gebhart/patrepeval huggingface dataset:
Bacteriophage applications: where are we now? (2010)

Bacteriophages are bacterial viruses and have been used for almost a century as antimicrobial agents. In the West, their use diminished when chemical antibiotics were introduced, but they remain a common therapeutic approach in parts of eastern Europe. Increasing antibiotic resistance in bacteria has driven the demand for novel therapies to control infections and led to the replacement of antibiotics in animal husbandry. Alongside this, increased pressure to improve food safety has created a need for faster detection of pathogenic bacteria. Hence, there has been a resurgence of interest in bacteriophage applications, and this has encouraged the emergence of a large number of biotech companies hoping to commercialize their use. Research in Europe and the United States has increased steadily, leading to the development of a range of applications for bacteriophage agents for the healthcare, veterinary and agricultural sectors. This article will attempt to answer the question of whether bacteriophages are now delivering on their potential.
3-(α<i>R</i>)-α-((2<i>S</i>,5<i>R</i>)-4-Allyl-2,5-dimethyl-1-piperazinyl)-3-hydroxybenzyl)-<i> N</i>-alkyl-<i>N</i>-arylbenzamides:  Potent, Non-Peptidic Agonists of Both the μ and δ Opioid Receptors (2003)

Opioid analgesics with both micro and delta opioid receptor activation represent a new approach to the treatment of severe pain with an improved safety profile. Compounds with this profile may exhibit strong analgesic properties due to micro agonism, with a reduced side effect profile resulting from delta agonism. Replacing the p-diethylamide of the known potent delta opioid receptor selective agonist BW373U86 with a m-diethylamide resulted in a compound with agonist activity at both the micro and delta opioid receptors. Modifying the amide to an N-methyl-N-phenylamide increased agonist potency at both receptors. A series of 3-(alphaR)-alpha-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-hydroxybenzyl)-N-alkyl-N-arylbenzamides have been made to explore the structure-activity relationship (SAR) around the N-methyl-N-phenylamide. Several potent agonists of both the micro and delta opioid receptors have been identified, including (+)-3-((alphaR)-alpha-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl)-3-hydroxybenzyl)-N-(4-fluorophenyl)-N-methylbenzamide (23), which has EC50 values of 0.67 and 1.1 nM at the micro (guinea pig ileum assay) and delta (mouse vas deferens assay) opioid receptors, respectively.
Ultrafast imaging of ultraviolet laser ablation and etching of polymethylmethacrylate (1989)

Ablation and etching of the surface of polymethylmethacrylate (PMMA) by pulses of 248 nm laser radiation [∼20 ns full width at half maximum (FWHM)] have been probed by pulses of visible laser radiation (596 nm; &lt;1 ns FWHM). The results were recorded photographically. Modification of the surface structure of the polymer is first visible at 12 ns and appears to be complete in about 60 ns. Emerging solid material, preceded by a shock wave which first becomes visible at 60 ns, reaches a maximum in intensity at 6 μs and continues until about 20 μs. The average velocity of the solid material, which is probably a low molecular weight polymer of PMMA, is 1.5×104 cm/s.
Smell and taste dysfunction following minor stroke: a case report. (2008)

