gebhart/patrepeval huggingface dataset:
Detection of mRNA of the Cyclin D1 Breast Cancer Marker by a Novel Duplex-DNA Probe (2013)

Previously, we have described 5-((4-methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6, as a fluorescent uridine analogue exhibiting a 3000-fold higher quantum yield (Φ 0.12) and maximum emission (478 nm) which is 170 nm red-shifted as compared to uridine. Here, we utilized 6 for preparation of labeled oligodeoxynucleotide (ODN) probes based on MS2 and cyclin D1 (a known breast cancer mRNA marker) sequences. Cyclin D1-derived labeled-ssODN showed a 9.5-fold decrease of quantum yield upon duplex formation. On the basis of this finding, we developed the ds-NIF (nucleoside with intrinsic fluorescence)-probe methodology for detection of cyclin D1 mRNA, by which the fluorescent probe is released upon recognition of target mRNA by the relatively dark NIF-duplex-probe. Indeed, we successfully detected, a ss-deoxynucleic acid (DNA) variant of cyclin D1 mRNA using a dark NIF-labeled duplex-probe, and monitoring the recognition process by fluorescence spectroscopy and gel electrophoresis. Furthermore, we successfully detected cyclin D1 mRNA in RNA extracted from cancerous human cells, using ds-NIF methodology.
Occurrence of 'attaching and effacing' lesions in the small intestine of calves experimentally infected with bovine isolates of verocytotoxic E coli (1989)

Nine calves (five colostrum-fed, four colostrum-deprived) were challenged with two field strains of Escherichia coli which produced either verocytotoxin 1 (VT1) or verocytotoxin 2 (VT2). Although three colostrum-fed calves had blood and mucus in their faeces, no diarrhoea was observed. Three of the four colostrum-deprived calves had diarrhoea and in two of them severe lesions were detected in the small intestine. Focal changes were detected in the colon of three calves. E coli were associated with the lesions in the small and large intestine and were shown by transmission electron microscopy to be intimately attached to the enterocyte surface with effacement of microvilli (attaching and effacing lesions). This is the first report of E coli which produce VT2 being associated with disease in calves.
Reproducibility of flow and wall shear stress analysis using flow‐sensitive four‐dimensional MRI (2011)

Flow-sensitive 4D MRI-based analysis of aortic blood flow can be performed with good reproducibility. Robustness of global and regional WSS quantification was limited, but spatio-temporal WSS distributions could reliably be replicated.
Dehydrozingerone, Chalcone, and Isoeugenol Analogues as in Vitro Anticancer Agents (2006)

Twenty-eight compounds related to dehydrozingerone (1), isoeugenol (3), and 2-hydroxychalcone (4) were synthesized and evaluated in vitro against human tumor cell replication. Except for isoeugenol analogues 27-35, most compounds exhibited moderate or strong cytotoxic activity against KB, KB-VCR (a multidrug-resistant derivative), and A549 cell lines. In particular, chalcone 15 showed significant cytotoxic activity against the A549 cell line with an IC50 value of 0.6 microg/mL. Furthermore, dehydrozingerone analogue 11 and chalcones 16 and 17 showed significant and similar cytotoxic activity against both KB (IC50 values of 2.0, 1.0, and 2.0 microg/mL, respectively) and KB-VCR (IC50 values of 1.9, 1.0, and 2.0 microg/mL, respectively) cells, suggesting that they are not substrates for the P-glycoprotein drug efflux pump.
Detection and measurement of inflammatory cytokines in implant crevicular fluid: a pilot study. (1997)

Peri-implantitis has been shown to possess clinical characteristics similar to those of periodontitis. This pilot study was conducted to determine levels of inflammatory cytokines in crevicular fluid from healthy implants and those implants affected by peri-implantitis. Fifty implants from 13 patients were examined. A clinical examination was performed, and gingival crevicular fluid samples were collected and analyzed for cytokines. Implants were categorized clinically as healthy, early peri-implantitis, or advanced peri-implantitis. Interleukin-1 beta was detected in the crevicular fluid of implants in all three groups (healthy = 59.47 +/- 15.55 pg/site; early peri-implantitis = 460.77 +/- 35.67 pg/site; and advanced peri-implantitis = 191.10 +/- 21.60 pg/site [mean +/- SEM]). These results indicate that interleukin-1 beta is present in implant gingival crevicular fluid and may be modulating attachment loss in implants suffering from peri-implantitis. Thus, interleukin-1 beta may be used to monitor disease progression.
Atmospheric Corrosion of Copper and Silver (1981)

