gebhart/patrepeval huggingface dataset:
Lauryl-poly-L-lysine: A New Antimicrobial Agent? (2014)

The development of multiple antibiotic resistance is a global problem. It is necessary to find new tools whose mechanisms of action differ from those of currently used antibiotics. It is known that fatty acids and cationic polypeptides are able to fight bacteria. Here, we describe the synthesis of fatty acids linked to a polypeptide with antibacterial activity. The linkage of fatty acids to a polypeptide is reported to increase the antibacterial effect of the linked fatty acid in comparison with free fatty acids (FA) or free poly-L-lysine (PLL) or a mixture of both (FA free + PLL free). A number of C6-C18 fatty acids were linked to PLL to obtain new synthetic products. These compounds were assessed in vitro to evaluate their antibacterial activity. Some fatty acid-PLLs showed a good ability to fight bacteria. Their bactericidal activity was evaluated, and, lauryl linked to PLL was found to be the most active product against both Gram-positive and Gram-negative bacteria. This new active component showed a good degree of specificity and reproducibility and its minimum inhibitory concentration (MIC) was comparatively good. The antibacterial activity of the lauryl-PLL compound suggests that it is a new and promising antimicrobial agent.
Neural stem cells deriving from chick embryonic hindbrain recapitulate hindbrain development in culture (2018)

Neural stem cells (NSCs) are self-renewing multipotent cells that line the neural-tube and generate all the nervous system. Understanding NSC biology is fundamental for neurodevelopmental research and therapy. Many studies emphasized the need to culture NSCs, which are typically purified from mammalian embryonic/adult brains. These sources are somewhat limited in terms of quantity, availability and animal ethical guidelines. Therefore, new sources are needed. The chick is a powerful system for experimental embryology which contributed enormously to neurodevelopmental concepts. Its accessibility, genetic/molecular manipulations, and homology to other vertebrates, makes it valuable for developmental biology research. Recently, we identified a population of NSCs in the chick hindbrain. It resides in rhombomere-boundaries, expresses Sox2 and generates progenitors and neurons. Here, we investigated whether these cells can recapitulate hindbrain development in culture. By developing approaches to propagate and image cells, manipulate their growth-conditions and separate them into subpopulations, we demonstrate the ordered formation of multipotent and self-renewing neurospheres that maintain regional identity and display differential stem/differentiation/proliferation properties. Live imaging revealed new cellular dynamics in the culture. Collectively, these NSC cultures reproduce major aspects of hindbrain development in-vitro, proposing the chick as a model for culturing hindbrain-NSCs that can be directly applied to other neural-tube domains and species.
Prediction of<b><i>in vivo</i></b>drug interactions with eplerenone in man from<b><i>in vitro</i></b>metabolic inhibition data (2004)

1: The inhibition kinetics of eplerenone (EP) 6beta-hydroxylation by 10 drugs were determined in vitro using human liver microsomes. Inhibition factors were calculated from in vitro inhibition constant (Ki) and three different inhibitor Cmax values (liver Cmax of total and unbound inhibitor, and maximum influx concentration of inhibitor into the liver). Subsequently, the inhibition factors were compared with available pharmacokinetic data derived from clinical interaction trials conducted by Pfizer involving EP and these drugs. EP was also evaluated for its effect on the metabolism of 10 drugs in vitro, and again the in vitro data were compared with results from the clinical trials. 2: The Ki values for the inhibition of EP 6beta-hydroxylation by cisapride, cyclosporine, digoxin, erythromycin, fluconazole, ketoconazole, midazolam, saquinavir, simvastatin and verapamil were 2.90, 1.24,>75.0, 9.50, 59.0, 0.160, 8.10, 0.546, 6.23 and 13.3 microM, respectively. Among the three methods, inhibition factors (Rb) calculated using the Ki and estimated liver Cmax values of the unbound drug were best correlated with the in vivo area under the curve-fold increases of EP in humans. The Rb values for the drugs listed above were 1.04, 1.69, 1.00, 2.17, 2.24, 4.90, 1.00, 1.82, 1.01 and 1.04, respectively, and the in vivo area under the curve-fold increases of EP by these drugs were 1.04, 1.16, 0.930, 2.87, 2.24, 5.39, 1.00, 2.07, 1.03 and 1.98, respectively. 3: EP did not have any significant effects on the drugs tested in vitro or in the clinic. 4: Using in vitro metabolic interaction data, human in vivo pharmacokinetic interactions involving EP could be predicted nearly quantitatively. The lack of effects of EP on the pharmacokinetics of other drugs in man was also suggested in the in vitro data.
A quantitative assessment of the relative speaker discriminating properties of phonemes (2002)

