gebhart/patrepeval huggingface dataset:
Structure-Activity Relationship of Cinnamaldehyde Analogs as Inhibitors of AI-2 Based Quorum Sensing and Their Effect on Virulence of Vibrio spp (2011)

Several new and more active cinnamaldehyde analogs were discovered and they were shown to affect Vibrio spp. virulence factor production in vitro and in vivo. Although ligands for LuxR have not been identified so far, the nature of different cinnamaldehyde analogs and their effect on the DNA binding ability of LuxR suggest that these compounds act as LuxR-ligands.
Nanocrystal–ligand interactions deciphered: the influence of HSAB and pKa in the case of luminescent ZnO (2020)

Despite all the efforts made by the scientific community to rationalize the interaction of organic molecules with nanocrystals (Ncs), we are still at the level of the empirical recipe when the material behavior in solution is concerned. In an effort to address this issue, the analysis of the luminescence measurements of ZnO Ncs in the presence of various organic substrates using a Langmuir adsorption model was carried out to determine for the first time the affinity constants and the number of binding sites as well as to rank the interaction strengths of these substrates with regard to ZnO Ncs. The results were confirmed by NMR spectroscopic studies, which, besides, provided a deep understanding of the substrate-ZnO Nc interactions. Analysis of the results using p<i>K</i> <sub>a</sub> and HSAB theory demonstrates that the interaction of a given substrate can be determined by its p<i>K</i> <sub>a</sub> <i>versus</i> the p<i>K</i> <sub>a</sub> of the organic molecules present at the surface of pristine Ncs and that the hard or soft character of the substrates can govern the emission intensity of the ZnO Ncs.
Towards practical deteministic write-all algorithms (2001)

The problem of performing t tasks on n asynchronous or undependable processors is a basic problem in parallel and distributed computing. We consider an abstraction of this problem called the Write-All problem— using n processors write 1's into all locations of an array of size t. The most efficient known deterministic asynchronous algorithms for this problem are due to Anderson and Woll. The first class of algorithms has work complexity of Ο(t . n ε), for n ≰ ty and any ε > 0, and they are the best known for the full range of processors (n = t). To schedule the work of the processors, the algorithms use sets of q permutations on [q] (q ≰ n) that have certain combinatorial properties. Instantiating such an algorithm for a specific ε either requires substantial pre-processing (exponential in 1/ε2) to find the requisite permutations, or imposes a prohibitive constant (exponential in 1/ε3) hidden by the asymptotic analysis. The second class deals with the specific case of t = nu, u ≰ 2, and these algorithms have work complexity of Ο(t log t). They also use sets of permutations with the same combinatorial properties. However instantiating these algorithms requires exponential in n preprocessing to find the permutations. To alleviate this costly instantiation Kanellakis and Shvartsman proposed a simple way of computing the permutation schedules. They conjectured that their construction has the desired properties but they provided no analysis.
Quantitation of small-animal (124)I activity distributions using a clinical PET/CT scanner. (2004)

This study indicates the feasibility of performing quantitative imaging on murine (124)I antibody fragment PET images using a large-bore clinical scanner, which enables high-throughput studies to evaluate the performance of PET tracers in a timely and cost-effective manner by imaging multiple animals simultaneously. Tracers deemed promising by this screening method can then be further evaluated using traditional necropsy studies. Our group is currently conducting time-dependent (124)I diabody PET and necropsy comparative studies with larger numbers of mice.
Landowners, Lawyers, and Land Law Reform in Nineteenth-Century England (1977)

Landowners, Lawyers, and Land Law Reform in Nineteenth-Century England Get access Eileen Spring, M.A. Eileen Spring, M.A. *The Johns Hopkins University Search for other works by this author on: Oxford Academic Google Scholar American Journal of Legal History, Volume 21, Issue 1, January 1977, Pages 40–59, https://doi.org/10.2307/844924 Published: 01 January 1977
Characterization of nanoparticle electrocatalysts using X-ray absorption spectroscopy (2015)

