gebhart/patrepeval huggingface dataset:
Protein Interactions at the Tight Junction (1999)

Defining how the molecular constituents of the tight junction interact is a prerequisite to understanding tight junction physiology. We utilized in vitro binding assays with purified recombinant proteins and immunoprecipitation analyses to define interactions between ZO-1, ZO-2, ZO-3, occludin, and the actin cytoskeleton. Actin cosedimentation studies showed that ZO-2, ZO-3, and occludin all interact directly with F-actin in vitro, indicating that actin is engaged in multiple interactions at the tight junction. Low speed sedimentation analyses demonstrated that neither ZO-2, ZO-3, nor occludin act as F-actin cross-linking proteins, and further evidence indicates that these proteins do not bind to actin filament ends. The binding interactions of ZO-2, ZO-3, and occludin were corroborated in vivo by immunofluorescence colocalization experiments which showed that all three proteins colocalized with actin aggregates at cell borders in cytochalasin D-treated Madin-Darby canine kidney cells. Exploration of other tight junction protein interactions demonstrated that ZO-2 binds directly to both ZO-1 and occludin. Contrary to previous beliefs, our immunoprecipitation results indicate that ZO-1, ZO-2, and ZO-3 exist in situ primarily as independent ZO-1.ZO-2 and ZO-1.ZO-3 complexes rather than a trimeric ZO-1.ZO-2.ZO-3 grouping. These studies elucidate direct binding interactions among tight junction-associated proteins, giving insight into their organization as a multimolecular structure.
OBIWAN-a visual interface for prompted query refinement (2002)

Typically, users submit very simple search queries to digital document data collections. Often, these queries can result in extremely broad answers or answers in which document relevance is hard to assess. Our group has developed a suite of tools which build sophisticated indexes to document collections. These tools can be used to provide cues to help users formulate more effective queries. In order to present these cues and manage the process of query refinement, we have developed a Java-based client-server system which uses these indexes and tools. One of the most powerful parts of our system is its ability to recognize domain-specific multi-word names and terms, using heuristic methods, and to index these vocabulary items in such a way that we can look up vocabulary items that commonly are related to the original query terms. This system responds to an initial query by suggesting additional items, based on a lexical network, that the user can use to focus the query. It has a simple "one-button" user interface, named OBIWAN (One-Button Interface With Associated Network).
Clinical Significance of CD200 and CD56 in Patients with Acute Lymphoblastic Leukemia (2016)

To analyze CD200 and CD56 expression by flow cytometry in acute lymphoblastic leukemia patients and whether their overexpression had prognostic impact individually and in combination with each other. Seventy newly diagnosed patients were assessed, of whom 27 were adult ALL and 43 pediatric ALL. Forty seven of 70 cases (67%) showed CD200 expression, and 7 cases (10%) showed CD56 expression but only 3 cases (4.3%) had expression for CD200+ and CD56+. Significance differences were found between CD200& CD56 expression in whole ALL patients group compared to control group (P<0.0001and P<0.001respectively). Splenomegaly and lower hemoglobin and platelet were more frequently observed in CD200+ patients whose also associated with significant increase of myeloid marker CD34 frequency. There were significant differences in overall survival (P= 0.042, P= 0.006) and disease-free survival (P= 0.005, P= 0.002 ) between the CD200+ and CD200- patients in total ALL patients and adult ALL . Whereas, in pediatric ALL OS of CD200+ patients 35.7% compared to 86.2% in CD200-, P= 0.032 but DFS showed non-significant difference (P=0.099). On the other hand, CD56+ patients had lower complete remission rate (14.3% vs. 63.5%, P= 0.018). CD56+ had significant influence on overall than those of CD56- (28.6% with mean 4.7 months vs. 41.1% with mean=11.8 months, P= 0.003) and disease free survival (40% with mean=6.26months vs. 54.9% with mean=14.16, P = 0.006). In respect to combination of two CDs positive had very inferior OS and DFS (mean =0.533 month and 0.150 month). In addition to, increased frequency of CD34 was associated with CD200+, CD56+ patients.
Fiber-Core-Matched Three-Dimensional Adiabatic Tapered Couplers for Integrated Photonic Devices (2010)

A three-dimensional (3-D) adiabatic tapered coupler is demonstrated to improve light coupling between single-mode fibers (SMF) and an integrated photonic chip. This 3-D taper, made by polymer via a fabrication process using mode extrusion in combination with photolithography, can have a large coupling area matching with a fiber core. For a silicon oxynitride waveguide coupling to a SMF, the measured coupler loss was 3 dB. The fiber misalignment tolerance is 3.5 m and 3 to 5 m for the lateral and vertical offset, respectively, according to a 3-dB loss window.
New Delhi Metallo-β-Lactamase in<i>Klebsiella pneumoniae</i>and<i>Escherichia coli,</i>Canada (2010)

