gebhart/patrepeval huggingface dataset:
Expression of human gene coding RORγT receptor depends on the Sp2 transcription factor (2016)

Th17 cells are involved in the immune response against pathogens, autoimmunity, and tumor progression. The differentiation of human Th17 cells requires the upregulation of RORγT, which in human cells is still not well understood. We identified 2 putative binding motifs for specificity protein transcription factors from the specificity protein/Kruppel-like factor family in the promoter of human RORγT and investigated the involvement of specificity proteins in the transcriptional regulation of this gene. To this end, a human lymphocytic cell line and in vitro-differentiated Th17 cells were used in promoter activity assays, in situ mutagenesis, chromatin immunoprecipitation, and real-time RT-PCR assays. In some experiments, specificity protein expression and activity was inhibited by siRNA and mithramycin A. The results showed that the transcription factor specificity protein 2 recognized binding motifs in the human RORγT promoter, which was critical for maintaining expression. Furthermore, specificity protein 2 was necessary for maximum IL-17 expression in in vitro-differentiated Th17 cells. These observations demonstrate the significant role of specificity protein 2 in the regulation of the Th17 signature transcription factor RORγT and the maintenance of the Th17 phenotype. The findings also suggest that specificity protein 2 plays a role in Th17-dependent physiologic and pathologic immune responses and might serve as a potential novel target for their modulation.
Synthesis and Evaluation of (2‐Phenethyl‐2H‐1,2,3‐triazol‐4‐yl)(phenyl)methanones as Kv1.5 Channel Blockers for the Treatment of Atrial Fibrillation. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Design of Photocontrolled RNA‐Binding Peptidomimetics (2012)

Positively constrained: the first examples of photocontrolled RNA binding peptides are described. The large number of positively charged sides chains in the Rev response element (RRE) of an HIV type I targeting α-helix imposes constraints on the choice of azobenzene-derived crosslinker.
MolScore: A scoring and evaluation framework for de novo drug design (2023)

MolScore is an open-source Python framework for scoring and evaluating molecules in the context of goal-directed generative models as used in de novo drug design. MolScore includes many relevant scoring functions for de novo drug design such as molecular similarity, docking software, predictive models, and synthesizability, as well as commonly used performance metrics to evaluate generative model performance based on chemistry generated. Integration into an existing generative model framework is simple, requiring just three lines of code, and graphical user interfaces are provided for objective configuration and for monitoring de novo molecules generated. As a real-world demonstration of its use, we use it to design selective 5-HT2a ligands using 266 pre-trained off-target predictive models. MolScore can also be used for generative model evaluation as we demonstrate by analysing and selecting fine-tuning epochs of an RNN-based generative model. Moreover, the use of configuration files allows the sharing of objectives within the community for the purposes of reproducibility, comparison, and benchmarking; making it easier to propose drug discovery relevant objective functions as benchmark tasks. The code is freely available and hosted on GitHub, https://github.com/MorganCThomas/MolScore.
Exploration of the effect of pulmonary fibrosis on erectile function in rats: A study based on bioinformatics and experimental research (2021)

First, the bioinformatics database was used to predict the potential targets and signaling pathways of pulmonary fibrosis (PF) leading to erectile dysfunction (ED), and bleomycin sulfate was used to create a PF rat model. Then, enzyme-linked immunosorbent assay (ELISA), Western blotting, Real-time fluorescent quantitative reverse transcription polymerase chain reaction (RT-qPCR) were used to detect the expression of sex hormones and related proteins and mRNA, and Hematoxylin and eosin (H&E) staining was used to compare the pathological changes of penile tissue. The results showed that, compared with group A, cyclic guanosine phosphate (cGMP) content in group B decreased, protein kinase CGMP-dependent 1(PKG1) and nitric oxide synthase 3 (eNOS) protein and mRNA expression were down-regulated, and phosphodiesterase 5A (PDE5A) protein and mRNA expression was up-regulated (p < .05); the penile tissue of rats in group B had pathological damage. And there was no change in sex hormone-related indicators in the two groups (p > .05). Therefore, PF inhibits erectile function by inhibiting the cGMP-PKG pathway and reducing the expression of eNOS and PKG1 protein and mRNA. And by up-regulating the expression of PDE5A to impair erectile function.
Two-dimensional particle displacement tracking in particle imaging velocimetry (1991)