The aim of the study described in this paper is to provide a thorough and quantitative assessment of the relative speaker discriminating properties of phonemes. A VQ codebook based approach to speaker modeling is used in conjunction with a phonetically hand-labelled database to produce phoneme rankings based on speaker verification scores. In broad groupings the nasals and vowels are found to provide the best speaker recognition performance, followed by the fricatives, affricates and approximants, with the stops providing the worst performance of all. A comparison at the individual phoneme level produces a more detailed ranking and of particular interest is the surprisingly good performance of the unvoiced fricative /s/. The ranking of phonemes is found to be largely unaffected by changes in experimental parameters such as the model size, the feature type and the speaker population.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Deep learning segmentation of major vessels in X-ray coronary angiography (2019)

X-ray coronary angiography is a primary imaging technique for diagnosing coronary diseases. Although quantitative coronary angiography (QCA) provides morphological information of coronary arteries with objective quantitative measures, considerable training is required to identify the target vessels and understand the tree structure of coronary arteries. Despite the use of computer-aided tools, such as the edge-detection method, manual correction is necessary for accurate segmentation of coronary vessels. In the present study, we proposed a robust method for major vessel segmentation using deep learning models with fully convolutional networks. When angiographic images of 3302 diseased major vessels from 2042 patients were tested, deep learning networks accurately identified and segmented the major vessels in X-ray coronary angiography. The average F1 score reached 0.917, and 93.7% of the images exhibited a high F1 score > 0.8. The most narrowed region at the stenosis was distinctly captured with high connectivity. Robust predictability was validated for the external dataset with different image characteristics. For major vessel segmentation, our approach demonstrated that prediction could be completed in real time with minimal image preprocessing. By applying deep learning segmentation, QCA analysis could be further automated, thereby facilitating the use of QCA-based diagnostic methods.
Effects of xanthan gum on atomization and deposition characteristics in water and Silwet 408 aqueous solution (2018)

In order to investigate the effects of viscosity on spray formation and utilization of pesticide, different concentrations of xanthan gum (XG) were added into water and 0.1% Silwet 408 aqueous solution. Droplet size, relative span (RS), fan angle, length of breakup and maximum retention (Rm) were measured with the LU120-02 nozzle spraying under the pressure of 0.3 MPa. The dynamic spreading of the different solutions on maize leaves was tested using a 5 μL micro-injector. The results showed: VMD, RS, length of breakup and Rm went up as the increasing of XG concentration in the range of 0-0.5% with the same solution, while the fan angle of nozzle and spreading area on maize leaf showed the opposite tendency. Silwet 408 could reduce the surface tension of liquid, which could alter the dominant mode of spray formation and lead to earlier sheet breakup, especially in low viscosity solutions. Under the same concentration of XG the addition of Silwet 408 could reduce the RS of drop size spectrum but has no effect on VMD or fan angle. In water solution, there was no difference with different concentrations of XG in the spreading time on maize leaf. Besides, in the 0.1% Silwet 408 aqueous solution, the spraying time and area were several-fold of that in water with same XG concentration. Moreover, with the same XG concentration, the smaller surface tension liquid indicated lower Rm, and the difference was magnified as the concentration increases. This work has demonstrated that initial spray characteristics such as droplet size and RS, fan angle, length of breakup, Rm and spreading area can vary depending on the viscosity of spray liquids. Therefore, by transforming the viscosity of the spray liquid to adjust the droplet spectrum to reduce drift, increasing the Rm and spreading area to improve liquid utilization and reduce the usage of pesticides.
Keywords: atomization, xanthan gum, spray, droplet size, breakup length, dynamic spreading
DOI: 10.25165/j.ijabe.20181103.3802

