gebhart/patrepeval huggingface dataset:
The Pseudomonas aeruginosa oxidative stress regulator OxyR influences production of pyocyanin and rhamnolipids: protective role of pyocyanin (2009)

The LysR-type transcriptional regulator (LTTR) OxyR orchestrates the defence of the opportunistic pathogen Pseudomonas aeruginosa against reactive oxygen species. In previous work we also demonstrated that OxyR is needed for the utilization of the ferrisiderophore pyoverdine, stressing the importance of this regulator. Here, we show that an oxyR mutant is unable to swarm on agar plates, probably as a consequence of absence of production of rhamnolipid surfactant molecules. Another obvious phenotypic change was the increased production of the phenazine redox-active molecule pyocyanin in the oxyR mutant. As already described, the oxyR mutant could not grow in LB medium, unless high numbers of cells (&gt;10 8 ml −1 ) were inoculated. However, its growth in Pseudomonas P agar (King's A), a medium inducing pyocyanin production, was like that of the wild-type, suggesting a protective action of this redox-active phenazine compound. This was confirmed by the restoration of the capacity to grow in LB medium upon addition of pure pyocyanin. Although both rhamnolipid and pyocyanin production are controlled by quorum sensing, no obvious changes were observed in the production of N -acylhomoserine lactones or the Pseudomonas quinolone signal (PQS). Complementation of rhamnolipid production and motility, and restoration of normal pyocyanin levels, was only possible when the oxyR gene was in single copy, while pyocyanin levels were increased when oxyR was present in a multicopy vector. Conversely, plating efficiency was increased only when the oxyR gene was present in multicopy, but not when in single copy in the chromosome, due to lower expression of oxyR compared with the wild-type, suggesting that some phenotypes are differently affected in function to the levels of OxyR molecules in the cell. Analysis of transcripts of oxidative stress-response enzymes showed a strong decrease of katB , ahpC and ahpB expression in the oxyR mutant grown in LB, but this was not the case when the mutant was grown on P agar, suggesting that the OxyR dependency for the transcription of these genes is not total.
Multimedia structured reporting employing natural language processing to improve the efficiency of data entry (2018)

Poster: ECR 2018 / C-2810 / Multimedia structured reporting employing natural language processing to improve the efficiency of data entry by: D. J. Vining, A. Pitici, C. Popovici, A. Prisacariu, M. Kontak; Houston, TX/US
Synthesis and Quality of Cr-doped AIN Thin Films Grown by RF Sputtering (2007)

The AlCrN films were grown by RF reactive sputtering method under the selected conditions. The Cr concentration was varied by the number of Cr pieces placed on the Al target. The sample quality has been studied by XRD, Auger spectroscopy, optical absorption and electrical resistant measurements. The XRD and Auger results show that the samples consist of a major phase with the <TEX>$Al_{1-x}Cr_xN$</TEX> formula, which has a hexagonal structure, and a few percents at. of oxygen, which may form <TEX>$Al_2O_3$</TEX>. There exist the Cr clusters in the samples with high concentration of Cr. The optical absorption measurement provides the information about the band gap that relates strongly to the quality of samples. The quality of samples is also clearly reflected in electrical measurement, i.e., the temperature dependence of resistance exhibits a semiconductor characteristic only for the samples that have no Cr cluster. In these cases, the values of ionization energies <TEX>$E_a$</TEX> can be derived from R(T) plots by using the function R(T) = Ro exp <TEX>$(E_a/k_BT)$</TEX>.
Overcoming the "Memory Wall" by improved system design exploration and a link to process technology options (2004)

Data transfer and storage issues "take the centre stage" in information and communication systems because of the increasing complexity and data dominance typically associated to them. In this paper, we summarise a systematic methodology for the power critical storage modules such as local SRAMs. We focus on their memory organisation (access schedule and data assignment) together with an exploration of the effect that the interconnect technology may have on the energy consumed by these local memory organisations in deep sub-micron technologies.
Reply to J. Devulder (1991)

Department of Neurosurgery, Johns Hopkins University, Baltimore, MD 21205 U.S.A. ∗Correspondence to: Richard B. North, M.D., Assoc. Prof., Department of Neurosurgery, Johns Hopkins University, 600 North Wolfe Street, Baltimore, MD 21205, U.S.A. Submitted April 22, 1991; accepted May 8, 1991.
Effect of AXS-05 (Dextromethorphan-Bupropion) in Major Depressive Disorder: A Randomized Double-Blind Controlled Trial (2022)