A new particle imaging velocimetry data acquisition and analysis system, which is an order of magnitude faster than any previously proposed system, has been constructed and tested. The new particle displacement tracking (PDT) system is an all electronic technique employing a video camera and a large memory buffer frame-grabber board. Using a simple encoding scheme, a time sequence of single exposure images is time coded into a single image and then processed to track particle displacements and determine 2-D velocity vectors. Use of the PDT technique in a counterrotating vortex flow produced over 1100 velocity vectors in 110 s when processed on an 80386 PC.
Real‐time 3D reconstruction of guidewires and stents using two update X‐ray projections in a rotating imaging setup (2023)

This dose efficiency combined with the ability to reconstruct complex arrangements of interventional material makes the presented algorithm a promising candidate to enable 3D fluoroscopy.
Anticorrelation between the splitting and polarization of the exciton fine structure in single self-assembled InAs/GaAs quantum dots (2011)

We report on a systematic correlation between the fine-structure splitting and polarization anisotropy of excitons in InAs/GaAs quantum dots, but with an unexpected reversal in order of the polarization eigenaxes. Such an anticorrelation is explained by a large valence-band-mixing induced splitting due to the shape and strain anisotropies. The strength and phase of valence band mixing are also found to play an important role in the tuning of fine structure splitting using an in-plane magnetic field.
Site-Isolated Redox Reactivity in a Trinuclear Iron Complex (2012)

The symmetric, high-spin triiron complex ((Ph)L)Fe(3)(THF)(3) reacts with mild chemical oxidants (e.g., Ph(3)C-X, I(2)) to afford an asymmetric core, where one iron bears the halide ligand ((Ph)L)Fe(3)X(L) and the hexadentate ((Ph)L = MeC(CH(2)NPh-o-NPh)(3)) ligand has undergone significant rearrangement. In the absence of a suitable trapping ligand, the chlorine and bromine complexes form (μ-X)(2)-bridged structures of the type [((Ph)L)Fe(3)(μ-X)](2). In the trinuclear complexes, the halide-bearing iron site sits in approximate trigonal-bipyramidal (tbp) geometry, formed by two ((Ph)L) anilides and an exogenous solvent molecule. The two distal iron atoms reside in distorted square-planar sites featuring a short Fe-Fe separation at 2.301 Å, whereas the distance to the tbp site is substantially elongated (2.6-2.7 Å). Zero-field, (57)Fe Mössbauer analysis reveals the diiron unit as the locus of oxidation, while the tbp site bearing the halide ligand remains divalent. Magnetic data acquired for the series reveal that the oxidized diiron unit comprises a strongly coupled S = (3)/(2) unit that is weakly ferromagnetically coupled to the high-spin (S = 2) ferrous site, giving an overall S = (7)/(2) ground state for the trinuclear units.
Simultaneous multi-frame MAP super-resolution video enhancement using spatio-temporal priors (2003)

A simultaneous multi-frame super-resolution video reconstruction procedure, utilizing spatio-temporal smoothness constraints and motion estimator confidence parameters is proposed. The ill-posed inverse problem of reconstructing super-resolved imagery from the low resolution, degraded observations is formulated as a statistical inference problem and a Bayesian, maximum a-posteriori (MAP) approach is utilized for its approximate solution. The inclusion of motion estimator confidence parameters and temporal constraints result in higher quality super-resolution reconstructions with improved robustness to motion estimation errors.
Differential effects of angiotensin II on atherogenesis at the aortic sinus and descending aorta of apolipoprotein-E-deficient mice (2005)