Citation: Wang S L, He X K, Song J L, Wang S S, Jia X M, Ling Y. Effects of xanthan gum on atomization and deposition characteristics in water and Silwet 408 aqueous solution. Int J Agric & Biol Eng, 2018; 11(3): 29–34.
Augmented marker tracking for peri-acetabular osteotomy surgery (2017)

We developed and validated a small, easy to use and cost-effective augmented marker-based hybrid navigation system for peri-acetabular osteotomy (PAO) surgery. The hybrid system consists of a tracking unit directly placed on the patient's pelvis, an augmented marker with an integrated inertial measurement unit ('MU) attached to the patient's acetabular fragment and the host computer. The tracking unit sends a live video stream of the marker to the host computer where the marker's pose is estimated. The augmented marker with the 'MU sends its pose estimate to the host computer where we apply sensor fusion to compute the final marker pose estimate. The host computer then tracks the orientation of the acetabular fragment during peri-acetabular osteotomy surgery. Anatomy registration is done using a previously developed registration device. A Kalman filter-based sensor fusion was added to complete the system. A plastic bone study was performed for validation between an optical tracking-based navigation system and our proposed system. Mean absolute difference for inclination and anteversion was 1.63 degrees and 1.55 degrees, respectively. The results show that our system is able to accurately measure the orientation of the acetabular fragment.
ErbB2 overexpression in an ovarian cancer cell line confers sensitivity to the HSP90 inhibitor geldanamycin. (2002)

ErbB2 is overexpressed in 25-30% of breast and ovarian cancers, correlates with poor prognosis and lower survival and has also been associated with chemoresistance. We have established an isogenic pair of human ovarian cells that differ only in the expression of erbB2 protein in order to elucidate the role of the protein in determining cellular sensitivity to various drugs and agents. These included cisplatin and paclitaxel, the main drugs used in the treatment of ovarian cancer, and also various signal transduction inhibitors affecting the ras and P13K pathways. Transfection of erbB2 resulted in cells stably overexpressing the protein and showing increased motility compared to the empty vector control cells. In cells overexpressing erbB2, the most notable effect on chemosensitivity was that of significantly increased (5-fold) sensitivity to the heat shock protein 90 (HSP90) molecular chaperone inhibitor geldanamycin. In contrast, erbB2-overexpressing cells showed statistically significant resistance to cisplatin, the P13K inhibitor LY294002 and the tyrosine kinase inhibitor emodin. No significant difference in growth inhibition was observed after exposure to paclitaxel, two additional HSP90 inhibitors radicicol and 17AAG, the cyclin-dependent kinase inhibitor flavopiridol, the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor PD153035, the mek inhibitor U0126 or the famesyl transferase inhibitor R115777. Exposure of cells to geldanamycin, 17AAG, emodin, LY294002 and cisplatin led to depletion of erbB2 in the transfected cells. These data suggest that erbB2 status in ovarian cancr may contribute to chemosensitivity, in some cases leading to increased sensitivity (as with geldanamycin) but in other cases leading to resistance (as with cisplatin).
Optimization of SAM-based multilayer SERS substrates for intracellular analyses: the effect of terminating functional groups (2011)