The corrosion rate of copper in laboratory tests is shown to be a sensitive function of relative humidity, sulfur dioxide, hydrogen sulfide, ozone, hydrogen chloride, and chlorine concentrations. Observed indoor corrosion rates obey log normal statistics over the field population of this study. Also, the observed indoor rates correlate reasonably well with the measured reduced sulfur concentrations (, ). The corrosion rate of silver is shown not to be humidity dependent. Hydrogen sulfide, ozone, chlorine, and hydrogen chloride concentrations substantially influence its corrosion rate. The observed indoor rates obey log normal statistics and correlate well with the reduced sulfur gas concentration. In contrast to copper, where indoor rates are 1% of outdoor values, silver often corrodes faster indoors than outdoors. Its sensitivity to sulfur gases and insensitivity to relative humidity is proposed as a plausible explanation for these findings. It is proposed that metallic silver is stable in polluted acidic atmospheric environments and therefore is the dominant surface species while is present on the surface of copper. The thermochemistry and kinetics of these two surfaces will control the stability of silver and copper, respectively, in the presence of pollutants.
An ontology for a Robot Scientist (2006)

EXPO in XML and OWL formats is at: http://sourceforge.net/projects/expo/. All materials about the Robot Scientist project are available at: http://www.aber.ac.uk/compsci/Research/bio/robotsci/.
Quantification of hydrogen cyanide in humid air by selected ion flow tube mass spectrometry (2004)

Following our recent observation that Pseudomonas bacteria in vitro emit hydrogen cyanide, we have found it necessary to investigate the ion chemistry of this compound and to extend the kinetics database for selected ion flow tube mass spectrometry (SIFT-MS) to allow the accurate quantification of HCN in moist air samples, including exhaled breath. Because of the proximity of the proton affinities of HCN and H2O molecules, the presence of water vapour can significantly distort HCN analysis in the presence of water vapour and a more sophisticated analytical procedure has to be developed. Thus, the reactions of H3O+(H2O)0,1,2,3 ions with HCN molecules have been studied in the presence of varying concentrations of water vapour, reactions on which SIFT-MS analysis of HCN relies. The results of these experiments have allowed an analytical procedure to be developed which has extended the kinetics database of SIFT-MS, such that HCN can now be quantified in humid air and in exhaled breath.
Periparturient Hypocalcemia in Cows: Effects on Peripheral Blood Neutrophil and Lymphocyte Function (1989)

Periparturient dairy cows are quite susceptible to intramammary infections and clinical mastitis, epidemiologic evidence indicates that parturient paresis (milk fever) greatly increases the risk of mastitis, although a causal relationship has not been established. In the present experiment the effects of hypocalcemia at parturition on the immune status of dairy cows were investigated. Ten healthy, multiparous Holstein cows were fed a high Ca diet prepartum to induce hypocalcemia at parturition. Five of these cows received intramuscular parathyroid hormone (crude synthetic N-terminus 1-34) to prevent hypocalcemia at parturition. Effects of hypocalcemia on various neutrophil and lymphocyte functions were determined during the periparturient period, ranging from 6 wk prepartum to 5 wk postpartum. All cows exhibited severe loss of immune cell function in the weeks surrounding parturition. Hypocalcemia or the development of parturient paresis did not exacerbate the immune cell dysfunction. This implies that the degree of hypocalcemia observed did not have a large or irreversible influence on neutrophil and lymphocyte function in periparturient cows.
Porous mesocarbon microbeads with graphitic shells: constructing a high-rate, high-capacity cathode for hybrid supercapacitor (2013)