In patients with major depression, dextromethorphan-bupropion (AXS-05) significantly improved depressive symptoms compared with bupropion and was generally well tolerated.
Compatibility of polysilicon with HFO2-BASED gate dielectrics for CMOS applications (2003)

The compatibility of HfO 2 gate dielectric films using polysilicon deposited under varying conditions as gate electrode has been systematically studied. Gate leakage current of capacitors was monitored as a metric for compatibility. Measurements after activation anneals show that for HfO 2 films, low temperature amorphous depositions show low leakage while with crystalline polySi depositions shorted capacitors resulted. For the HfO 2 films covered by a capping layer, the crystalline poly depositions show lower leakage than amorphous depositions. The high leakage with crystalline polysilicon electrodes is speculated as being due to the presence of weak spots or defects in the film which in the presence of a reducing ambient during polySi deposition become high-leakage conduction paths. The presence of Si within the HfO 2 film detected by TOF-SIMS supports this hypothesis.
Evidence for electric field-assisted dissociation of the excited singlet state into charge carriers in MEH–PPV (1998)

Electric field-modulated time-resolved fluorescence was measured in films of MEH–PPV. For excitation near the absorption edge, the applied field leads only to a decrease of fluorescence lifetimes, leaving the initial fluorescence amplitude unaffected, which indicates direct dissociation of the excited states into electron–hole pairs. For higher energy excitation, a small reduction in the initial fluorescence amplitude is also observed. In this case, energy migration from higher to lower energy sites results in a small amplitude quenching. These experimental results are difficult to reconcile with the band model, which suggests direct generation of electron–hole pairs by optical excitation.
CTGF directs fibroblast differentiation from human mesenchymal stem/stromal cells and defines connective tissue healing in a rodent injury model (2015)

Fibroblasts are ubiquitous cells that demonstrate remarkable diversity. However, their origin and pathways of differentiation remain poorly defined. Here, we show that connective tissue growth factor (CTGF; also known as CCN2) is sufficient to induce human bone marrow mesenchymal stem/stromal cells (MSCs) to differentiate into fibroblasts. CTGF-stimulated MSCs lost their surface mesenchymal epitopes, expressed broad fibroblastic hallmarks, and increasingly synthesized collagen type I and tenacin-C. After fibroblastic commitment, the ability of MSCs to differentiate into nonfibroblastic lineages - including osteoblasts, chondrocytes, and adipocytes - was diminished. To address inherent heterogeneity in MSC culture, we established 18 single MSC-derived clones by limiting dilution. CTGF-treated MSCs were alpha-SMA-, differentiating into alpha-SMA+ myofibroblasts only when stimulated subsequently with TGF-beta1, suggestive of stepwise processes of fibroblast commitment, fibrogenesis, and pathological fibrosis. In rats, in vivo microencapsulated delivery of CTGF prompted postnatal connective tissue to undergo fibrogenesis rather than ectopic mineralization. The knowledge that fibroblasts have a mesenchymal origin may enrich our understanding of organ fibrosis, cancer stroma, ectopic mineralization, scarring, and regeneration.
Advances in Drug Design of Radiometal-Based Imaging Agents for Bone Disorders (2011)

Nuclear medicine bone imaging has been the optimum diagnosis for the detection of bone disorders because the lesion could be detectable before the appearance of symptomatic and radiographic changes. Over the past three decades, (99m)Tc-MDP and (99m)Tc-HMDP have been used as bone scintigraphic agents because of their superior biodistribution characteristics, although they are far from optimal from a chemical and pharmaceutical point of view. Recently, a more logical drug design has been proposed as a concept of bifunctional radiopharmaceuticals in which the carrier molecules (bisphosphonates) and radiometal chelating groups are separated within a molecule, specifically, (99m)Tc-mononuclear complex-conjugated bisphosphonate. Some of the (99m)Tc-mononuclear complex-conjugated bisphosphonate compounds showed superior biodistribution in preclinical studies. Moreover, the drug design concept could be applied to (68)Ga PET bone imaging agents. These studies would provide useful information for the development of radiometal-based imaging and therapeutic agents for bone disorders such as bone metastases.
Urban Sensing or Personal and Participatory Sensing (2009)