Surface-enhanced Raman scattering (SERS) has become an attractive analytical tool for intracellular analyses due to its minimally invasive nature and molecular specificity. However, highly reproducible and optimized SERS substrates have been seen as a key to developing SERS as a reliable analytical methodology. This research focuses on optimizing self assembled monolayer (SAM)-based multilayer SERS substrates for a wide range of applications, including ultratrace detection of biomolecules within individual living cells. Multilayer SERS substrates are comprised of alternating layers of metal film and dielectric spacer cast on a monolayer of nanostructures. Using these substrates, varying degrees of SERS enhancement factors (EF) have been achieved, some as large as 10-fold relative to optimized single film over nanostructures substrates. To gain a mechanistic understanding of multilayered SERS enhancements, SAMs have been used to systematically vary spacer thickness. The results revealed spacer-dependent SERS EFs. To further the understanding of multilayer SERS enhancement, this work discusses the use of terminating functional groups in the optimization of SAM multilayer SERS substrates. SAMs having various functional groups were used as dielectric spacers to systematically vary the dielectric constant. To investigate the effect of the pH on the uniformity of the SAMs and their multilayer SERS enhancement, SAMs were formed in alkylthiol solutions of different pH and the subsequent SERS enhancement were evaluated. It was found that using alklythiol SAMs with appropriate terminating functional groups the SAM multilayer can achieve SERS EFs ranging between 10<sup>8</sup> and10<sup>10</sup> and the substrates yielded highly reproducible SERS signals. The effect of the pH on the SERS enhancement is selective on the type of the terminating functional group of the alkylthiol used for SAM formation.
A Discrete Choice Model for Ordered Alternatives (1987)

A generalization of the multinomial logit (MNL) model is developed for cases in which discrete alternatives are ordered so as to induce stochastic correlation among alternatives in close proximity.The model belongs to the Generalized Extreme Value class introduced by McFadden, and is therefore consistent with random utility maximization.If the true model is nearly MNL, iterative estimation on an ordinary MNL computer package provides approximate parameter estimates and a test for the hypothesized failure of the MNL's "independence from irrelevant alternatives" assumption.A straightforward extension can handle cases where observations have been selected on the basis of a truncated choice set.The model's properties are investigated through a numerical example, and through two empirical applications whose rather unsatisfactory results are very briefly described.
Automatic adjustment of visuomotor readiness (2007)

Participants initiated a reaching movement to a single target more rapidly than to an odd-color target among distractors when the two trial types were presented in separate blocks, reflecting differentiated states of sensorimotor readiness for a relatively easy (single target) versus harder (odd-color target) tasks. This pattern was eliminated when the two trial types were randomly mixed. Latencies for the easy single trials increased, and those for the harder odd-color trials decreased, showing homogenization. The faster movement initiation in the odd-color target task was accompanied by curved trajectories, directed toward a distractor initially but corrected in midflight. Two possible hypotheses could account for this differentiated adjustment in visuomotor readiness: (1) explicit knowledge of upcoming trial types and (2) implicit leaning derived from history of the very recent past, that is, repetition of the same type of trials. To distinguish between these two accounts, we included a third condition where the trial types were predictably alternated. Contrary to the explicit knowledge hypothesis, this also led to homogenization of initiation latencies, and curved trajectories. We conclude that visuomotor readiness is automatically adjusted by the recent experience of trial difficulty.
Design of a scanning tunneling microscope for biological applications (1988)

A scanning tunneling microscope (STM) designed for biological application and operating at ambient pressure is described. It is combined with a light microscope, monitoring the specimen through a transparent support, which is used to search for specimen areas of interest. Glass or mica coated with a thin conductive layer (e.g., carbon) are used as a specimen support. The STM itself, is essentially a Besocke-type STM; modifications include a convenient and reliable mechanism for sample approach to the tip (z adjustment).
Bcl-2: an antidote to programmed cell death. (1992)

