gebhart/patrepeval huggingface dataset:
Cross-talk between β-adrenoreceptor and α7-nicotinic acetylcholine receptor (α7-nAChR) signaling in gastric carcinogenesis (2008)

2238 Cigarette smoking is associated with various cancers, but it is unclear which component(s) imposed the carcinogenic effect in stomach. Nicotine, the major component in cigarette smoke, has been shown to exert mitogenic effect on tumor growth and angiogenesis. Moreover, nicotine-derived nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), is carcinogenic in lung cancer. However, there are few studies that examined the effects of these two components in gastric carcinogenesis. The aim of this study is to determine if nicotine and/or NNK would promote gastric tumor growth and to delineate the molecular mechanism(s) involved, which may shed light on new gastric cancer drug discovery. Human gastric carcinoma cells (AGS) were incubated with nicotine and NNK at various concentrations for 5 hours. High dose of nicotine (200 μg/ml) and NNK (100 nM) significantly increased cell proliferation by 40% and 96%, respectively. The increased cancer growth is due to the modulation of several G1 regulatory proteins, leading to the cell cycle transitions. Cyclin D1 expression and its association with cyclin-dependent kinases (CDK4/6) was analyzed by immunoprecipitation. The complexes immunoprecipitated with anti-cyclin D1 antibody exhibited higher amounts of CDK4 in NNK than nicotine treatment. Furthermore, phosphorylation of retinoblastoma protein (Rb) was activated which released the transcription factor E2F and DP-1 to form heterodimers and facilitate cell cycle progression. Pretreatment with a selective COX-2 inhibitor (SC-236) prevented the upregulation of G1 regulatory proteins and caused cell cycle arrest at G1 phase. Furthermore, nicotine- and NNK-induced COX-2 activity and protein expressions were abrogated by SC-236. The increased production of PGE 2 was blocked by SC-236. Pretreatment of cells with propranolol (non-specific β-adrenoreceptor antagonist), but not α-bungarotoxin (α-BTX, α7nAChR antagonist), abolished the nicotine-induced cell proliferation. On the other hand, α-BTX suppressed COX-2 and PGE 2 production in NNK-induced cell proliferation, and was partially abrogated by propranolol. These results pointed to the importance of adrenergic and nicotinic receptors in gastric tumor growth promoted by cigarette smoke. These data revealed that nicotine and NNK are two major components in cigarette smoke that are responsible for the tumor promoting effects on gastric carcinogenesis through the cooperation of different receptors to regulate the progression of cell cycle via COX-2 dependent pathway.
Een nieuwe vorm van participatie: de zorggebruikersvereniging (2004)

We leven in een tijd van snelle ontwikkelingen. Die ontwikkelingen raken alle onderdelen van de samenleving. Zo ook de gehandicaptenzorg.
Study on span configurations for long-distance 40Gb/s-based WDM transmissions with all-Raman amplification (2002)

We have investigated various span configurations suitable for a distributed all-Raman amplification system over long distance. By our proposed configuration, 6,050-km WDM transmission of 32 chtimes42.7 Gb/s signals was achieved with a practical symmetrical-structure
Supplementary Data from Chk1 Inhibition Potently Blocks STAT3 Tyrosine705 Phosphorylation, DNA-Binding Activity, and Activation of Downstream Targets in Human Multiple Myeloma Cells (2023)

Supplementary Data from Chk1 Inhibition Potently Blocks STAT3 Tyrosine705 Phosphorylation, DNA-Binding Activity, and Activation of Downstream Targets in Human Multiple Myeloma Cells
Molecular Biology of the H-2 Histocompatibility Complex (1986)

The H-2 histocompatibility complex of the mouse is a multigene family, some members of which are essential for the immune response to foreign antigens. The structure and organization of these genes have been established by molecular cloning, and their regulation and function is being defined by expression of the cloned genes.
Data Supplement from TLR9 Is Critical for Glioma Stem Cell Maintenance and Targeting (2023)