Li₄Ti₅O₁₂/activated carbon hybrid supercapacitor can combine the advantages of both lithium-ion battery and supercapacitor, which may meet the requirements for developing high-performance hybrid electric vehicles. Here we proposed a novel "core-shell" porous graphitic carbon (PGC) to replace conventional activated carbon for achieving excellent cell performance. In this PGC structure made from mesocarbon microbead (MCMB), the inner core is composed of porous amorphous carbon, while the outer shell is graphitic carbon. The abundant porosity and the high surface area not only offer sufficient reaction sites to store electrical charge physically, but also can accelerate the liquid electrolyte to penetrate the electrode and the ions to reach the reacting sites. Meanwhile, the outer graphitic shells of the porous carbon microbeads contribute to a conductive network which will remarkably facilitate the electron transportation, and thus can be used to construct a high-rate, high-capacity cathode for hybrid supercapacitor, especially at high current densities.
Antimicrobial properties of porphyrins (2001)

A large number of natural and synthetic porphyrins of diverse chemical compositions and characteristics can be isolated from nature or synthesised in the laboratory. Antimicrobial and antiviral activities of porphyrins are based on their ability to catalyse peroxidase and oxidase reactions, absorb photons and generate reactive oxygen species (ROS) and partition into lipids of bacterial membranes. Light-dependent, photodynamic activity of natural and synthetic porphyrins and pthalocyanines against Gram-positive and Gram-negative bacteria has been well demonstrated. Some non-iron metalloporphyrins (MPs) possess a powerful light-independent antimicrobial activity that is based on the ability of these compounds to increase the sensitivity of bacteria to ROS or directly produce ROS. MPs mimic haem in their molecular structure and are actively accumulated by bacteria via high affinity haem-uptake systems. The same uptake systems can be used to deliver antibiotic-porphyrin and antibacterial peptide-porphyrin conjugates. Haemin, the most well known natural porphyrin, possesses a significant antibacterial activity that is augmented by the presence of physiological concentrations of hydrogen peroxide or a reducing agent. Natural and synthetic porphyrins have relatively low toxicity in vitro and in vivo. The ability for numerous chemical modifications and the large number of different mechanisms by which porphyrins affect microbial and viral pathogens place porphyrins into a group of compounds with an outstanding potential for discovery of novel agents, procedures and materials active against pathogenic microorganisms.
The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines (2012)

Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic beta cells are killed by infiltrating immune cells and by cytokines released by these cells. Signaling events occurring in the pancreatic beta cells are decisive for their survival or death in diabetes. We have used RNA sequencing (RNA-seq) to identify transcripts, including splice variants, expressed in human islets of Langerhans under control conditions or following exposure to the pro-inflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). Based on this unique dataset, we examined whether putative candidate genes for T1D, previously identified by GWAS, are expressed in human islets. A total of 29,776 transcripts were identified as expressed in human islets. Expression of around 20% of these transcripts was modified by pro-inflammatory cytokines, including apoptosis- and inflammation-related genes. Chemokines were among the transcripts most modified by cytokines, a finding confirmed at the protein level by ELISA. Interestingly, 35% of the genes expressed in human islets undergo alternative splicing as annotated in RefSeq, and cytokines caused substantial changes in spliced transcripts. Nova1, previously considered a brain-specific regulator of mRNA splicing, is expressed in islets and its knockdown modified splicing. 25/41 of the candidate genes for T1D are expressed in islets, and cytokines modified expression of several of these transcripts. The present study doubles the number of known genes expressed in human islets and shows that cytokines modify alternative splicing in human islet cells. Importantly, it indicates that more than half of the known T1D candidate genes are expressed in human islets. This, and the production of a large number of chemokines and cytokines by cytokine-exposed islets, reinforces the concept of a dialog between pancreatic islets and the immune system in T1D. This dialog is modulated by candidate genes for the disease at both the immune system and beta cell level.
Capacity of Data Collection in Arbitrary Wireless Sensor Networks (2010)

How to efficiently collect sensing data from all sensor nodes is critical to the performance of wireless sensor networks. In this paper, we aim to understand the theoretical limitations of data collection in terms of possible and achievable maximum capacity. Previously, the study of data collection capacity has only concentrated on large-scale random networks. However, in most of practical sensor applications, the sensor network is not deployed uniformly and the number of sensors may not be as huge as in theory. Therefore, it is necessary to study the capacity of data collection in an arbitrary network. In this paper, we derive the upper and constructive lower bounds for data collection capacity in arbitrary networks. The proposed data collection method can lead to order-optimal performance for any arbitrary sensor networks. We also examine the design of data collection under a general graph model and discuss performance implications.
Denoising non-steady state dynamic PET data using a feed-forward neural network (2020)