The maintenance of homoeostasis in normal tissues reflects a balance between cell proliferation and cell death. The importance of both positive and negative regulators of cell growth has been well documented in neoplasia. bcl-2 argues for the existence of a new category of oncogenes, regulators of programmed cell death. The bcl-2 gene was identified at the chromosomal breakpoint of t(14;18) bearing B cell lymphomas. Bcl-2 has proved to be unique among proto-oncogenes in being localized to mitochondria and in blocking programmed cell death rather than affecting proliferation. In adults, bcl-2 is topographically restricted to progenitor cells and long-lived cells in tissues characterized by apoptotic cell death. Bcl-2 is confined to the zones of surviving B cells in germinal centres. Within thymus, bcl-2 is present in the surviving mature thymocytes of the medulla but absent from the majority of immature cortical thymocytes, most of which die by apoptosis. Transgenic mice that overexpress bcl-2 in the B cell lineage demonstrate extended cell survival and prolonged immune responses and indicate a role for bcl-2 in B cell memory. Transgenic models that overexpress bcl-2 in the thymus have expanded the involvement of bcl-2 to multiple apoptotic pathways and indicate its involvement in thymocyte maturation. Moreover, the development of tumours in transgenic mice that overexpress bcl-2 indicates the potential importance of oncogenes in interfering with programmed cell death. Alterations in genes that regulate cell death may prove to be key events in neoplasia, extending the life span of cells and thus increasing their opportunity to acquire additional genetic aberrations.
A study on the data privacy and operation performance for cloud collaborative editing systems (2012)

This paper deals with the problem of collaboratively secure document editing in cloud environment. Using cloud document editing service, several users can create and edit a document collaboratively. However, as the cloud service provider is not trusted to guarantee the confidentiality of these documents, existing methods encrypt the documents before uploading them to the cloud. While these approaches can be inefficient for collaborative editing, we propose to organize the content of a document using a Red-Black tree and encrypt each block of data separately, so as to improve the performance of collaborative editing systems. Although creating and maintaining the Red-Black tree introduces extra cost, compared to the whole document encryption strategy the experimental results show that for text editing operations, such as insertion and removal, the use of Red-Black tree algorithm improves efficiency by 31.04% if 3DES encryption is applied and by 23.94% if applying AES encryption.
Inclusive Islamic financial planning: a conceptual framework (2016)

Purpose This paper aims to develop a conceptual framework of inclusive Islamic financial planning (IFP) by combining the traditional Islamic institutions of zakat and awqaf with contemporary notions of financial planning, financial inclusion and financial literacy that caters to the short-term and long-term financial goals of the poor. Design/methodology/approach Being a conceptual article, an inclusive IFP framework is described, analyzed and developed by integrating modern notions of financial inclusion, financial planning and financial literacy with the concepts of zakat and awqaf . Findings Using the notion of a hierarchy of needs and a financial planning model, an inclusive IFP framework that can be used by the poor is outlined. The complementary role of the non-poor households who provide funds for zakat and awqaf is also identified. Research limitations/implications The applicability of an inclusive IFP would require Islamic financial instruments and products, institutional development and existence of a social planner who can integrate zakat , awqaf and financial planning to serve the financial needs of the poor. Social implications Application of an inclusive IFP that can mitigate poverty would necessitate integrating financial planning skills and knowledge with traditional institutions of zakat and awqaf to provide holistic financial advice and services to the poor households. Originality/value Discussion of financial planning in financial inclusion literature is scant. The paper explores and offers a novel approach of poverty mitigation by utilizing the full spectrum of IFP that considers the financial needs and allows for the creation of a personalized financial plan for low-income households.
The Role of Toll-Like Receptor 4 in Infectious and Noninfectious Inflammation (2016)

Toll-like receptor 4 (TLR4) belongs to the family of pattern recognition receptors (PRRs). They are highly conserved receptors that recognize conserved pathogen-associated molecular patterns (PAMPs), thus representing the first line of defense against infections. TLR4 has been long recognized as the sensing receptor for gram-negative lipopolysaccharide (LPS). In addition, it also binds endogenous molecules produced as a result of tissue injury. Hence, TLR4 represents a key receptor on which both infectious and noninfectious stimuli converge to induce a proinflammatory response. TLR4-mediated inflammation, triggered by exogenous or endogenous ligands, is also involved in several acute and chronic diseases, having a pivotal role as amplifier of the inflammatory response. This review focuses on the research progress about the role of TLR4 activation in infectious and noninfectious (e.g., sterile) inflammation and the effects of TLR4 signaling in some pathological conditions.