&lt;p&gt;Figure S1. Increased TLR9 expression in induced glioma spheres. Figure S2. TLR9 and STAT3 form a feed-forward loop in GSCs. Figure S3. Stat3 silencing by local CpG-Stat3siRNA delivery inhibits tumor growth. Figure S4. Stat3 silencing by local CpG-Stat3siRNA delivery inhibits GSCs. Figure S5. Targeting Brain tumors systemically with CpG-siRNA reaches the tumor site.&lt;/p&gt;
7α-Iodo and 7α-Fluoro Steroids as Androgen Receptor-Mediated Imaging Agents (1999)

We have synthesized several 7alpha-fluoro (F) and 7alpha-iodo (I) analogues of 5alpha-dihydrotestosterone (5alpha-DHT) and 19-nor-5alpha-dihydrotestosterone (5alpha-NDHT) and tested them for binding to the androgen receptor and for their biological activity in an in vitro assay with cells that have been engineered to respond to androgens. The relative binding affinity to the androgen receptor determined in competition assays showed that in the androstane series the fluoro steroids have the highest affinity and that F-17alpha-CH3-DHT (4) has a higher affinity than 5alpha-DHT. All other steroids were somewhat less potent than 5alpha-DHT with F-DHT (2) = I-17alpha-CH3-DHT (3) >/= F-NDHT (6) > F-17alpha-CH3-NDHT (8) = I-DHT (1) >/= I-NDHT (5) > I-17alpha-CH3-NDHT (7). The relative biological activity in cells transfected with the androgen receptor and an androgen responsive reporter gene is 4 >> 5alpha-DHT > 2 > 6 > 3 >/= 1 >/= 8 >/= 5 > 7. The iodinated compound, I-17alpha-CH3-DHT (3), with the highest binding activity was synthesized labeled with 125I and was shown to bind with high affinity, Ka = 1.9 x 10(10) L/mol, and low nonspecific binding to the androgen receptor in rat prostatic cytosol. However, when radiolabeled [125I]-17alpha-CH3-DHT ([125I]3) was injected into castrated male rats, it showed very poor androgen receptor-mediated uptake into the rat prostate. This was unexpected in light of its superior receptor binding properties and its protection by the 17alpha-methyl group from metabolic oxidation at C-17. However, the biological potency of I-17alpha-CH3-DHT (3) was not as high as would have been expected. When I-DHT (1) and I-17alpha-CH3-DHT (3) were incubated in aqueous media at 37 degrees C they rapidly decomposed, but they were stable at 0 degrees C. The fluorinated analogue 4 treated similarly at 37 degrees C was completely stable. The products of the decomposition reaction of I-DHT (1) at 37 degrees C were identified as iodide and principally 17beta-hydroxy-5alpha-androst-7-en-3-one. The temperature dependence of this elimination reaction explains the inconsistency between the high binding to the androgen receptor (measured at 0 degrees C) and the low biological activity, as well as the poor androgen receptor mediated concentration in vivo. The fluorinated analogue F-17alpha-CH3-DHT (4) has both high affinity for the androgen receptor and high stability in aqueous media. Of the compounds tested, 4 has the highest affinity for the androgen receptor as well as the highest androgenic activity. Thus it is likely that F-17alpha-CH3-DHT 4 labeled with 18F will be an excellent receptor-mediated diagnostic imaging agent.
The X-ray structure of (MeBm2t)1-cyclosporin complexed with cyclophilin A provides an explanation for its anomalously high immunosuppressive activity (1994)

