant conformational change needed in the cellodextrin ligand near this site for catalysis. Moreover, aromatic residue mutations in the Cel7A and Cel7B active sites display only small differences in binding affinity, but the ligand flexibility and enzyme-ligand interactions are only locally affected in Cel7A, whereas the entire ligand is significantly affected when any aromatic residue is mutated in Cel7B.
Assessing consistency across functional screening datasets in cancer cells (2021)

Supplementary data are available at Bioinformatics online.
Properties of acetylcholine-receptor activation in human Duchenne muscular dystrophy myotubes (1989)

In human myotubes cultured from biopsies of normal subjects and dystrophic patients we investigated, with the patch-clamp technique, the activation properties of the nicotinic acetylcholine receptor (AChoR) in the presence of acetylcholine and suberyldicholine. The single-channel conductance and the lifetime of the openings were not found to differ. In contrast, the average frequency of openings was about four times higher in Duchenne muscular dystrophy (DMD) myotubes in the presence of equal amounts of acetylcholine, but not of suberyldicholine. The most reasonable conclusion from this observation is that the behaviour of the AChoR is not altered in DMD cells but that there is a greater average concentration of ACho molecules present around AChoRs. This leads to the tentative conclusion that the activity of the enzyme acetylcholinesterase (AChoE) is impaired by some unknown mechanism in the dystrophic myotube.
Performance Maximization of In-Memory Reinforcement Learning with Variability-Controlled Hf1-xZrxO2 Ferroelectric Tunnel Junctions (2019)

We develop strategies to maximize the performance and reliability of in-memory reinforcement learning (RL) with Hf <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (HZO) ferroelectric tunnel junction (FTJ) by structural and material engineering. Simulation results of RL suggest that small cycle-to-cycle variability is desirable for effective policy finding while large operation voltage margin (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> ), which is the difference between breakdown voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BD</sub> ) and set voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">set</sub> ), facilitates V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">set</sub> tuning for performance maximization. HZO thinning is effective to reduce the variability as a result of reduced effect of traps on the current, while V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> can be increased with decreasing Zr concentration. We also found that device size scaling enables low-power, high-density, and high-reliability RL with keeping the learning performance.
Application of Enzymes in Industrial Organic Synthesis (1997)

Aminopeptidase- and amidase-based methods for the production of enantiomerically pure amino acids, intermediates for pharmaceuticals and agrochemicals, are discussed. Furthermore, enzymatic syntheses of the dipeptide sweetener aspartame and semisynthetic antibiotics (such as ampicillin, amoxicillin, cephalexin, and cefadroxil) are highlighted.
Thermal characterization of the inter-die thermal resistance of hybrid Cu/dielectric wafer-to-wafer bonding (2016)

In this paper, we present the design of a passive test chip with thermal test structures in the Metal 1 layer of the back-end of Line (BEOL) for the experimental thermal characterization of the inter-die thermal resistance of wafer-pairs fabricated by hybrid Cu/dielectric wafer-to-wafer bonding. The thermal test structures include heater elements and temperature sensors. The measurement data is combined with a modeling study to extract the thermal resistance of the bonded interface for the fabricated bonded wafer pair. The extracted thermal resistance of the die-die interface created by hybrid wafer-to-wafer bonding is compared to literature data on µbump stacking. The low thermal resistance of the thin bonded dielectric interface indicates that hybrid Cu/dielectric bonding is a promising technology to create 3D chip stacks with a low thermal die-to-die resistance.
Focal Enterocyte Vacuolization: A New Microscopic Finding in the Acquired Immune Deficiency Wasting Syndrome (1993)

Vacuolization of duodenal enterocytes was found by light microscopic examination in five patients meeting the Centers for Disease Control criteria for the acquired immunodeficiency wasting syndrome. Four of these patients had chronic diarrhea and malabsorption as documented by an abnormal D-xylose test, whereas one patient had no diarrhea or malabsorption. Enterocyte vacuolization was patchy in distribution, although affected cells were most notable on villous tips. Staining with period acid-Schiff, acid-fast bacilli, periodic acid-Schiff following diastase treatment, Congo red, and alcian blue were negative, suggesting that vacuolization is due to lipid accumulation. Immunoperoxidase staining for the human immunodeficiency virus envelope protein gp41 was positive in lamina propria mononuclear cells in all five patients. The authors hypothesize that lipid accumulation represents an enterocyte response to injury, possibly by an indirect effect of the human immunodeficiency virus.
EventCube (2013)