Smell (olfactory) and taste (gustatory) are key senses in the regulation of nourishment and individual safety. Olfactory and gustatory dysfunctions have been infrequently reported together in patients following stroke (Landis et al., 2006; Leopold et al., 2006). This case report details two patients who experienced smell and taste dysfunction following minor stroke events. Symptoms reported included hyposmia (diminished sense of smell) and anosmia (complete loss of smell), and dysgeusia (distorted taste). Patients' sense of smell and taste were assessed in an ambulatory care stroke prevention clinic eight months following their strokes. Patient A presented with minor stroke due to a lesion in the anterior circulation, patient B with a lesion in the posterior circulation. Both patients reported intense olfactory and gustatory dysfunction immediately following their strokes. Examination revealed a general inability to detect subtle odours and the ability to identify only 'sweet' tastes for both patients. In addition, both patients reported heavily salting or sweetening their food to mask the distorted and unpleasant taste, which also impacted comorbid conditions such as hypertension and diabetes. Patients and their spouses reported a decrease in their appreciation of family-related activities due to the patients' olfactory and gustatory dysfunction. Patients reported weight loss, lack of energy and strength, likely due to poor nutrition. Olfactory and gustatory dysfunctions are potentially deleterious outcomes following minor stroke and should be assessed by health care professionals prior to patient discharge. Assistance may be required to promote the health and well-being of patients and their carers if smell and taste are impacted by the stroke event.
An enzyme labelled nuclear antigen immunoassay for detection of cytomegalovirus IgM antibodies in human serum: Specific and non‐specific reactions (1987)

A mu-capture enzyme linked immunosorbent assay was developed for detection of IgM antibody to cytomegalovirus (CMV). Virus-specific IgM was detected using horseradish peroxidase labelled nuclear CMV antigen (CMV-ELA). False-positive reactions caused by Paul-Bunnell-Davidsohn (PBD) positive sera and antinuclear antibody (ANA) positive sera were identified in a combination assay employing enzyme labelled nuclear control antigen (CO-ELA) in parallel to the CMV-ELA. Four of five PBD positive and 30 of 31 ANA positive sera reactive with the CMV-ELA were identified as false positive reactions in the combined ELA-assay. The reactivity in PBD-positive sera could not be explained by antigenic cross reactivity between CMV and Epstein-Barr virus, and the results further suggested that different cell specified components of the CMV-ELA were responsible for the reactivity of PBD-positive as compared to ANA-positive sera. One of 314 healthy blood donors, 12 of 12 patients with primary CMV infection, and 11 of 15 patients with secondary CMV infection had detectable CMV IgM antibodies. Comparison of different CMV-ELAs revealed that pronounced differences in specificity as well as sensitivity may exist.
Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition (2015)

T-cell receptors (TCR) play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR), which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation.
Direct modulation of tumor suppressor connexin 26 gene by human chorionic gonadotropin in rat mammary glands. (1998)

Human chorionic gonadotropin (hCG) has been shown to reduce the incidence of carcinogen-induced rat mammary tumors. Because connexin 26 (Cx26), a tumor suppressor gene candidate, can be up-regulated in mammary epithelial cells during lactation, we examined the in vivo and ex vivo effects of hCG on Cx26 expression in rat mammary tissues and used its effect on the expressions of beta-casein and Cx43 as controls. The Cx26 mRNA and protein expressions were up-regulated by daily administrations of 100 units of hCG, starting on day 5 and reaching a 14-fold maximum increment on days 16 through 21. It remained elevated above the basal level even 20 days after hCG withdrawal. The changes in beta-casein expression ran parallel to that of Cx26, whereas the expression of Cx43 was down-regulated. There was no correlation between steroidal hormone levels and Cx26 expression, except for the first 5 days of hCG treatment. In the ex vivo organ culture system, exposure of mammary glands to 10 units/ml hCG for 5 days up-regulated Cx26 but had no effect on beta-casein expression. These results imply a direct induction of the tumor suppressor Cx26 gene by hCG in mammary epithelial cells, a mechanism unrelated to lactation.
CUDA-OpenGL Interoperability to Visualize Electromagnetic Fields Calculated by FDTD (2012)

In this contribution, a compute unified device architecture (CUDA) implementation of a two-dimensional finite-difference time-domain (FDTD) program is presented along with the OpenGL interoperability to visualize electromagnetic fields as an animation while an FDTD simulation is running. CUDA, which runs on a graphics processing unit (GPU) card, is used for electromagnetic field data generation and image manipulation, while OpenGL is used to draw field distribution on the screen. Since CUDA and OpenGL both run on GPU and share data through common memory in the framebuffer, the CUDA-OpenGL interoperability is very efficient in visualization of electromagnetic fields. Step by step details of implementation of this interoperability are demonstrated.
Evading cellular data monitoring with human movement networks (2010)