Privacy is important Individuals should be able to control their time/space accountability. Our Personal Data Vault (PVD) will support individual privacy, help document data ownership, and provide visibility for data processing and inferences.Within the PDV, The TraceAudit logs and reveals all activities on the data.Adaptive filters dynamically resample data feeds to selectively share data with service providers.
Current Hot Potatoes in Atrial Fibrillation Ablation (2012)

Atrial fibrillation (AF) ablation has evolved to the treatment of choice for patients with drug-resistant and symptomatic AF. Pulmonary vein isolation at the ostial or antral level usually is sufficient for treatment of true paroxysmal AF. For persistent AF ablation, drivers and perpetuators outside of the pulmonary veins are responsible for AF maintenance and have to be targeted to achieve satisfying arrhythmia-free success rate. Both complex fractionated atrial electrogram (CFAE) ablation and linear ablation are added to pulmonary vein isolation for persistent AF ablation. Nevertheless, ablation failure and necessity of repeat ablations are still frequent, especially after persistent AF ablation. Pulmonary vein reconduction is the main reason for arrhythmia recurrence after paroxysmal and to a lesser extent after persistent AF ablation. Failure of persistent AF ablation mostly is a consequence of inadequate trigger ablation, substrate modification or incompletely ablated or reconducting linear lesions. In this review we will discuss these points responsible for AF recurrence after ablation and review current possibilities on how to overcome these limitations.
Supplementary Figure 1 from Using Tandem Mass Spectrometry in Targeted Mode to Identify Activators of Class IA PI3K in Cancer (2023)

&lt;p&gt;PDF file - 203K&lt;/p&gt;
Tumor-penetrating drug delivery for cancer therapy. (2010)

e13590 Background: Poor drug penetration is a major problem in cancer treatment that leads to ineffective therapy and drug resistance. We have discovered a tumor-specific tissue penetration system that solves this problem. It is based on a tumor-penetrating peptide, iRGD (amino acid sequence: CRGDK/RGPDC), which carries an attached payload specifically to tumors, and subsequently, deep into tumor parenchyma. Two overlapping peptide motifs account for this activity: RGD, which mediates binding to alpha-v integrins on tumor vessels, and RXXR/K (the CendR element), which induces tissue penetration through binding to neuropilin-1. We will report clinical applications of the iRGD tumor targeting system. Methods: Whole body tumor imaging and systemic treatment studies were performed in a panel of mouse xenograft tumors. The applicability of the system to human cancer was evaluated in ex vivo tumor penetrating assays using freshly excised human appediceal tumor samples according to an IRB-approved protocol. Results: iRGD significantly improved the contrast of tumor imaging agents and enhanced the activity of anticancer drugs in mice. Incubating fresh human appendiceal tumors in culture media containing the iRGD peptide or iRGD-coated phage allowed the compounds to penetrate into the tumor tissue up to about 4 mm in 90 min. Conclusions: The tumor homing iRGD peptide penetrates human tumors as well as mouse tumors. The penetration occurs even in the absence of circulation by initiating an active transport pathway. The technology can be used to enhance both systemic and local delivery of drugs into tumor tissue. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration ACT, CTI VSB Invitrogen, NCI ICMIC
The kinetics of inactivation of spheroidal microbial cells by pulsed electric fields (2007)

The nature of non-exponential kinetics in microbial cells inactivation by pulsed electric fields (PEF) is discussed. It was demonstrated that possible mechanism of non-exponential kinetics can be related to orientational disorder in suspension of microbial cells of anisotropic form. A numerical studies of spheroidal cell suspensions was carried out. The most pronounced deviations from the exponential kinetics were observed for disordered suspensions of prolate spheroids at small electric field strength $E$ or at large aspect ratio $a$. For partially oriented suspensions, efficiency of inactivation enhances with increasing of order parameter and field strength. A possibility of the PEF-induced orientational ordering in microbial suspensions is discussed.
Structural Basis for the Recognition of para‐Benzoyl‐L‐phenylalanine by Evolved Aminoacyl‐tRNA Synthetases (2007)