A large portion of real world data is either text or structured (e.g., relational) data. Moreover, such data objects are often linked together (e.g., structured specification of products linking with the corresponding product descriptions and customer comments). Even for text data such as news data, typed entities can be extracted with entity extraction tools. The EventCube project constructs TextCube and TopicCube from interconnected structured and text data (or from text data via entity extraction and dimension building), and performs multidimensional search and analysis on such datasets, in an informative, powerful, and user-friendly manner. This proposed EventCube demo will show the power of the system not only on the originally designed ASRS (Aviation Safety Report System) data sets, but also on news datasets collected from multiple news agencies, and academic datasets constructed from the DBLP and web data. The system has high potential to be extended in many powerful ways and serve as a general platform for search, OLAP (online analytical processing) and data mining on integrated text and structured data. After the system demo in the conference, the system will be put on the web for public access and evaluation.
Somatic Gene Therapy for Diabetes With an Immunological Safety System for Complete Removal of Transplanted Cells (1992)

To develop somatic gene therapy for diabetes, we studied an animal model with proinsulin-producing fibroblasts with an immunological safety system. Cultured mouse fibroblasts of the Ltk- cell line were transfected first with the efficient human proinsulin expression vector pBMG-Neo-Ins. Initially, 2 x 10(6) cells with a proinsulin-production rate of 91 ng.24 h-1.10(6) cells-1 were transplanted i.p. into streptozocin-induced diabetic C3H mice. The blood glucose concentrations improved between the first and the 28th day, but the animals died of hypoglycemia between the 29th and 46th days. The proinsulin-producing Ltk- cells were further transfected with a second plasmid, pHEBo-CD8.2, encoding BALB/c mouse T-cell differentiation antigen. The CD8.2 allotype is different from CD8.1 allotype by only one amino acid substitution and should be only slightly antigenic to the recipient C3H mice. Somatic gene therapy with these doubly transfected cells followed by the consecutive administration of a monoclonal antibody to CD8.2 resulted in an initial decrease of blood glucose concentrations followed by the permanent recurrence of hyperglycemia, thus proving the complete removal of the transplanted cells. Cultured fibroblasts were thus proven capable of supplying sufficient proinsulin to lower the blood glucose concentrations in diabetic animals. The immunological safety system with a combination of artificial expression of cell surface antigen and the administration of the specific monoclonal antibody was an effective safety system for somatic gene therapy.
Lithium Ion Conducting Polymeric Hybrids (1984)

Abstract Plastic solid electrolytes were prepared from inorganic lithium salts and polymer matrixes, and their ionic conductivity was discussed in relation to the ordering or the space distribution state of conduction column. When the hybrids took the micro-segregated structure with the continuous cylindrical conduction column embedded in supporting polymer matrixes, the ionic conductivity was enhanced. Thus formulated polymeric hybrids gave the ionic conductivity of 10–5 S/cm and excellent processibility.
Effect of nitrogen plasma on the surface of indium oxide nanowires (2012)

The change in the atomic nitrogen concentration on a semiconducting nanowire's surface and the consequent changes in the electrical characteristics of a nanowire transistor were investigated by exposing In(2)O(3) nanowires to nitrogen (N(2)) plasma. After plasma was applied at N(2) flow rates of 20, 40, and 70 sccm with a fixed source power of 50 W, the In(2)O(3) nanowire transistor exhibited changes in the threshold voltage (V(th)), subthreshold slope (SS), and on-current (I(on)). In particular, after treatment at an N(2) flow rate of 40 sccm, V(th) shifted positively by ~2.3 V, the SS improved by ~0.24 V/dec, and I(on) increased by ~0.8 μA on average. The changes are attributed to the combination of nitrogen ions produced by the plasma with oxygen vacancies or indium interstitials on the nanowires. Optimization of the plasma treatment conditions is expected to yield desirable device characteristics by a simple, nondestructive process.
Adversarial Examples that Fool both Computer Vision and Time-Limited Humans (2018)

Machine learning models are vulnerable to adversarial examples: small changes to images can cause computer vision models to make mistakes such as identifying a school bus as an ostrich. However, it is still an open question whether humans are prone to similar mistakes. Here, we address this question by leveraging recent techniques that transfer adversarial examples from computer vision models with known parameters and architecture to other models with unknown parameters and architecture, and by matching the initial processing of the human visual system. We find that adversarial examples that strongly transfer across computer vision models influence the classifications made by time-limited human observers.
Radical chain reactions in pyrolytic cleavage of the ether linkages of lignin model dimers and a trimer (2009)