The quality of reconstructed dynamic PET images, as well as the statistical reliability of the estimated pharmacokinetic parameters is often compromised by high levels of statistical noise, particularly at the voxel level. Many denoising strategies have been proposed, both in the temporal and spatial domain, which substantially improve the signal to noise ratio of the reconstructed dynamic images. However, although most filtering approaches are fairly successful in reducing the spatio-temporal inter-voxel variability, they may also average out or completely eradicate the critically important temporal signature of a transient neurotransmitter activation response that may be present in a non-steady state dynamic PET study. In this work, we explore an approach towards temporal denoising of non-steady state dynamic PET images using an artificial neural network, which was trained to identify the temporal profile of a time-activity curve, while preserving any potential activation response. We evaluated the performance of a feed-forward perceptron neural network to improve the signal to noise ratio of dynamic [<sup>11</sup>C]raclopride activation studies and compared it with the widely used highly constrained back projection (HYPR) filter. Results on both simulated Geant4 Application for Tomographic Emission data of a realistic rat brain phantom and experimental animal data of a freely moving animal study showed that the proposed neural network can efficiently improve the noise characteristics of dynamic data in the temporal domain, while it can lead to a more reliable estimation of voxel-wise activation response in target region. In addition, improvements in signal-to-noise ratio achieved by denoising the dynamic data using the proposed neural network led to improved accuracy and precision of the estimated model parameters of the lp-ntPET model, compared to the HYPR filter. The performance of the proposed denoising approach strongly depends on the amount of noise in the dynamic PET data, with higher noise leading to substantially higher variability in the estimated parameters of the activation response. Overall, the feed-forward network led to a similar performance as the HYPR filter in terms of spatial denoising, but led to notable improvements in terms of temporal denoising, which in turn improved the estimation activation parameters.
Green tea catechins such as (−)‐epicatechin and (−)‐epigallocatechin accelerate Cu<sup>2+</sup>‐induced low density lipoprotein oxidation in propagation phase (1997)

Effects of (-)-epicatechin (EC) and (-)-epigallocatechin (EGC) on Cu2+-induced low density lipoprotein (LDL) oxidation were studied in initiation and propagation phases. When 1.5 microM EC or EGC was added to the mixture of isolated human LDL and Cu2+ in the initiation phase, the oxidation of LDL was inhibited in agreement with previous findings. In contrast, in the propagation phase, 1.5 microM of EC or EGC worked as an accelerator of the oxidation, and acceleration ratios (maximum about 6 times) were modified depending on the concentrations of catechin used and the oxidation process in the propagation phase. The evidence was obtained from formation of thiobarbituric acid reactive substances (TBARS), detecting conjugated diene measured by absorbance at 234 nm and investigating fragmentation of apoprotein B (apo B) in LDL. Even in the propagation phase of LDL oxidation, the elevated concentrations of EC or EGC worked as inhibitors: after 40 min incubation of LDL with Cu2+, 10.0 microM EC or 2.0 microM EGC inhibited LDL oxidation. Yet, nitric oxide (NO) released from 5 microM zwitterionic polyamine/NO adducts had an inhibitory in all phases of LDL oxidation. These results indicate that catechins such as EC and EGC can act as free radical terminators (reducing agents) or accelerators (oxidizing agents) under oxidation circumstances, which is a different character from NO. From the above evidence, further investigations are needed on many natural flavonoids, the most potent antioxidative compounds in foods.
Phase shift in an atom interferometer induced by the additional laser lines of a Raman laser generated by modulation (2012)