Angiotensin (Ang) II infusion increases atherosclerosis and leads to the formation of abdominal aortic aneurysms in apolipoprotein E-deficient (ApoE-/-) mice. Conversely, blockade of the renin-angiotensin system (RAS) decreases atherosclerosis in this model. However, there are conflicting data in the literature concerning responses to both Ang II infusion and RAS blockade which may depend on age, sex, dose, duration of treatment, and the site at which lesion area was measured. In the present study we examined the effects of Ang II infusion on lesion formation in male ApoE-/- mice both at the aortic sinus and in the descending aorta, starting at different ages, and varying in duration. We also tested the effects of the Ang II receptor antagonist losartan at different doses in both males and females. Blood pressure and plasma renin concentration (PRC) were measured as indicators of the hemodynamic and neurohormonal effects of these treatments. Administration of Ang II increased lesion area much more in the descending aorta than at the aortic sinus. However, spontaneous lesion development at the aortic sinus was much greater than in more distal regions of the aorta. Aneurysms were observed in all treatment groups but were less severe in animals treated from 4 weeks age, possibly because of protective remodeling. Losartan treatment reduced lesion area at the aortic sinus, although differences were only significant in female mice. These findings demonstrate regional and temporal differences in the sensitivity of the aorta to the effects of RAS stimulation and blockade, and may help to explain some of the discrepancies between previous reports from other laboratories.
Cognitive Neuroscience of Human Systems (2014)

While there have been tremendous advances in our scientific understanding of the brain, this work has been largely academic, and often oriented toward clinical publication. Cognitive Neuroscience of Human Systems: Work and Everyday Life addresses the relationship between neurophysiological processes and the performance and experience of humans in e
Schaumcharakterisierung mit optischen Messtechniken und PC-gestützter Bildverarbeitung (Foam Characterization by Optical Measuring Techniques and Computer-Aided Image Processing) (2004)

Abstract In diesem Beitrag wird ein optisches Mess- und Aufnahmeverfahren mit anschließender automatischer Bildverarbeitung am PC zur Charakterisierung stabiler und zerfallender Schäume beschrieben, die Aussagen über deren Morphologie, Poren- bzw. Blasengrößenverteilung, Zerfallsprozess, Alterungseigenschaften usw. zulässt. Hierzu wird eine Messanordnung verwendet, die aus einer hoch auflösenden monochromen CCD-Kamera mit einem telezentrischen Objektiv, einer koaxialen, diffusen Beleuchtung mit optionaler Blitzlichtsteuerung und einer schnellen Framegrabber-Karte besteht. Die Bilder werden automatisch am PC mit einer speziell von uns entwickelten Software hinsichtlich folgender Charakteristika ausgewertet: (a) fraktale Dimensionen von Schäumen, die deren Körnigkeit und somit ihre Morphologie kennzeichnen, (b) Flüssigkeitsanteil beim Zerfallsprozess instabiler Schäume durch Auswertung zeitlich aufeinander folgender Schaumbilder und (c) Änderung der Blasengrößenverteilungen bei Alterung des Schaums.
The Influence of Refining History of Waste NSSC Paper on its Recyclability (2013)

The effects of refining history and recycling times of NSSC pulp as a representative of semi-chemical pulps were studied. The results indicated that NSSC behaved as would be expected for a chemical pulp in all aspects. In fact, increasing the recycling cycles decreased the apparent density, tensile index, burst index, tear index, water retention value (WRV), and increased the hornification. In the current research, 400 mL CSF was judged to be the most suitable treatment among the refining levels considered. In the case of virgin pulp 400 mL CSF yielded better results than 500 mL CSF in all aspects (apparent density, tensile index, burst index, tear index, WRV and hornification). Also, there was not much difference with 300 mL CSF in these properties. Generally, a refining history of 400 mL CSF gave rise to the least negative influence on different properties compared to 500 and 300 mL CSF in 1 st , 2 nd , and 3 rd recycling cycles of NSSC.
P2P-based PVR Recommendation using Friends, Taste Buddies and Superpeers (2005)

In this paper we present a novel distributed recommendation method based on exchanging similar playlists among taste buddies, which takes into account the limited availability of peers, lack of trust in P2P networks, and dynamic identities of peers, etc. Our preliminary experiment shows that only exchanging a small portion of similar playlists from taste buddies could lead to an efficient way to calculate recommendations within a context of P2P networks.
High temperature piezoelectric properties of yttrium calcium oxyborate single crystals (2010)