X-ray absorption spectroscopy (XAS) is a non-destructive spectroscopic technique commonly used with synchrotron radiation source and measures the changes of absorption coefficient as the function of the x-ray energy. Its unique power is that it can reveal the internal structure of nanoparticles, even if the particle is made up of several elements. By analyzing the results, interatomic distances and coordination numbers for each element are obtained, and their values and relationships indicate whether the elements in the nanoparticle are in a homogeneous solution, physically separated, or form a core-shell particles in which certain elements are mostly located in the core, and the other in the shell. The latter type of nanoparticles is of particular interest for the electrocatalysts as it reduces the precious metal content in the nanoparticles by replacing the precious metal in the the nanoparticles' core with less expensive alternatives. This paper describes the internal structure characterization of the nanoparticle electrocatalysts by in situ XAS, and gives certain examples of systems composed of two or three metals.
Chromosome-Specific Single-Locus FISH Probes Allow Anchorage of an 1800-Marker Integrated Radiation-Hybrid/Linkage Map of the Domestic Dog Genome to All Chromosomes (2001)

We present here the first fully integrated, comprehensive map of the canine genome, incorporating detailed cytogenetic, radiation hybrid (RH), and meiotic information. We have mapped a collection of 266 chromosome-specific cosmid clones, each containing a microsatellite marker, to all 38 canine autosomes by fluorescence in situ hybridization (FISH). A 1500-marker RH map, comprising 1078 microsatellites, 320 dog gene markers, and 102 chromosome-specific markers, has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present a karyotype in which each chromosome is identified by one meiotic linkage group and one or more RH groups. This updated integrated map, containing a total of 1800 markers, covers >90% of the dog genome. Positional selection of anchor clones enabled us, for the first time, to orientate nearly all of the integrated groups on each chromosome and to evaluate the extent of individual chromosome coverage in the integrated genome map. Finally, the inclusion of 320 dog genes into this integrated map enhances existing comparative mapping data between human and dog, and the 1000 mapped microsatellite markers constitute an invaluable tool with which to perform genome scanning studies on pedigrees of interest.
Hypnotic analgesia reduces R-III nociceptive reflex: further evidence concerning the multifactorial nature of hypnotic analgesia (1995)

Mechanisms of hypnotic analgesia were investigated by examining changes in the R-III, a nociceptive spinal reflex, during hypnotic reduction of pain sensation and unpleasantness. The R-III was measured in 15 healthy volunteers who gave VAS-sensory and VAS-affective ratings of an electrical stimulus during conditions of resting wakefulness, suggestions for hypnotic analgesia, and attempted suppression of the reflex during non-hypnotic conditions. The H-reflex was also measured to monitor and control for general changes in alpha-motoneuron excitability. Hypnotic sensory analgesia was related to reduction in the R-III after controlling for changes in the H-reflex (R2 = 0.51, P < 0.003), suggesting that hypnotic sensory analgesia is at least in part mediated by descending antinociceptive mechanisms that exert control at spinal levels in response to hypnotic suggestion. The relationship between hypnotic affective analgesia and reduction in R-III approached significance (R2 = 0.26; P = 0.053). Reduction in R-III was 67% as great and accounted for 51% of the variance in reduction of pain sensation. In turn, reduction in pain sensation was 75% as great and accounted for 77% of the variance in reduction of unpleasantness. The results suggest that 3 general mechanisms may be involved in hypnotic analgesia. The first, implicated by reductions in R-III, is related to spinal cord antinociceptive mechanisms. The second, implicated by reductions in pain sensation over and beyond reductions in R-III, may be related to brain mechanisms that serve to prevent awareness of pain once nociception has reached higher centers, as suggested by Hilgard.(ABSTRACT TRUNCATED AT 250 WORDS)
Comparison of system impedance estimating methods (2011)