For most of the cyclosporin A (CsA) analogs, there is generally a good correlation between cyclophilin binding and immunosuppression. However, this relationship does not seem to hold for 4-[(E)-2-butenyl]-4,4,N-trimethyl-L-threonine1 (MeBm2t)1-CsA. Its affinity for cyclophilin was reported to be approximately 1% that of CsA and its immunosuppressive activity in vitro was shown to be approximately 30% that of CsA. We report here the crystal structure of a complex between recombinant human cyclophilin A (CypA) and (MeBm2t)1-CsA which has been determined by X-ray crystallography at 2.2 A resolution and refined to an R-factor of 16.3%. (MeBm2t)1-CsA shows a similar bound conformation and network of interactions to CypA as CsA. The measured lower affinity for CypA cannot therefore be explained by a different mode of binding. We propose that the poor affinity to CypA could be accounted for by the existence of an equilibrium in aqueous solution between a 'cyclophilin bound conformation' and a 'non-binding conformation' of (MeBm2t)1-CsA. The relatively high immunosuppressive activity is suggested to result from slight conformational differences observed in the effector domain.
Experiment and model for deviation from Pelgrom scaling relation in device width (2014)

Through modeling, simulations, and experimental data, we show that FETs exhibit several width dependent characteristics purely due to un-correlated random variations among sub-threshold currents in different width segments. They include unit-width median sub-threshold current and constant-current threshold voltage. The width scaling relation for threshold voltage mismatch is different from Pelgrom scaling relation for sufficiently large variation when compared to the thermal voltage.
Investigation on Feedback Channel State Information for Interference Rejection Combining Receiver in LTE-Advanced Downlink (2014)

This paper investigates a scheme for deriving feedback information for the interference rejection combining (IRC) receiver, which can suppress inter- cell interference, in order to perform adaptive modulation and coding (AMC), user scheduling, and transmission precoding at the serving eNodeB appropriately in the LTE/LTE-Advanced downlink. In this paper, we evaluate the negative impact of inappropriate feedback information for the IRC receiver, i.e., not including the interference suppression effect, and the effectiveness of appropriate feedback information on the user throughput performance. Simulation results assuming two transmitter/receiver antenna branches and an uncorrelated channel show that interference suppression for the IRC receiver does not affect the precoding matrix selection when selecting a common precoding matrix for the transmission bandwidth. Furthermore, even when the IRC receiver calculates the feedback information excluding the effect of interference suppression, the user throughput improves compared to that for the conventional MMSE receiver, which cannot suppress the inter-cell interference. However, when comparing the performance of the IRC receivers that calculate the feedback information when including and excluding the effect of interference suppression, the results show that the degree of improvement in the user throughput when excluding the interference suppression effect degrades due to inappropriate feedback information.
Resist system based on the cationic photocrosslinking of poly(4‐hydroxystyrene) and polyfunctional electrophiles (1993)

Abstract New resist systems based on acid‐catalyzed, electrophilic aromatic substitution are described. These new resists show high sensitivity to deep UV and E‐beam radiation with values approaching 2 mJ/cm 2 and 2 μC/cm 2 , respectively. The resists are based on a three component system consisting of poly(4‐hydroxystyrene), a polyfunctional, low molecular weight, latent electrophile, and a photoactive onium salt used as an acid generator. Irradiation of the resist film produces a latent image of acid dispersed in the matrix. During the postbaking step the photo‐generated acid reacts with the latent polyfunctional electrophile and releases a reactive carbocationic intermediate with concomitant liberation of acetic acid. The carbocationic intermediate then reacts with neighboring phenolic moieties in a crosslinking reaction. The substitution reaction liberates a proton, making the process catalytic in nature, thus incorporating the concept of chemical amplification. These highly sensitive materials can be used as nonswelling negative multipurpose resists that function in deep‐UV, x‐ray or E‐beam modes. © 1993 John Wiley &amp; Sons, Inc.
THE COMPLEMENT SYSTEM IN TRAUMA-RELATED AND ISCHEMIC TISSUE DAMAGE (1994)