Nichtnatürliche Wechselwirkungen: Die Röntgenkristallstruktur einer mutierten Aminoacyl-tRNA-Synthase, die selektiv para-Benzoyl-L-phenylalanin erkennt, wurde gelöst. Die Mutationen im Enzym führen zu neuen hydrophoben Wechselwirkungen mit der nichtnatürlichen Aminosäure und zum Verlust von spezifischen Wasserstoffbrückenwechselwirkungen mit Tyrosin, ohne dass eine signifikante Änderung in der Konformation des Polypeptid-Rückgrats auftritt.
Towards markerless surgical tool and hand pose estimation (2021)

: To the best of our knowledge, we propose the first synthetic and real data generation pipelines to generate hand and object pose labels for open surgery. We present three baseline models for RGB based object and object/hand pose estimation based on RGB frames. Our realistic synthetic data generation pipeline may contribute to overcome the data bottleneck in the surgical domain and can easily be transferred to other medical applications.
ON THE RATE OF CONVERGENCE OF THE SPHERICAL-HARMONICS METHOD IN THE MILNE PROBLEM (1958)

The extrapolated end point, z 0 , and the ratio of current to flux at the free surface, j(0)/ρ(0), for the Milne problem are evaluated by the spherical-harmonics method in the P N approximation, N being odd. It is shown that, for N large, the approximations to these quantities are related to the exact values by[Formula: see text]in which c is the number of secondaries per collision, f 1 (c) and f 3 (c) are independent of N, and ζ 1 and ζ 2 are the absolutely lesser and greater roots of[Formula: see text]κ being the exact inverse diffusion length. The relation (A) is subject to the restrictions[Formula: see text]
Prolepsis (2006)

Abstract This chapter provides an analytical framework for the concept of prolepsis designed to take the term forward from Genette's influential account in such a way that it is capable of accounting for effects formerly considered as metafictional. Prolepsis, for Genette, is a moment in a narrative in which the chronological order of story events is disturbed and the narrator narrates future events out of turn. The complications in the definition of prolepsis are reported. Performative prolepsis produces the future in the act of envisaging it, so that the possible transforms itself into the actual. The relationship of Prolepsis 1 and Prolepsis 3 is the axis between time and self-consciousness, since storytelling is not just self-distance but temporal self-distance; and, on this subject, narratology has much to learn from the philosophy of time.
A novel biomarker harvesting nanotechnology identifies Bak as a candidate melanoma biomarker in serum (2010)

Our study links serum proteome analysis with confocal microscopic clinical in vivo histologic classification of melanomas. Bak has not been previously measured in serum. Bak differential expression among melanoma subtypes confirms the importance of the apoptotic pathway as a contributor to melanoma aggressiveness.
Design and Synthesis of RNA-Specific Groove-Binding Cations: Implications for Antiviral Drug Design (1994)

As as initial step in the design of structure-specific RNA-interactive molecules as potential antiviral agents, we have focused on the synthesis of molecules that exhibit strong and preferential binding to duplex RNA. A series of polycationic ligands have been synthesized, and the degree of preferential binding to RNA has initially been determined by thermal denaturation (delta Tm) with both RNA [poly(A).poly(U)] and DNA [poly(dA).poly(dT)] polymers at a variety of pH values. Seven compounds from the series exhibit a substantial degree of RNA-selective binding. The relatively high delta Tm values obtained suggest a specific mode of interaction between these ligands and the RNA helix. By contrast, the much lower delta Tm values with poly(dA).poly(dT) DNA reflect a more nonspecific interaction mode. A viscometric titration study with poly(A).poly(U) confirms that they do not bind by intercalation. The results, combined with the known structure and electronegative potential of duplex RNA, suggest that these molecules bind in the major groove via specific electrostatic and/or hydrogen-bonded interactions.
Duration of Rhinovirus Shedding in the Upper Respiratory Tract in the First Year of Life (2014)

Although rhinovirus infections are common in healthy infants, prolonged presence of rhinovirus RNA in the respiratory tract after an upper respiratory infection was uncommon (<5%). Detection of rhinovirus RNA in an infant most likely represents an infection within a 30-day period.
Measurement of multipath interference in the coherent cross-talk regime (2004)