Abstract The piezoelectric single crystal yttrium calcium oxyborate, YCa 4 O(BO 3 ) 3 , was studied as a function of orientation and temperature. The resistivity of Y‐cut samples was found to be 2.7 × 10 7 Ω cm at 950 °C, three orders of magnitude higher than langatate crystals. The electromechanical coupling k 26 and piezoelectric d 26 were found to be 22% and 10 pC/N at room temperature for (ZXw)‐30°‐cut samples, respectively, maintaining similar values at elevated temperature of 950 °C, exhibiting temperature independent behavior. Furthermore, the highest temperature frequency coefficient was obtained in (ZXw)‐33°‐cut samples, being –91 ppm/K. The temperature independent piezoelectric properties, together with the high resistivity and mechanical quality factor Q (∼2000 at 950 °C), suggest the YCOB crystal to be a good candidate for high temperature sensing applications. (© 2010 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Oxidative Degradation of Dimeric Lignin Model Compounds (2001)

The oxidation of dimeric lignin model compounds (arylglycerol - β - aryl ethers and phenylcoumarans) by molecular oxygen, catalyzed by [N, N′ - bis(salicylidene) - ethane - 1, 2-diaminato] cobalt(II), [Co(salen)], was studied in order to find novel processes for the production of chemicals by degradation of polyphenols contained in waste waters from the pulp and paper industry. All the studied compounds reacted at room temperature in chloroform with high conversion already after 30 minutes; after 48 h the reaction was essentially complete and interesting low molecular weight compounds were isolated with good yields. An EPR investigation of the reaction mixtures indicates the presence of a phenoxy cobalt radical, [CoIII(salen)(RO-)(RO•)], as a reactive intermediate for ROH as phenolic substrate. The electron donor properties of the phenolic substrate and the stability of the phenoxy radical control the yields of the oxidation products.
Domain repertoires as a tool to derive protein recognition rules (2000)

Several approaches, some of which are described in this issue, have been proposed to assemble a complete protein interaction map. These are often based on high throughput methods that explore the ability of each gene product to bind any other element of the proteome of the organism. Here we propose that a large number of interactions can be inferred by revealing the rules underlying recognition specificity of a small number (a few hundreds) of families of protein recognition modules. This can be achieved through the construction and characterization of domain repertoires. A domain repertoire is assembled in a combinatorial fashion by allowing each amino acid position in the binding site of a given protein recognition domain to vary to include all the residues allowed at that position in the domain family. The repertoire is then searched by phage display techniques with any target of interest and from the primary structure of the binding site of the selected domains one derives rules that are used to infer the formation of complexes between natural proteins in the cell.
Drug Discovery in Oncology (2001)

Drug discovery in oncology has undergone profound changes over the past 20 yr; the rate of change has markedly accelerated over the last 5 yr, and it is therefore appropriate to take stock of these changes, and to ask what the next steps in this evolving landscape of concepts, skills, and technologies are likely to be. More than ever, drug discovery in oncology finds itself at the crossroads of academic research, industrial research and development (with a growing share by the biotech industry), clinical research, regulatory authorities, and public health, including major partners, such as the National Cancer Institute (NCI). All of these partners are driven, more than ever, by the forces related to productivity, i.e., a relentless drive for quality at manageable cost, within minimal time frames. These forces are behind the technological revolution that is still taking place, the drive to secure competitive patent positions, the drive to be faster on the market through streamlined R&D processes, the drive for a more efficient approval process and flexible handling of market access by health authorities, and the importance of pharmacoeconomic aspects for the payors at large, even in disease states, such as advanced cancer, in which the medical need is undisputed.
Outgassing Issues in Acetal Resist Design. (2000)

The outgassing issues that have long plagued conventional acetal resist designs are shown to be significantly mitigated depending on the structure of the acetal-blocked polymer. Resists formulated with acetal-blocked polymers based on low molecular weight vinyl ethers such as ethyl vinyl ether and t-butyl vinyl ether deblock during exposure resulting in considerable outgassing inside the stepper and attendant film shrinkage. By modifying the acetal structure, deblocking can be completely prevented during exposure, in which case the resist requires post-exposure baking to initiate the deblocking reaction as with conventional high activation energy systems. Such systems also show superior plasma etch resistance compared to conventional lower molecular weight acetals.
A fixed-point neural network for keyword detection on resource constrained hardware (2015)