Multidrug-resistant Klebsiella pneumoniae and Escherichia coli isolates harboring New Delhi metallo-β-lactamase (NDM-1) were isolated from a patient who had returned to Canada from India. The NDM-1 gene was found on closely related incompatibility group A/C type plasmids. The occurrence of NDM-1 in North America is a major public health concern.
In Silico Approach for Predicting Toxicity of Peptides and Proteins (2013)

ToxinPred is a unique in silico method of its kind, which will be useful in predicting toxicity of peptides/proteins. In addition, it will be useful in designing least toxic peptides and discovering toxic regions in proteins. We hope that the development of ToxinPred will provide momentum to peptide/protein-based drug discovery (http://crdd.osdd.net/raghava/toxinpred/).
A poly(arylene ether sulfone) hybrid membrane using titanium dioxide nanoparticles as the filler (2016)

Poly(arylene ether sulfone) (PES)–titanium dioxide (TiO 2 ) hybrid membranes were prepared via solution blending method using TiO 2 nanoparticles as inorganic filler. The chemical structure and thermal stability of the matrix polymer were characterized by proton nuclear magnetic resonance, Fourier transform infrared, differential scanning calorimetry, and thermogravimetric analysis. The crystal structure, morphology, mechanical properties, and gas separation performance of hybrid membranes were characterized in detail. As shown in scanning electron microscopic images, TiO 2 nanoparticles dispersed homogeneously in the matrix. Although the mechanical properties of hybrid membranes decreased certainly compared to the pure PES membranes, they are strong enough for gas separation in this study. All gas permeability coefficients of PES-TiO 2 hybrid membranes were higher than pure PES membranes, attributed to the nanogap caused by TiO 2 nanoparticles, for instance, oxygen and nitrogen permeability coefficients of Hybrid-3 (consists of PES with 4-amino-phenyl pendant group and hexafluoroisopropyl (Am-PES)-20 and TiO 2 nanoparticles, 5 wt%) increased from 2.57 and 0.33 to 5.88 and 0.63, respectively. In addition, the separation factor increased at the same time attributed to the stimulative transfer effect caused by the interaction of hydroxyl groups on the TiO 2 nanoparticle and polar carbon dioxide molecules.
Tensile properties of human knee joint cartilage: I. Influence of ionic conditions, weight bearing, and fibrillation on the tensile modulus (1986)

The flow-independent (intrinsic) tensile modulus of the extracellular matrix of human knee joint cartilage has been measured for normal, fibrillated, and osteoarthritic (removed from total knee joint replacements) cartilage. The modulus was determined in our isometric tensile apparatus and measured at equilibrium. We found a linear equilibrium stress-strain behavior up to approximately 15% strain. The modulus was measured for tissues from the high and low weight-bearing areas of the joint surfaces, the medial femoral condyle and lateral patello femoral groove, and from different zones (surface, subsurface, middle, and middle-deep) within the tissue. For all specimens, the intrinsic tensile modulus was always less than 30 MPa. Tissues from low weight-bearing areas (LWA) are stiffer than those from high weight-bearing areas (HWA). The tensile modulus of the ECM correlates strongly with the collagen/proteoglycan ratio; it is higher for LWA than for HWA. Osteoarthritic cartilage from total knee replacement procedures has a tensile stiffness less than 2 MPa.
Role of immune interferon in the monocytic differentiation of human promyelocytic cell lines induced by leukocyte conditioned medium (1985)

Conditioned medium (CM) from lectin-stimulated human leukocytes contains factors that induce human promyelocytic cell lines to differentiate along the monocytic pathway. In this report, we show that human promyelocytic cell lines are also induced to differentiate along this pathway by immune interferon (IFN gamma). Various preparations of IFN alpha tested did not induce this differentiation. In cultures containing IFN gamma, the cells are induced to coordinately express monocyte markers and functions such as monocyte-specific surface antigens, HLA-DR antigens, nonspecific esterase, receptors for the Fc fragment of IgG, and the ability to mediate antibody-dependent cell- mediated cytotoxicity. Our data indicate that differentiation induced by IFN gamma is not secondary to an arrest of growth of promyelocytic cell lines, but rather that a proportion of cells is induced along a programmed pathway of terminal differentiation similar to that of normal monocytes. CM contains IFN gamma, but its ability to induce differentiation is greater than expected on the basis of its content of IFN gamma. Treatments at 56 degrees C or at pH 2.0, which abolish IFN gamma activity, abrogate the differentiation ability of CM. The antiviral activity and the differentiation activity contained in the CM are coeluted from gel filtration and reverse-phase columns. Monoclonal antibodies anti-IFN gamma, which completely abrogate the differentiation ability of IFN gamma and the antiviral activity in the CM, completely suppress the induction of some monocyte markers by CM, but only reduce the expression of others. When IFN gamma is added to CM, promyelocytic cell lines are induced to differentiate to a much greater extent than that induced by either IFN gamma or IFN gamma- depleted CM alone. These results show that the differentiation activity of leukocyte CM is due to the synergistic effect of IFN gamma and other factors not yet identified.
Laser photocoagulation combined with subtenon injection of triamcinolone acetonide for diabetic cystoid macular edema. (2009)