We compare various techniques to measure MPI in devices exhibiting distributed coherent crosstalk. Such devices are susceptible to deterministic noise as well as intermittent fading, and the measurement technique employed must capture both these manifestations of MPI. We evaluate several measurement techniques used to characterise MPI in few mode fibers. The coherent, distributed nature of MPI in few-mode fibers leads to fast fluctuations, manifesting in deterministic noise, as well as slow variations, reminiscent of fading in mobile communications systems. Slow temporal intensity variations of a CW DFB laser captures most of the relevant information.
Copolymerization of carbon monoxide and norbornadiene with a palladium catalyst (1997)

Carbon monoxide (CO) and norbornadiene (NBD) with Pd(CH3CN)4(BF4)2 were copolymerized under various conditions at 50°C. Elemental analysis, infrared spectra, UV, Raman, and NMR spectra showed that the copolymers contained both ketone and unsaturated ring structures. Bidentate nitrogen ligands and phosphorus ligands proved to be more effective at stabilizing catalytic activity than monodentate arsenic ligands or phosphorus ligands. Methanol, protic acid, and an oxidant served as the coinitiator and chain transfer agent, respectively. X-ray diffraction analysis showed the copolymer to be partially crystalline. Thermogravimetric analysis showed that the TG curve for the NBD/CO copolymer has two stages with two maxima peaks at 251 and 470°C. This phenomenon was probably due to increased instability of the copolymers as CO content is increased. Hydrogenation of norbornadiene/CO copolymer with LiAlH4 and Pd/C in THF yields a hydroxyl-containing polymer and norbornene/CO copolymer, respectively. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 1157–1166, 1997
Functional Magnetic Resonance Imaging (2005)

Functional Magnetic Resonance Imaging 

edited by Scott A. Huettel, Allen W. Song, and Gregory McCarthy, 492 pp., Sunderland, MA, Sinauer Associates, 2004, $79.95

Not long ago, if one planned to teach a course on MRI, it was necessary to come up with original lecture notes and assign primary readings because MRI was such a novel (and peculiar) mix of physics, imaging, and high-tech gadgets. Then came the explosion of applications of MRI, notably studies of brain function using blood oxygen level-dependent (BOLD) fMRI, and along with these advances came many books on the topic. The problem of selecting a textbook suddenly reversed; there were too many books (some of them very good) …
Learning Causal Effects on Hypergraphs (2022)

Hypergraphs provide an effective abstraction for modeling multi-way group interactions among nodes, where each hyperedge can connect any number of nodes. Different from most existing studies which leverage statistical dependencies, we study hypergraphs from the perspective of causality. Specifically, in this paper, we focus on the problem of individual treatment effect (ITE) estimation on hypergraphs, aiming to estimate how much an intervention (e.g., wearing face covering) would causally affect an outcome (e.g., COVID-19 infection) of each individual node. Existing works on ITE estimation either assume that the outcome on one individual should not be influenced by the treatment assignments on other individuals (i.e., no interference), or assume the interference only exists between pairs of connected individuals in an ordinary graph. We argue that these assumptions can be unrealistic on real-world hypergraphs, where higher-order interference can affect the ultimate ITE estimations due to the presence of group interactions. In this work, we investigate high-order interference modeling, and propose a new causality learning framework powered by hypergraph neural networks. Extensive experiments on real-world hypergraphs verify the superiority of our framework over existing baselines.
WordGesture-GAN: Modeling Word-Gesture Movement with Generative Adversarial Network (2023)

Word-gesture production models that can synthesize word-gestures are critical to the training and evaluation of word-gesture keyboard decoders. We propose WordGesture-GAN, a conditional generative adversarial network that takes arbitrary text as input to generate realistic word-gesture movements in both spatial (i.e., (x, y) coordinates of touch points) and temporal (i.e., timestamps of touch points) dimensions. WordGesture-GAN introduces a Variational Auto-Encoder to extract and embed variations of user-drawn gestures into a Gaussian distribution which can be sampled to control variation in generated gestures. Our experiments on a dataset with 38k gesture samples show that WordGesture-GAN outperforms existing gesture production models including the minimum jerk model [37] and the style-transfer GAN [31, 32] in generating realistic gestures. Overall, our research demonstrates that the proposed GAN structure can learn variations in user-drawn gestures, and the resulting WordGesture-GAN can generate word-gesture movement and predict the distribution of gestures. WordGesture-GAN can serve as a valuable tool for designing and evaluating gestural input systems.