There is increasing evidence that the complement system plays an important role in tissue damage associated with trauma and ischemia. In the present review we focus on some principles of importance for a basic understanding of the complement system, particularly aimed at those not working in this field. Complement is activated by its ability to discriminate between self and non-self, primarily as a defense against microorganisms. The activation induces an inflammatory reaction which may lead to harmful effects on the host, either as local tissue damage or, in case of an extensive systemic activation, as breakdown of homeostatic mechanisms. Complement-mediated inflammation is important not only in specific immunological defense reactions, but also in the induction of tissue injury by ischemia, hypothermia or other general tissue-damaging factors. Major trauma leads to systemic complement activation and complications to trauma may enhance the activation and increase the risk of development of the whole body inflammatory reaction and even of a fatal outcome. To protect the host against self-damage, complement activation is controlled by a series of regulatory proteins inhibiting at the various levels of the cascade. Intervening with complement activation using regulatory proteins like soluble complement receptor 1 has provided direct evidence for the importance of complement in tissue damage in various experimental models. Therapeutic complement intervention using a similar approach may be a useful tool in selected patients to attenuate the degree of complement activation and thereby reduce the total inflammatory load.
Liposomal dry powders as aerosols for pulmonary delivery of proteins (2020)

The purpose of this research was to develop liposomal dry powder aerosols for protein delivery. The delivery of stable protein formulations is essential for protein subunit vaccine delivery, which requires local delivery to macrophages in the lungs. β-Glucuronidase (GUS) was used as a model protein to evaluate dry powder liposomes as inhaled delivery vehicles. Dimyristoyl phosphatylcholine:cholesterol (7∶3) was selected as the liposome composition. The lyophilization of liposomes, micronization of the powders, aerosolization using a dry powder inhaler (DPI), and in vitro aerodynamic fine particle fraction upon collection in a twinstage liquid impinger were evaluated. After lyophilization and jet-milling, the total amount of GUS and its activity, representing encapsulation efficiency and stability, were evaluated. The GUS amount and activity were measured and compared with freshly-prepared liposomes in the presence of mannitol, 43% of initial GUS amount, 29% of GUS activity after lyophilization and 36% of GUS amount, 22% of activity after micronization were obtained. Emitted doses from dry powder inhaler were 53%, 58%, 66%, and 73% for liposome powder:mannitol carrier ratios of 1∶0, 1∶4, 1∶9, and 1∶19. Fifteen percent of the liposome particles were less than 6.4 μm in aerodynamic diameter. The results demonstrate that milled liposome powders containing protein molecules can be aerosolized effectively at a fixed flow rate. Influences of different cryoprotectants on lyophilization of protein liposome formulations are reported. The feasibility of using liposomal dry powder aerosols for protein delivery has been demonstrated but further optimization is required in the context of specific therapeutic proteins.
SemantiLynx (2010)

Typical web navigation techniques tend to support undirected web browsing, a depth-first search of information pages. This search strategy often results in the unintentional behavior of 'web surfing', where a user starts in search of information, but is sidetracked by tangential links. A mobile user in particular, would prefer to extract the desired information quickly and with minimal mental effort. In this paper, we introduce 'SemantiLynx' to visually augment hyperlinks on web pages for better supporting the task of directed searches on small-screen ubiquitous platforms. Our algorithm comprises four parts: establishing the context of information related to a hyperlink, retrieving relevant imagery based on this context, applying image simplification, and finally compositing a visual icon for the given hyperlink.
The Liver Tumor Segmentation Benchmark (LiTS) (2019)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.
Characteristics of Scar-Related Ventricular Tachycardia Circuits Using Ultra-High-Density Mapping (2018)

VT circuits identified were complex, some of them having multiple entrances, exits, and dead ends. The barriers to conduction in the isthmus seem to be partly functional in 75% of circuits. Conduction velocity in the VT isthmus slowed at isthmus entrances and exits when compared with the mid isthmus. Isthmus voltage is often higher in VT than in sinus or paced rhythms.
Unlocking the potential for extreme solar concentration via subcell segmentation (2022)