Cellular networks are centrally administered, enabling service providers and their governments to conduct system-wide monitoring and censorship of mobile communication. This paper presents HUMANETS, a fully decentralized, smartphone-to-smartphone (and hence human-to-human) message passing scheme that permits unmonitored message communication even when all cellular traffic is inspected. HUMANET message routing protocols exploit human mobility patterns to significantly increase communication efficiency while limiting the exposure of messages to mobile service providers. Initial results from tracedriven simulation show that 85 % of messages reach their intended destinations while using orders of magnitude less network capacity than naïve epidemic flooding techniques. 1
ANGULAR MOMENTUM IN QUANTUM MECHANICS (2008)

This book offers a concise introduction to the angular momentum, one of the most fundamental quantities of quantum mechanics.Beginning with the quantization of angular momentum (spin and orbit), the author goes on to discuss the Clebsch-Gordan coefficients for a two-component system.The theory of spherical tensors and tensor operators is developed, and then the vector-coupling coefficients (3-j, 6-j and 9-j coefficients) and their properties are investigated.The author provides practical applications to atomic, molecular and nuclear physics.This book, published first in 1957 (see the review in Zbl 0079.42204), has always been and remains to be a standard source reference for those working in quantum theory of angular momentum and its applications in physics.
Chiral Preparation of Polyoxygenated Cyclopentanoids (2000)

A series of polyoxygenated cyclopentanoids, including 2,2-dimethyl-3a,6a-dihydro-4H-cyclopenta[d][1,3]dioxol-4-one, has been prepared in both enantiomeric forms from cyclopentadiene by employing lipase-mediated kinetic resolution as the key step. Thus, cyclopentadiene is first transformed into racemic cis-4-cumyloxycyclopent-2-en-1-ol which is resolved under transesterification conditions in the presence of lipase PS. After transformation into the corresponding tert-butyldimethylsilyl (TBS) ethers, each of the enantiomers is cis-dihydroxylated diastereoselectively from the less hindered face which is transformed into the 2,3-O-isopropylidene-1,4-di-O-protected (trans-1,2 : cis-2,3 : trans-3,4)-1,2,3,4-cyclopentanetetraol. Selective removal of the 1,4-protecting group gives the corresponding 2,3,4-O-protected cyclopentanols which are further transformed into the 2,3,4-O-protected cyclopentanones on oxidation without suffering β-elimination. Exposure of the cyclopentanones to warm acetic acid allows β-elimination to give rise to the dehydration product 2,2-dimethyl-3a,6a-dihydro-4H-cyclopenta[d][1,3]dioxol-4-one having the corresponding chirality without losing their original chiral integrity.
Game programming by demonstration (2013)

The increasing adoption of smartphones and tablets has provided tens of millions of users with substantial resources for computation, communication and sensing. The availability of these resources has a huge potential to positively transform our society and empower individuals. Unfortunately, although the number of users has increased dramatically, the number of developers is still limited by the high barrier that existing programming environments impose.
Inhibition of dexamethasone-induced cytochrome P450-mediated mutagenicity and metabolism of aflatoxin B1 by Chinese medicinal herbs (1993)