This paper introduces and compares three impedance estimation techniques: FFT, PSD and CWT. The impedance of proposed system is calculated by using the injected step current transient and the measured voltage response. Both steady and noisy situation is simulated by Matlab/Simulink and the characteristics of each impedance analyzing method are demonstrated by the achieved impedance results.
Formal ratification of the Global Boundary Stratotype Section and Point (GSSP) for the Chibanian Stage and Middle Pleistocene Subseries of the Quaternary System: the Chiba Section, Japan† (2021)

by Yusuke Suganuma, Makoto Okada, Martin J. Head, Koji Kameo, Yuki Haneda, Hiroki Hayashi, Toshiaki Irizuki, Takuya Itaki, Kentaro Izumi, Yoshimi Kubota, Hiroomi Nakazato, Naohisa Nishida, Masaaki Okuda, Yasufumi Satoguchi, Quentin Simon, and Yoshihiro Takeshita. Episodes 2021;44:317-47. https://doi.org/10.18814/epiiugs/2020/020080
S129 Predicting outcome from HIV-associated pneumocystis pneumonia (2010)

<h3>Background</h3> The presentation of <i>Pneumocystis jirovecii</i> pneumonia (PCP) ranges from mild to severe. The former responds to antimicrobial therapy, the latter has a high mortality rate despite treatment. Several studies have described clinical and laboratory factors that are predictive of death from PCP. Our objectives were to create a prognostic scoring model to aid the clinician in predicting outcome from HIV-associated PCP. <h3>Methods</h3> A prognostic scoring model was built using risk factors identifiable at/soon after hospitalisation, that is, ‘by the bedside’— which have previously been identified as being associated with mortality from PCP (a repeat episode of PCP, the patient9s age, their haemoglobin (Hb), PaO<sub>2</sub> (breathing room air), both on admission, the presence of co-morbidity (Comorb), such as lymphoma or pregnancy, and the presence of pulmonary Kaposi sarcoma (PKS) (Walzer PD, <i>et al</i> CID 2008;46:625–33). The model was built from data concerning 592 consecutive episodes of PCP that had occurred among 540 patients presenting to a specialist inpatient HIV treatment centre. <h3>Results</h3> The prognostic scoring model was: [25.5 + (age in years/10) + 2 (if a repeat episode of PCP) + 4 (if PKS detected) + 4 (if Comorb present)−PaO<sub>2</sub> – Hb]. The prognostic model produced scores ranging from 0 to 20; median (IQR)=9 (7–11). Testing interactions between risk factors and time showed the model to be applicable across all time periods. Patients were divided into five groups according to prognostic score: 0–3.9=group 1, 4–7.9=group 2, 8–11.9=group 3, 12–15.9=group 4, 16 or greater =group 5. Abstract S129 Table 1 shows mortality rates among the 540 patients with PCP, grouped according to their prognostic scores. <h3>Conclusions</h3> While this prognostic scoring model requires further validation in patient cohorts from other healthcare institutions, it is potentially a simple ‘by the bedside’ method of identifying patients early in their hospital admission who are at high and low risk of in-hospital death from PCP and so may aid the clinician in assessing the severity of illness and in deciding on treatment strategies.
Copper-67 labeled porphyrin localization in inflamed tissues (1989)

A series of experiments compared the uptake of 5,10,15,20-tetrakis(4-carboxyphenyl) porphinato (/sup 67/Cu) copper(II), /sup 67/CuTCPP, by the lymph nodes of inflamed and two sets or control rats. The results demonstrate that /sup 67/CuTCPP localizes in greater concentration in inflamed lymph nodes than in noninflamed control lymph nodes. This enhanced uptake of /sup 67/CuTCPP by inflamed lymph nodes was 3.6 times greater than was the uptake by control lymph nodes. A time course study demonstrated that the uptake of /sup 67/CuTCPP inflamed lymph nodes reached the maximum level by 24 hours post-injection of /sup 67/CuTCPP and remained constant throughout the 96 hours examined. It was also found that the uptake of /sup 67/CuTCPP by inflamed lymph nodes was not exclusively dependent upon an increase in the weight of inflamed lymph nodes. These studies show that /sup 67/CuTCPP has potential as a lymphoscintigraphy agent. 29 refs., 5 figs., 1 tab.
The Complexity of Animal Model Generation for Complex DiseasesANIMAL MODEL GENERATION FOR COMPLEX DISEASES (2010)