Abstract β-Ether-type dimers, [1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)-1-propanol and 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1-propanol], and an α,β-diether-type trimer [1-(4-(3,4-dimethoxybenzyloxy)-3-methoxyphenyl) -2- (2-methoxyphenoxy) -1-propanol] were pyrolyzed in a closed ampoule reactor (N 2 /250–400°C/2 min). 1-Phenylpropenes (C α =C β ) and 1-phenylpropanones (C α =O) were obtained as the major β-ether-cleaved products. Radical chain mechanisms are proposed in which hydrogen abstraction at the phenolic O- H and C α - H s occurs, respectively. The former reaction which gives rise to three radical species was much more effective than the latter. As the effective reaction increases the radical concentration, cleavage of the β-ether linkage in the phenolic dimer is achieved at a much lower temperature (260°C) than that of the non-phenolic type (360°C). Radical chain reactions are initiated in the case of the trimer with a weak C α -O bond at lower temperature (320°C) than those of the non-phenolic (methylated) dimer, since homolysis of the C α -O bond produces the phenoxy type dimer and 3,4-dimethoxybenzyl radicals as initiators. However, some of the dimer phenoxyl radical was stabilized by H-abstraction (to form dimer) or by recombination with a 3,4-dimethoxybenzyl radical (to form C-benzylated products) so that the chain depolymerization via quinone methide intermediate was suppressed.
Ultra Low-Energy SRAM Design for Smart Ubiquitous Sensors (2012)

Medical diagnosis and healthcare are at the onset of a revolution fueled by improvements in smart sensors and body area networks. Those sensor nodes' computation and memory requirements are growing, but their energy resources do not increase; thus, more energy-efficient memories and processors are required. New circuit-design techniques that drastically reduce the static RAM (SRAM) memories' energy consumption while still achieving tens of megahertz of operation are discussed.
C(3)-cyclopropyl cephems and carbacephems. (1989)

A series of C(3)-cyclopropyl cephems and carbacephems has been prepared by palladium catalyzed addition of diazomethane to the corresponding C(3)-vinyl derivatives. The phenylglycyl cyclopropyl cephem derivatives exhibit better Gram-positive activity than cephalexin or cefaclor, while the aminothiazole oxime cyclopropyl cephem derivatives were not as active as the corresponding C(3)-vinyl cephems.
Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production (2015)

In the current study, an L-ascorbic acid pathway using D-galacturonic acid as a precursor was introduced to a microorganism for the first time. This is also the first report on an engineered filamentous fungus for L-ascorbic acid production and a proof-of-concept of consolidated bioprocess for the production.
A Context Sharing Message Broker Architecture to Enhance Interoperability in Changeable Environments (2009)

With the growing number of mobile devices connected to the network, demand for appropriate services according to the situational contexts of users is increasing. However, building such context-aware applications is costly because both the environments of users in the real world and available services on the network are dynamically changing. In this paper, we propose a Context Sharing Message Broker Architecture which supports applications in changeable environments which cooperate with each other. The message broker provides a common context model which applications can share. A context model works not only as a common interface to the real world context, but also as a common interface to the applications which share the context model. Applications only access the context model, and they do not directly communicate with each other. This approach has three advantages; this architecture reduces the complexity of distributed context-aware systems; the architecture keeps applications independent from each other; applications can maintain their common context model cooperatively. These advantages enable applications to cooperate, and yet keep applications independent from each other.
Surface Tension Effects In Microlithography - Striations (1986)

Surface tension plays a role in many areas of lithography. One of them has been found to be formation of Benard cells in photoresist coatings at the center of a wafer. A relationship between these cells and ,&apos;riations is proposed. Observations of the effects of evaporation, gravity, radius, dispense flow, spiv, lme, spin speed, type of solvent, type of solute and concentration of surfactant suggest that the formation of cells and striations follows the same principles that are active in conventional thick coatings. Surface tension measurements are reported that support this conclusion.
Novel "Dual Hit" Rat Model of Diabetic Cardiomyopathy (2018)