Oldenlandia diffusa (OD) and Scutellaria barbata (SB) have been used in traditional Chinese medicine for treating liver, lung and rectal tumours. We previously showed that they inhibited mutagenesis, DNA binding and metabolism of aflatoxin B1 (AFB1) and benzo(a)pyrene (BaP) bioactivated by Aroclor 1254-induced rat S9. The purpose of this study was to investigate the effects of OD and SB on the mutagenicity of AFB1 in Salmonella typhimurium TA100 using dexamethasone (DXM)-induced rat hepatic S9, on cytochrome P450-linked aminopyrine N-demethylase (APND) activity in DXM-induced hepatic microsomes and on the metabolism of AFB1 by DXM-induced S9 using high-performance liquid chromatography (HPLC). The experimental results showed that OD and SB consistently inhibited the mutagenicity of AFB1 bioactivated by either non-induced or DXM-induced S9. These effects correlated with the inhibition of cytochrome P450-linked APND activity in DXM-induced microsomes and with an inhibition of DXM-induced S9 mediated metabolism of [3H]AFB1 as determined by HPLC. Since DXM treatment has been associated with an induction of the CYP3 enzyme family, these results suggest that OD and SB may possess antimutagenic and antitumorigenic activity towards AFB1 through an inhibition of CYP3-mediated metabolism of AFB1.
P1–200: Systemic markers of inflammation and cognitive decline in old age (2006)

Several lines of investigation suggest that inflammation is involved in the pathogenesis of cognitive decline and dementia. To investigate whether circulating levels of C–reactive protein (CRP), interleukin–6 (IL–6), and α1–antichymotrypsin (ACT) are associated with cognitive function and decline in old age. We used linear regression analyses to investigate the associations of inflammatory markers with cognitive function and decline in two independent population–based cohort studies, the Rotterdam Study (3874 individuals, mean age 72), and the Leiden 85–plus Study (491 individuals, all aged 85). In both studies global cognition, executive function and memory were assessed. In the Rotterdam Study, higher levels of hsCRP and IL–6 were cross–sectionally associated with worse global cognition and executive function (p<0.05). ACT was not associated with cognitive function. In the Leiden 85–plus Study cross–sectional estimates for CRP were similar to those in the Rotterdam Study, though not statistically significant. In the longitudinal analysis, higher IL–6 levels were related to a steeper annual decline in memory function in the Leiden 85–plus Study (p<0.05). The effect of higher IL–6 levels on global and memory function decline was stronger in APOE–ϵ4 carriers than in non APOE–ϵ4 carriers (p–interaction 0.011, respectively 0.048). In the Rotterdam Study, higher IL–6 levels were related to a steeper annual decline in global cognition in APOE–ϵ4 carriers only. Systemic markers of inflammation are modestly associated with cognitive function and decline, and tend to be stronger in carriers of the APOE–ϵ4 allele. Systemic markers of inflammation are not suitable for risk stratification.
<title>Three-dimensional segmentation of bone structures in CT images</title> (1999)

This work is concerned with the implementation of a fully 3D-consistent, automatic segmentation of bone structures in CT images. The morphological watersheds algorithm has been chosen as the base of the low-level segmentation. The over- segmentation, a phenomenon normally involved with this transformation, has been sorted out successfully by inserting modifying modules that act already within the algorithm. When dealing with a maxillofacial image, this approach also includes the possibility to provide two different divisions of the image: a fine-grained tessellation geared to the following high-level segmentation and a more coarse-grained one for the segmentation of the teeth. In the knowledge-based high-level segmentation, probabilistic considerations make use of specific properties of the 3D low-level regions to find the most probable tissue for each region. Low-level regions that cannot be classified with the necessary certainty are passed to a second stage, where--embedded in their respective environment--they are compared with structural patterns deduced from anatomical knowledge. The tooth segmentation takes the coarse-grained tessellation as its starting point. The few regions making up each tooth are grouped to 3D envelopes--one envelope per tooth. Matched filtering detects the bases of these envelopes. After a refinement they are fitted into the fine- grained, high-level segmented image.
Role of Glycogen Synthase Kinase 3β in Rapamycin-Mediated Cell Cycle Regulation and Chemosensitivity (2005)