This study, with a follow-up of 6 months, suggests that subtenon injection of triamcinolone combined with macular photocoagulation provides a better chance of stabilizing vision loss in patients with diabetic cystoid macular edema than photocoagulation alone.
Unmet Supportive Care Needs after Non-Small Cell Lung Cancer Resection at a Tertiary Hospital in Seoul, South Korea (2023)

The aim of this study is to identify the prevalence and predictors of unmet needs of non-small cell lung cancer (NSCLC) patients undergoing surgical resection in Seoul, South Korea. A total of 949 patients who completed survey questionnaires that included the Cancer Survivors' Unmet Needs Korean version (CaSUN-K), fear of cancer recurrence (FCR) inventory-short form, and European Organization for Research and Treatment of Cancer Quality of Life Core Questionnaire (EORTC QLQ-C30) were recruited from January to October 2020. Multivariable logistic regression was used to determine the potential correlation of significant unmet needs, defined as any moderate or strong need, for each domain of CaSUN-K. Of the 949 participants, the mean age was 63.4 ± 8.8 years old, and 529 (55.7%) were male. Overall, 91.8% of participants reported one or more unmet need. The highest domains of moderate-to-strong unmet needs were existential survivorship (59.1%), comprehensive cancer care (51.2%), and information (49.7%). High FCR and poor emotional function were associated with moderate-to-strong unmet needs across all domains of CaSUN-K. NSCLC survivors with a recent diagnosis had more frequent disease-related unmet needs. Interventions to reduce the unmet needs of NSCLC patients should focus on relieving FCR and improving emotional functioning. Furthermore, emphasis should be placed on decreasing disease-related needs, particularly for early survivors of lung cancer during the re-entry phase.
[Substantiation of radiation quality coefficient dependence on LET in application to the assessment of early radiobiological effects]. (1998)

Radiobiological studies targeted at determination of the coefficients of relative biological effectiveness (RBE) of various radiations in comparison with the standard X-ray radiation at 180-250 keV maximum were reviewed. Comparison of reactions of the body as a whole and its specific systems shortly after acute irradiation revealed the character of the relationship of RBE coefficients to LET. These data are essential for more careful estimation of radiation risk during space missions when, in parallel with chronic exposure to determinant sources, i.e. GCR and ERB, crew members may be also subjected to comparatively brief SCR attacks, particularly during solar proton events with high fluences.
Colour parameters, whiteness indices and physical features of marking paints for horizontal signalization (2005)

The present paper describes the assessment of colour parameters of industrial paints for horizontal signalization (designed as POM S1 and POM S2 / ZEB 1 and ZEB 2) of white colour hue, coming from two different producers ("Pomoravlje" and "Zorka") with reference to an independent sample (IND 0) and some physical properties of each sample. Colorimetric characterization of samples was performed using a reflectance spectrophotometer "Update Colour Eye 3000". Standard and modified test methods (ASTM) were performed to establish physical properties of the paints. The industrial paints show better values for the investigated parameters and properties and satisfy standards prescribed by law. POM S2 sample with dry film thickness, similar to the same of other samples, provides the best physical features maximizing quality and minimizing protection cost.
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes (2015)

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
Enforcing code security in database web applications using libraries and object models (2007)

Libraries are commonly though as toolboxes offering reusable components and algorithms. In this paper, we show that a properly designed library can also be used to enforce security, and hence to help in the creation of robust and secure applications. As an illustration, we choose database web applications, because they are the kind of applications that suffers from the highest amount of vulnerabilities. SQL injection or Cross Site Scripting are common examples. We present how a library can be designed in such a way to completely mitigate these vulnerabilities. We also show how a properly designed library does not only allow a programmer to write secure code, but can also make vulnerable code impossible to write. We validate our theories through the presentation of a concrete Java library named "Stones" that follows and applies our ideas. Finally, our approach is compared with related work and various practical results are stated.
Failure to replicate effect of kibra on human memory in two large cohorts of European origin (2008)