Under extreme solar concentrations, series resistance is a primary solar power loss mechanism for concentrator photovoltaic modules. In this paper, a detailed balance based approach demonstrates the mitigation of these losses by the application of subcell segmentation, a current matching architecture which divides each subcell into multiple pn junctions. By increasing the number of series-connected junctions, power extraction shifts from high current to high voltage, thus shifting theoretical efficiency peaks from hundreds to thousands of suns. Simultaneously, the high-efficiency bandgap design space expands across all concentrations by leveraging the current matching potential of subcell segmentation.
Generic global placement and floorplanning (1998)

We present a new force directed method for global placement. Besides the well-known wire length dependent forces we use additional forces to reduce cell overlaps and to consider the placement area. Compared to existing approaches, the main advantage is that the algorithm provides increased flexibility and enables a variety of demanding applications. Our algorithm is capable of addressing the problems of global placement, floorplanning, timing minimization and interaction to logic synthesis. Among the considered objective functions are area, timing, congestion and heat distribution. The iterative nature of the algorithm assures that timing requirements are precisely met. While showing similar CPU time requirements it outperforms Gordian by an average of 6 percent and TimberWolf by an average of 8 percent in wire length and yields significantly better timing results.
Phased array antenna design and characterization for next-generation radio telescopes (2009)

Instrumentation for radio astronomical observations is currently undergoing a transition from large reflectors with single-pixel feeds to multi-pixel phased arrays. Research efforts aimed at realizing the benefits of phased arrays for highly sensitive, calibrated astronomical measurements have opened up interesting challenges for antenna designers. This paper surveys recent theoretical and experimental results on characterization of beam equivalent noise temperature and efficiency, impedance matching to minimize front end noise, and beamforming and calibration algorithms for phased array feeds.
Fusion-product ash buildup in tokamak with radial electric field (1979)

A Lewis acid catalyzed [3+4]-annulation reaction between cyclopropane 1,1-diesters and anthranils has been developed. This annulation consists of a reaction sequence involving ring-opening/aromatization/nucleophilic addition. Thereinto, aromatization is the driving force for this annulation. Using this reaction, a series of 8-oxa-1-azabicyclo[3.2.1]octanes can be prepared conveniently with excellent diastereoselectivity.
High temperature selective emitters via critical coupling of weak absorbers (2023)

Tailoring the emission spectra of a solar thermophotovoltaic emitter away from that of a blackbody, thereby minimizing transmission and thermalization loss in the energy receiver, is a viable approach to circumventing the Shockley-Queisser limit to single junction solar energy conversion. Embodiments allow for radically tuned selective thermal emission that leverages the interplay between two resonant phenomena in a simple planar structure—absorption in weakly-absorbing thin films and reflection in multi-layer dielectric stacks. A virtual screening approach is employed based on Pareto optimality to identify a small number of promising structures for a selective thermal emitter from a search space of millions, several of which approach the ideal values of a step-function selective thermal emitter.
GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds (2021)

The current study describes the construction of various ligand-based machine learning models to be used for drug-repurposing against the family of G-Protein Coupled Receptors (GPCRs). In building these models, we collected > 500,000 data points, encompassing experimentally measured molecular association data of > 160,000 unique ligands against > 250 GPCRs. These data points were retrieved from the GPCR-Ligand Association (GLASS) database. We have used diverse molecular featurization methods to describe the input molecules. Multiple supervised ML algorithms were developed, tested and compared for their accuracy, F scores, as well as for their Matthews' correlation coefficient scores (MCC). Our data suggest that combined with molecular fingerprinting, ensemble decision trees and gradient boosted trees ML algorithms are on the accuracy border of the rather sophisticated deep neural nets (DNNs)-based algorithms. On a test dataset, these models displayed an excellent performance, reaching a ~ 90% classification accuracy. Additionally, we showcase a few examples where our models were able to identify interesting connections between known drugs from the Drug-Bank database and members of the GPCR family of receptors. Our findings are in excellent agreement with previously reported experimental observations in the literature. We hope the models presented in this paper synergize with the currently ongoing interest of applying machine learning modeling in the field of drug repurposing and computational drug discovery in general.