Keyword detection is typically used as a front-end to trigger automatic speech recognition and spoken dialog systems. The detection engine needs to be continuously listening, which has strong implications on power and memory consumption. In this paper, we devise a neural network architecture for keyword detection and present a set of techniques for reducing the memory requirements in order to make the architecture suitable for resource constrained hardware. Specifically, a fixed-point implementation is considered; aggressively scaling down the precision of the weights lowers the memory compared to a naive floating-point implementation. For further optimization, a node pruning technique is proposed to identify and remove the least active nodes in a neural network. Experiments are conducted over 10 keywords selected from the Resource Management (RM) database. The trade-off between detection performance and memory is assessed for different weight representations. We show that a neural network with as few as 5 bits per weight yields a marginal and acceptable loss in performance, while requiring only 200 kilobytes (KB) of on-board memory and a latency of 150 ms. A hardware architecture using a single multiplier and a power consumption of less than 10mW is also presented.
Endogenous bioactive lipids and the regulation of conventional outflow facility (2008)

Perturbation of paracrine signaling within the human conventional outflow pathway influences tissue homeostasis and outflow function. For example, exogenous introduction of the bioactive lipids, sphingosine-1-phosphate, anandamide or prostaglandin F(2α), to conventional outflow tissues alters the rate of drainage of aqueous humor through the trabecular meshwork, and into Schlemm's canal. This review summarizes recent data that characterizes endogenous bioactive lipids, their receptors and associated signaling partners in the conventional outflow tract. We also discuss the potential of targeting such signaling pathways as a strategy for the development of therapeutics to treat ocular hypertension and glaucoma.
Synthetic Promoter Screening Using Poplar Mesophyll Protoplast Transformation (2023)

Plant protoplasts are useful to study both transcriptional regulation and protein subcellular localization in rapid screens. Protoplast transformation can be used in automated platforms for design-build-test cycles of plant promoters, including synthetic promoters. A notable application of protoplasts comes from recent successes in dissecting synthetic promoter activity with poplar mesophyll protoplasts. For this purpose, we constructed plasmids with TurboGFP driven by a synthetic promoter together with TurboRFP constitutively controlled by a 35S promoter, to monitor transformation efficiency, allowing versatile screening of high numbers of cells by monitoring green fluorescent protein expression in transformed protoplasts. Herein, we introduce a protocol for poplar mesophyll protoplast isolation followed by protoplast transformation and image analysis for the selection of valuable synthetic promoters. Graphical overview.
Suppression of Lymphocyte Functions by Plasma Exosomes Correlates with Disease Activity in Patients with Head and Neck Cancer (2017)

<b>Purpose:</b> Head and neck cancers (HNCs) often induce profound immunosuppression, which contributes to disease progression and interferes with immune-based therapies. Body fluids of patients with HNC are enriched in exosomes potentially engaged in negative regulation of antitumor immune responses. The presence and content of exosomes derived from plasma of patients with HNC are evaluated for the ability to induce immune dysfunction and influence disease activity.<b>Experimental Design:</b> Exosomes were isolated by size-exclusion chromatography from plasma of 38 patients with HNC and 14 healthy donors. Morphology, size, numbers, and protein and molecular contents of the recovered exosomes were determined. Coculture assays were performed to measure exosome-mediated effects on functions of normal human lymphocyte subsets and natural killer (NK) cells. The results were correlated with disease stage and activity.<b>Results:</b> The presence, quantity, and molecular content of isolated, plasma-derived exosomes discriminated patients with HNC with active disease (AD) from those with no evident disease (NED) after oncologic therapies. Exosomes of patients with AD were significantly more effective than exosomes of patients with NED in inducing apoptosis of CD8<sup>+</sup> T cells, suppression of CD4<sup>+</sup> T-cell proliferation, and upregulation of regulatory T-cell (Treg) suppressor functions (all at <i>P</i> < 0.05). Exosomes of patients with AD also downregulated NKG2D expression levels in NK cells.<b>Conclusions:</b> Exosomes in plasma of patients with HNC carry immunosuppressive molecules and interfere with functions of immune cells. Exosome-induced immune suppression correlates with disease activity in HNC, suggesting that plasma exosomes could be useful as biomarkers of HNC progression. <i>Clin Cancer Res; 23(16); 4843-54. ©2017 AACR</i>.