Daniel M. Albert, MD, MS; Aneesh Neekhra, MD; Shoujian Wang, MD, PhD; Soesiawati R. Darjatmoko, BS; Christine M. Sorenson, PhD; Richard R. Dubielzig, DVM; Nader Sheibani, PhDObjectives To study the progressive changes of intense cyclic light–induced retinal degeneration and to determine whether it results in choroidal neovascularization (CNV).Methods Albino rats were exposed to 12 hours of 3000-lux cyclic light for 1, 3, or 6 months. Fundus examination, fundus photography, fluorescein and indocyanine green angiography, and optical coherence tomography were performed prior to euthanization. Light-exposed animals were euthanized after 1, 3, or 6 months for histopathological evaluation. Retinas were examined for the presence of 4-hydroxy-2-nonenal– and nitrotyrosine-modified proteins by immunofluorescence staining.Results Long-term intense cyclic light exposure resulted in retinal degeneration with loss of the outer segments of photoreceptors and approximately two-thirds of the outer nuclear layer as well as development of subretinal pigment epithelium neovascularization after 1 month. Almost the entire outer nuclear layer was absent with the presence of CNV, which penetrated the Bruch membrane and extended into the outer retina after 3 months. Absence of the outer nuclear layer, multiple foci of CNV, retinal pigment epithelial fibrous metaplasia, and connective tissue bands containing blood vessels extending into the retina were observed after 6 months. All intense light–exposed animals showed an increased presence of 4-hydroxy-2-nonenal and nitrotyrosine staining. Optical coherence tomographic and angiographic studies confirmed retinal thinning and leakiness of the newly formed blood vessels.Conclusions Our results suggest that albino rats develop progressive stages of retinal degeneration and CNV after long-term intense cyclic light exposure, allowing the detailed study of the pathogenesis and treatment of age-related macular degeneration.Clinical Relevance The ability to study the progressive pathogenesis of age-related macular degeneration and CNV will provide detailed knowledge about the disease and aid in the development of target-specific therapy.
Simultaneous Detection and Identification of Human Parainfluenza Viruses 1, 2, and 3 from Clinical Samples by Multiplex PCR (1998)

Reverse transcription (RT)-PCR assays have been widely described for use in the diagnosis of human parainfluenza viruses (HPIVs) and other respiratory virus pathogens. However, these assays are mostly monospecific, requiring separate amplifications for each HPIV type. In the present work, we describe multiplex RT-PCR assays that detect and differentiate HPIV serotypes 1, 2, and 3 in a combined reaction. Specifically, a mixture of three pairs of primers to conserved regions of the hemagglutinin-neuraminidase gene of each HPIV serotype was used for primary amplification, yielding amplicons with similar sizes. For typing, a second amplification was performed with a mixture of nested primers, yielding amplicons with sizes easily differentiated by agarose gel electrophoresis. A modified single-amplification RT-PCR assay with fluorescence-labeled nested primers, followed by analysis of the labeled products on an automated sequencing gel, was also evaluated. Fifteen temporally and geographically diverse HPIV isolates from the Centers for Disease Control and Prevention archives and 26 of 30 (87%) previously positive nasopharyngeal specimens (8 of 10 positive for HPIV serotype 1 [HPIV1], 9 of 10 positive for HPIV2, and 9 of 10 positive for HPIV3) were positive and were correctly typed by both assays. Negative results were obtained with naso- or oropharyngeal specimens and/or culture isolates of 33 unrelated respiratory tract pathogens, including HPIV4, enterovirus, rhinovirus, respiratory syncytial virus, adenovirus, influenza virus, and Streptococcus pneumoniae. Our multiplex RT-PCR assays provide sensitive, specific, and simplified tools for the rapid diagnosis of HPIV infections.
A Tale of Two Fashions: An Empirical Study on the Performance of Native Apps and Web Apps on Android (2017)