It was recently suggested that the Kibra polymorphism rs17070145 has a strong effect on multiple episodic memory tasks in humans. We attempted to replicate this using two cohorts of European genetic origin (n = 319 and n = 365). We found no association with either the original SNP or a set of tagging SNPs in the Kibra gene with multiple verbal memory tasks, including one that was an exact replication (Auditory Verbal Learning Task, AVLT). These results suggest that Kibra does not have a strong and general effect on human memory.
A client-side stub interpreter (1994)

We have built a research operating system in which all services are presented through interfaces described by an interface description language. The system consists of a micro-kernel that supports a small number of these interfaces, and a large number of interfaces that are implemented by user-level code. A typical service implements one or more interfaces, but is a client of many other interfaces that are implemented elsewhere in the system. We have an interface compiler that generates client-side and server-side stubs to deliver calls from clients to servers, providing location transparency if the client and server are in different address spaces. The code for client-side stubs was occupying a large amount of the text space of our clients, so a stub interpreter was written to replace the clientside stub methods. The result was that we traded 125K bytes of stub code for 13K bytes of stub descriptions and 4K bytes of stub interpreter. This paper describes the stub interpreter, the stub descriptions, and discusses some alternatives.
Microfluidic Colloidal Island Formation and Erasure Induced by Surface Acoustic Wave Radiation (2008)

Spatiotemporal patterns form in many nonlinear physicochemical or biological systems. Although unusual, microfluidic systems are no exception. We observe such patterns to form by colloids along the free surface of a drop beneath which surface acoustic waves propagate, and propose fundamental mechanisms to elucidate their formation. With increasing excitation amplitude, the colloids first assemble into concentric rings and then cluster into islands due to a combination of capillarity and surface acceleration. As the excitation is further increased, fluid streaming commences within the drop, inducing a transient metastable state in which the system alternates between colloidal island formation on the quiescent drop surface and subsequent erasure due to local vortex generation.
MCC950, a specific small molecule inhibitor of NLRP3 inflammasome attenuates colonic inflammation in spontaneous colitis mice (2018)

MCC950 a potent, highly specific small molecule inhibitor of canonical and noncanonical activation of NLRP3 inflammasome has been evaluated in a multitude of NLRP3 driven inflammatory diseases. However, the effect of MCC950 on colonic inflammation has not yet been reported. In the present study we investigated the effect of MCC950 in a spontaneous chronic colitis mouse model Winnie, which mimics human ulcerative colitis. Oral administration of 40 mg/kg MCC950 commencing at Winnie week seven for three weeks significantly improved body weight gain, colon length, colon weight to body weight ratio, disease activity index and histopathological scores. MCC950 significantly suppressed release of proinflammatory cytokines IL-1β, IL-18, IL1-α, IFNγ, TNF-α, IL6, IL17, chemokine MIP1a and Nitric Oxide in colonic explants. Moreover, MCC950 resulted in a significant decrease of IL-1β release and activation of caspase-1 in colonic explants and macrophage cells isolated from Winnie. Complete inhibition with MCC950 in Winnie colonic explants shows, for the first time, the contribution of inflammatory effects resulting exclusively from canonical and noncanonical NLRP3 inflammasome activation in colitis. Taken together, our results illustrate the efficacy of MCC950 in the treatment of murine ulcerative colitis and provides avenue for a potential novel therapeutic agent for human inflammatory bowel diseases.
Improved analysis method for broadband rectangular microstrip antenna geometry using E-plane gap coupling (1993)

An analysis method for the broadband rectangular microstrip antenna geometry using E-plane gap coupling is considered. The return loss of the designed broadband antenna is computed theoretically and compared with experimental results for illustrating the usefulness of this method.
Periodogram pattern feature-based seizure detection algorithm using optimized hybrid model of MLP and Ant Colony (2015)

Seizure detection with EEG analysis in the form of offline is an application of brain signal processing. In this paper, a seizure detection algorithm using pattern features of periodogram and an optimized hybrid model based on Ant Colony Optimization (ACO) and Multi-Layer Perceptron (MLP) neural network is proposed. In this algorithm, with introducing a novel feature extraction method, a feature vector based on periodogram is extracted. For this purpose, we define a novel color map of periodogram pattern based on windowing method and modified periodogram. Statistical and frequency features are computed for each one of five rhythms in EEG signals. These rhythms and features are extracted by using a novel scenario that is called Periodogram Pattern Feature (PPF). In this scenario, at first by making a color pattern of periodogram as an estimation of the spectral density, for each signal, a Time-Frequency layout is created. This pattern is divided to some epochs for decomposing the brain rhythms. Also, to optimize the feature vector, ACO algorithm in combination with MLP is used. At last, a perfect set of features with 5 valid items has provided. Moreover, seizure from non-seizure signal has been classified with accuracy of 94.4% using the final optimized features.