The pathogenesis of diabetic cardiomyopathy (DC) is poorly understood and new drugs targeting the myocardium are absent. This may be ascribed to the failure of available pre-clinical models to recapitulate essential clinical features of DC and heart failure. We hypothesized that the combination of experimental diabetes and pharmacologically induced cardiac stress might provide a novel rat model displaying a distinct profile of DC. Non-insulin dependent type 1 like diabetes mellitus was induced by partial (90%) pancreatectomy (Px). Pronounced hyperglycemia was established within two weeks (blood glucose levels of 23.3 ± 3.7 mM). Five weeks post Px or sham surgery, vehicle or the sympathomimetic agent, isoproterenol (Iso, 1 mg/kg, SC) was administered for 10 days. Ten weeks after surgery, the heart was isolated for detailed histological and molecular characterization. The relative weight of the left ventricle (LV) was significantly increased in Px-Iso rats compared to sham-vehicle treated control rats (0.22 ± 0.03 vs. 0.25 ± 0.02 mg/g BW, p&amp;lt;0.05), indicating Px-Iso-induced cardiac hypertrophy. Compared to sham-vehicle rats, cardiac muscle fibers of Px-vehicle rats had attenuated respiratory function and increased reliance upon oxidation of fatty acid substrates, measured by high-resolution respirometry. Interestingly, this aggravation was reversed in Px-Iso rats. Moreover, Iso induced cardiac fibrosis demonstrated by quantitative histology (area fraction; Px-vehicle vs. Px-Iso: 3.1 ± 0.2% vs. 6.3 ± 0.5%; Sham-vehicle vs. Sham-Iso: 3.7 ± 0.4% vs. 7.6 ± 0.5%, p&amp;lt;0.001). Echo- and electrocardiography as well as transcriptome analyses were applied to further assess LV remodeling and cardiac function. In conclusion, the Px-Iso rat model may provide a state-of-the-art model of DC displaying key features of the clinical condition. Hereby, this model may be useful in the evaluation of cardiovascular effects of novel compounds in the pre-clinical phase of drug development. Disclosure L. Thisted: Employee; Self; Gubra. R.T. Lindsay: None. K. Fosgerau: Stock/Shareholder; Self; Novo Nordisk A/S. Employee; Self; Gubra. Stock/Shareholder; Self; Gubra. T. Secher: Employee; Self; Gubra. Employee; Spouse/Partner; Novo Nordisk A/S. M.B. Thomsen: None. T. Jespersen: None. A.J. Murray: None. P.J. Pedersen: None. N. Vrang: Board Member; Self; Gubra. Employee; Self; Gubra. Stock/Shareholder; Self; Gubra. L.N. Fink: Employee; Self; Gubra. Stock/Shareholder; Self; Novo Nordisk A/S. T.X. Pedersen: Employee; Self; Gubra. N.E. Zois: Employee; Self; Gubra.
Considerations for development of sensing and monitoring tools to facilitate treatment and care of persons with lower-limb loss: A review (2014)

Sensing and monitoring technologies offer enormous potential to enhance the quality of healthcare provided to persons with lower-limb loss. Incorporation of these technologies into the rehabilitation process creates opportunities for a multidimensional exchange of timely, relevant, and meaningful health information between patients, their prostheses, and healthcare providers. Here, the authors envision a conceptual model for enhancing prosthetic rehabilitation through use of integrated physical and/or biological sensors and remote monitoring methods. Several specific applications that target treatment, diagnosis, and prognosis of health issues faced by persons with limb loss are proposed in an effort to demonstrate how collecting and using objective data can facilitate clinical decision making. Contemporary integrated sensors that may be used in these applications are reviewed and their limitations discussed. It is hoped that the considerations proposed here may serve to stimulate development of clinically useful monitoring and sensing technologies and promote their integration into routine amputation rehabilitation.
Evaluation of BART for measuring available bandwidth in an industrial application (2009)

We report results from a field study using the BART method for measuring available bandwidth in a local IP-network for use in train cars. The test was performed on physical hardware in a laboratory environment for a set of two cars. Test results indicate that BART measurement is viable.
Sonographic appearance of fallopian tube carcinoma (2005)

Fallopian tube carcinoma is the least common of gynecological malignancies. We report the case of a 56-year-old woman who presented with a 2 1/2-year history of intermittent vaginal bleeding and lower abdominal pain. Transvaginal sonography revealed a cystic lesion of the fallopian tube with papillary projections, distinct from the ovary and uterus. Doppler examination showed low vascular impedance (resistance index 0.50, pulsatility index 0.80). The suspicion of tubal malignancy was confirmed at surgery.
An Efficient and Rapid Chalcogenide‐Morita—Baylis—Hillman Process Promoted by TBDMSOTf and a Thiolane. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.