prevalent smartphones have become the major entrance to accessing services on the Internet. On smartphones, users can have two options as the clients, i.e., native apps and Web apps. There have been several debates about native apps and Web apps. However, major service providers such as Google, Amazon, and Facebook provide both native apps and Web apps to end-users. Essentially, the performance differences between these two types of apps haven't been addressed. Indeed, the performance differences make non-trivial impacts on apps development, deployment, and distribution. In this article, we conduct a measurement study on the performance of native apps and Web apps on Android smartphones. Specifically, we want to explore given the same functionalities, do Web apps always perform poorly compared to native apps. We select 328 services from some popular providers, covering various domains such as e-commerce, map, social networking, and entertainment. With HTTP-level trace analysis, we demystify the workflows on how native apps and Web apps deliver services on mobile devices, respectively. Then, we characterize the performance differences between native apps and Web apps with the metrics including the number of requests, response time, data drain, and energy consumption. We find that the performance of Web apps is better than native apps in more than 31 percent cases. Our derived knowledge can suggest some recommendations to improve the performance for mobile apps.
<b>PRODUCTION OF REGION-SPECIFIC ANTISERA TO HUMAN PRORENIN AND RENIN USING SYNTHETIC </b><b>PEPTIDES </b> (1987)

Based on the predicted amino acid sequence of human renal preprorenin (HRPR), two peptides corresponding to the prorenin-related (21-64) and renin/proreninrelated (337-360) sequences were synthesized by a solid-phase technique. The synthetic peptides were used as immunogens, which elicited antibodies in rabbits. Both anti-HRPR (21-64) serum R0066 and anti-HRPR (337-360) serum R0417 regularly immunostained cells in the juxtaglomerular apparatus in human adult and fetal renal tissues. The immunoreactive cells revealed by antiserum R0066 were identical with those detected by antiserum R0417, but the stainings with antiserum R0066 were less frequent and significantly weaker than those with antiserum R0417 and more strictly confined in the narrow perinuclear area of the cytoplasm. The present observations support the presence of prorenin or/and its amino-terminal fragment(s) in the Golgi apparatus in cells and suggest enzymatic degradation of the (21-64) portion in a rather early stage of prorenin processing. The results also validate the use of these antisera in further detailed studies on the prorenin-renin system.
Cadmium-Containing Quantum Dots Used in Electronic Displays: Implications for Toxicity and Environmental Transformations (2021)

Cadmium-containing quantum dot (QD) nanoparticles are integrated into electronic displays because of their ability to efficiently convert colors. There are conflicting accounts as to whether these particles present a hazard to the environment, as they have been studied either as (1) embedded QDs in display screen films or (2) as model QDs with small, hydrophilic ligands. Both approaches have limitations that we addressed by synthesizing QDs featuring the core–shell structure and the thick polymer coating present in commercial devices to probe the dissolution of QDs in response to two environmental factors (pH and dissolved oxygen) over 1 day and 6 months. Results show that QDs were chemically stable at circumneutral pH (0% Cd dissolution after 6 months), but low pH initiated rapid dissolution under both aerobic and anaerobic conditions (up to 100% Cd dissolution after 6 months). In addition to the presence of a capping polymer, the QD shell structure led to more chemically stable nanoparticles compared to nonshelled QDs, as the presence of ZnS shells decreased Cd dissolution by 75%. The dense aggregation of QDs into structures of ∼100 nm diameter over time was observed as well, which could lead to decreased bioavailability. To test this, we used liver cells to compare the toxicity of pristine QDs to those subjected to acid dissolution. Our results reveal that low-pH-exposed QDs separated from dissolved ions are less toxic than pristine QDs (half maximal inhibitory concentration, IC50, of 290 and 150 mg/L, respectively) and suggest a key role of dissolved ions and capping polymers for QD toxicity. These findings highlight the use of a commercially relevant nanoparticle structure to demonstrate fate and toxicity.
Style and Alignment in Information-Seeking Conversation (2018)

Analysis of casual chit-chat indicates that differences in conversational style---the way things are said---can significantly impact a participants» impressions of the conversation and of each other. However, prior work has not systematically analyzed how important style is in task-oriented, information-seeking exchanges of the sort we might have with a conversational search agent. We examine recordings from the MISC data set, where pairs of "users" and "intermediaries" collaborate on information-seeking tasks, and look for indications of style which can be computed at scale. We find that stylistic markers identified by Tannen in casual chat do exist in information-seeking dialogue, and that participants can be arranged along a single stylistic dimension: "considerate" to "involved". This labelling for style needs no manual intervention. Furthermore, we find that there is no clear best style; but that differences in style, previously thought to impede communication, are only a problem for shorter tasks. This result is likely due to alignment of conversational style over the course of an interaction.