The mammalian target of rapamycin is a serine-threonine kinase that regulates cell cycle progression. Rapamycin and its analogues inhibit the mammalian target of rapamycin and are being actively investigated in clinical trials as novel targeted anticancer agents. Although cyclin D1 is down-regulated by rapamycin, the role of this down-regulation in rapamycin-mediated growth inhibition and the mechanism of cyclin D1 down-regulation are not well understood. Here, we show that overexpression of cyclin D1 partially overcomes rapamycin-induced cell cycle arrest and inhibition of anchorage-dependent growth in breast cancer cells. Rapamycin not only decreases endogenous cyclin D1 levels but also decreases the expression of transfected cyclin D1, suggesting that this is at least in part caused by accelerated proteolysis. Indeed, rapamycin decreases the half-life of cyclin D1 protein, and the rapamycin-induced decrease in cyclin D1 levels is partially abrogated by proteasome inhibitor N-acetyl-leucyl-leucyl-norleucinal. Rapamycin treatment leads to an increase in the kinase activity of glycogen synthase kinase 3beta (GSK3beta), a known regulator of cyclin D1 proteolysis. Rapamycin-induced down-regulation of cyclin D1 is inhibited by the GSK3beta inhibitors lithium chloride, SB216763, and SB415286. Rapamycin-induced G1 arrest is abrogated by nonspecific GSK3beta inhibitor lithium chloride but not by selective inhibitor SB216763, suggesting that GSK3beta is not essential for rapamycin-mediated G1 arrest. However, rapamycin inhibits cell growth significantly more in GSK3beta wild-type cells than in GSK3beta-null cells, suggesting that GSK3beta enhances rapamycin-mediated growth inhibition. In addition, rapamycin enhances paclitaxel-induced apoptosis through the mitochondrial death pathway; this is inhibited by selective GSK3beta inhibitors SB216763 and SB415286. Furthermore, rapamycin significantly enhances paclitaxel-induced cytotoxicity in GSK3beta wild-type but not in GSK3beta-null cells, suggesting a critical role for GSK3beta in rapamycin-mediated paclitaxel-sensitization. Taken together, these results show that GSK3beta plays an important role in rapamycin-mediated cell cycle regulation and chemosensitivity and thus significantly potentiates the antitumor effects of rapamycin.
Determination of Potassium, Sodium, and Total Alkalies in Portland Cement, Fly Ash, Admixtures, and Water of Concrete by a Simple Flow Injection Flame Photometric System (2011)

A simple flow injection with flame photometric detection has been developed for determination of sodium, potassium, and total alkalies in portland cement, fly ash, admixtures, and water of concrete. A liquid sample or a digest of solid sample was injected into a water carrier stream which flowed to a flame photometer. A change in emission intensity at a selected wavelength was recorded as a peak. An amplifier circuit was fabricated, which helped improve sensitivity of the flame photometer. Calibration graphs in the range of 0.05-1.0 mg L(-1) and 1.0-20.0 mg L(-1) were obtained with a detection limit of 0.02 mg L(-1), for both potassium and sodium determination. Relative standard deviations for 11 replicates of injecting of 10 mg L(-1) potassium and sodium solutions were 1.69 and 1.79%, respectively. Sample throughput of 120 h(-1) was achieved. The proposed method was successfully applied to portland cement, fly ash, admixtures, and water samples validated by the ASTM standard method and certified reference materials of portland cement.
Near-field communication-based secure mobile payment service (2009)

The loss of customer account information makes headlines all too often. The Payment Card Industry (PCI) Data Security Standard (DSS) has generated resistance from merchants because of its cost and complexity. Unfortunately, innovating in the Point of Sale (PoS) space is hard because the protocols have been standardized, tightly constraining new ideas. Using mobile phones as payment devices opens up some opportunities, but any solution must minimize changes in the back-end processing. This paper describes a Near Field Communication (NFC) based mobile phone payment solution in a service-oriented environment, which provides the needed data protection without requiring costly changes to the payment processing infrastructure. In the payment transaction path, a personal mobile phone is viewed as a single, user-trusted touch point. Compared to other solutions available, our approach better protects user credentials, provides better user control over the transaction, and supports both proximity and remote transactions. The prototype has been integrated with an instore kiosk application and a HP multi-channel banking platform to demonstrate its value in the retail environment.