The use of a Raman laser generated by modulation for a light-pulse atom interferometer allows for a laser system that is compact and robust. However, the additional laser frequencies generated can perturb the atom interferometer. In this article, we present a precise calculation of the phase shift induced by the additional laser frequencies. The model is validated by comparison with experimental measurements on an atom gravimeter. The uncertainty of the phase-shift determination limits the accuracy of our compact gravimeter to $8\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}8}\phantom{\rule{0.28em}{0ex}}\text{m}/{\text{s}}^{2}$. We show that it is possible to reduce this inaccuracy considerably with a better control of experimental parameters or with particular interferometer configurations.
Retinal Vascularization Analysis on Optical Coherence Tomography Angiography before and after Intraretinal or Subretinal Fluid Resorption in Exudative Age-Related Macular Degeneration: A Pilot Study (2021)

The aim was to analyze the variations in macular vascularization on optical coherence tomography angiography (OCTA) according to the presence of intraretinal fluid (IRF) induced by exudative age-related macular degeneration (AMD). We included exudative AMD patients with IRF and/or subretinal fluid (SRF) and age-matched control eyes. All patients underwent a macular 6 × 6 mm swept-source OCTA. The mean perfusion density (MPD) and mean vascular density (MVD) were calculated in the superficial (SCP) and the deep (DCP) capillary plexus at two timepoints: during an episode of exudation (T0) and after its total resorption (T1). A total of 22 eyes in the IRF ± SRF group, 11 eyes in the SRF group and 11 eyes in the healthy group were analyzed. At T0, the IRF ± SRF group showed significantly lower MPD and MVD than healthy eyes in the SCP (<i>p</i> < 0.001) and DCP (<i>p</i> < 0.001). At T1, MPD and MVD significantly increased from T0 in the SCP (<i>p</i> = 0.027 and <i>p</i> = 0.0093) and DCP (<i>p</i> = 0.013 and <i>p</i> = 0.046) but remained statistically lower than in the healthy eyes. For the SRF group, only the DCP showed significantly lower MPD (<i>p</i> = 0.012) and MVD (<i>p</i> = 0.046) in comparison to the healthy eyes at T0. The present study shows that retinal vascular changes do occur in the case of exudative AMD.
Audiogram Digitization Tool for Audiological Reports (2022)

A number of private and public insurers compensate workers whose hearing loss can be directly attributed to excessive exposure to noise in the workplace. The claim assessment process is typically lengthy and requires significant effort from human adjudicators who must interpret hand-recorded audiograms, often sent via fax or equivalent. In this work, we present a solution developed in partnership with the Workplace Safety Insurance Board of Ontario to streamline the adjudication process. In particular, we present the first audiogram digitization algorithm capable of automatically extracting the hearing thresholds from a scanned or faxed audiology report as a proof-of-concept. The algorithm extracts most thresholds within 5 dB accuracy, allowing to substantially lessen the time required to convert an audiogram into digital format in a semi-supervised fashion, and is a first step towards the automation of the adjudication process. The source code for the digitization algorithm and a desktop-based implementation of our NIHL annotation portal is publicly available on GitHub (https://github.com/GreenCUBIC/AudiogramDigitization).
Quantum Dots at Room Temperature Carved out from Few-Layer Graphene (2012)

We present graphene quantum dots endowed with addition energies as large as 1.6 eV, fabricated by the controlled rupture of a graphene sheet subjected to a large electron current in air. The size of the quantum dot islands is estimated to be in the 1 nm range. The large addition energies allow for Coulomb blockade at room temperature, with possible application to single-electron devices.
Cancer Trials Revamp (2005)

A panel convened by the National Cancer Institute last week recommended a sweeping restructuring of NCI-funded clinical trials.

Among the most far-reaching of the group's 22 recommendations is to create scientific steering committees to coordinate all phase III trials for major cancers. “That's a huge change,” says panel member Richard Schilsky of the University of Chicago, noting that the varied ways trials are currently reviewed can lead to redundant studies.

The 77-page report also calls for a central database of trials with summary results, and it sets aside new funds for molecular medicine. Total costs of the restructuring plans are estimated at $113 million over 5 years. NCI Director Andrew von Eschenbach, who called for the review 18 months ago, said on 7 June that the reorganization “will change the future of clinical research.”
Impact of dorzolamide, benzalkonium-preserved dorzolamide and benzalkonium-preserved brinzolamide on selected biomarkers of oxidative stress in the tear film (2021)

Use of topical benzalkonium chloride-preserved carbonic anhydrase inhibitors increases oxidative stress in the tear film.