gebhart/patrepeval huggingface dataset:
The Prdm family: expanding roles in stem cells and development (2012)

Members of the Prdm family are characterized by an N-terminal PR domain that is related to the SET methyltransferase domain, and multiple zinc fingers that mediate sequence-specific DNA binding and protein-protein interactions. Prdm factors either act as direct histone methyltransferases or recruit a suite of histone-modifying enzymes to target promoters. In this way, they function in many developmental contexts to drive and maintain cell state transitions and to modify the activity of developmental signalling pathways. Here, we provide an overview of the structure and function of Prdm family members and discuss the roles played by these proteins in stem cells and throughout development.
Cynoglossum Birkinshawii J. S. Mill. (2005)

in Adansonia, ser. 3, 27: 115. 2005
Fast location of seismicity: A migration-type approach with application to hydraulic-fracturing data (2006)

Abstract We propose a new approach for the location of seismic sources using a technique inspired by Gaussian-beam migration of three-component data. This approach requires only the preliminary picking of time intervals around a detected event and is much less sensitive to the picking precision than standard location procedures. Furthermore, this approach is characterized by a high degree of automation. The polarization information of three-component data is estimated and used to perform initial-value ray tracing. By weighting the energy of the signal using Gaussian beams around these rays, the stacking is restricted to physically relevant regions only. Event locations correspond to regions of maximum energy in the resulting image. We have successfully applied the method to synthetic data examples with 20%–30% white noise and to real data of a hydraulic-fracturing experiment, where events with comparatively small magnitudes (&lt;0) were recorded.
DELAYED IMPLANTATION IN INTACT RATS TREATED WITH MEDROXYPROGESTERONE ACETATE (1964)

Summary. Intact, female Holtzman rats were treated daily with medroxyprogesterone acetate (map; Provera) in corn oil, beginning on the day of insemination. This caused delay of implantation in 14% (0·5 mg/day) to 100% (2·4 mg/day) of the animals tested. It is possible that map suppresses the synthesis or the release of luteinizing hormone (lh) from the pituitary gland and thus prevents the production of sufficient endogenous oestrogen to cause implantation. Implantation was achieved in 'delayed' rats by simultaneous administration of 1 μg of oestrone with the dose of map they had been receiving. The viability of foetuses in such animals varied inversely with the dose of map the mothers had received.
Combination of TLR1/2 and TLR3 ligands enhances CD4+ T cell longevity and antibody responses by modulating type I IFN production (2016)

Despite the possibility of combining Toll-like receptor (TLR) ligands as adjuvants to improve vaccine efficacy, it remains unclear which combinations of TLR ligands are effective or what their underlying mechanisms may be. Here, we investigated the mechanism of action of L-pampo, a proprietary adjuvant composed of TLR1/2 and TLR3 ligands. L-pampo dramatically increased humoral immune responses against the tested target antigens, which was correlated with an increase in follicular helper T cells and the maintenance of antigen-specific CD4(+) T cells. During the initial priming phase, in contrast to the induction of type I interferon (IFN) and pro-inflammatory cytokines stimulated by polyI:C, L-pampo showed a greatly diminished induction of type I IFN, but not of other cytokines, and remarkably attenuated IRF3 signaling, which appeared to be critical to L-pampo-mediated adjuvanticity. Collectively, our results demonstrate that the adjuvant L-pampo contributes to the promotion of antigen-specific antibodies and CD4(+) T cell responses via a fine regulation of the TLR1/2 and TLR3 signaling pathways, which may be helpful in the design of improved vaccines.
Local Area Prediction-Based Mobile Target Tracking in Wireless Sensor Networks (2014)

Tracking mobile targets in wireless sensor networks (WSNs) has many important applications. As it is often the case in prior work that the quality of tracking (QoT) heavily depends on high accuracy in localization or distance estimation, which is never perfect in practice. These bring a cumulative effect on tracking, e.g., target missing. Recovering from the effect and also frequent interactions between nodes and a central server result in a high energy consumption. We design a tracking scheme, named t-Tracking, aiming to achieve two major objectives: high QoT and high energy efficiency of the WSN. We propose a set of fully distributed tracking algorithms, which answer queries like whether a target remains in a “specific area” (called a “face” in localized geographic routing, defined in terms of radio connectivity and local interactions of nodes). When a target moves across a face, the nodes of the face that are close to its estimated movements compute the sequence of the target's movements and predict when the target moves to another face. The nodes answer queries from a mobile sink called the “tracker”, which follows the target along with the sequence. t-Tracking has advantages over prior work as it reduces the dependency on requiring high accuracy in localization and the frequency of interactions. It also timely solves the target missing problem caused by node failures, obstacles, etc., making the tracking robust in a highly dynamic environment. We validate its effectiveness considering the objectives in extensive simulations and in a proof-of-concept system implementation.
Polymyxin B sulfate modification of bacterial endotoxin: effects on the development of endotoxin shock in dogs (1979)

The effects of endotoxin (lipopolysaccharide [LPS]) on the pathogenesis of canine endotoxin shock were compared with those of LPS which had interacted with polymyxin B sulfate prior to administration. Both LPS and polymyxin B-modified LPS caused comparable early decreases in aortic blood pressure, leukocyte and platelet numbers, and serum complement levels. However, in dogs receiving polymyxin B-modified LPS the late hypotensive phase was significantly ameliorated and lethality was significantly decreased. These data indicate that polymyxin B-modified LPS, though significantly less lethal than unmodified LPS, was capable of major interactions with several components of the humoral defense system, and support the concept that such interactions are not determinative in the pathogenesis of canine endotoxin shock.
Glucokinase activators as new type 2 diabetes therapeutic agents (2008)

Background: Small molecule glucokinase activators (GKAs) represent a new strategy to treat type 2 diabetes. Glucokinase (GK) primarily exerts its effect through modulatory actions in the pancreatic β-cells and the liver. It couples insulin secretion in the pancreas with plasma glucose concentration, and improves glucose utilization in the liver, thus affecting two key aspects of glucose homeostasis. Objective and method: To review currently disclosed GKA structures and to classify them based on the key structural features. For this purpose, the data from patent disclosures and publications are used. Also, published in vitro findings on related lead GKAs are used to compare their effect on GK kinetics. Results and conclusion: The most common GKA pharmacophore consists of a center, which can be a carbon or an aromatic ring, and three attachments. Two of these are hydrophobic groups, with at least one of them being an aromatic ring. The third attachment, without exception, consists of an H-bond donor–acceptor pair in the form of a heterocyclic amine, or an N-acyl urea. These structurally diverse GKAs show important differences in their effects on the kinetic properties of GK.
Asymptotic Behaviors of Support Vector Machines with Gaussian Kernel (2003)

Support vector machines (SVMs) with the gaussian (RBF) kernel have been popular for practical use. Model selection in this class of SVMs involves two hyperparameters: the penalty parameter C and the kernel width sigma. This letter analyzes the behavior of the SVM classifier when these hyperparameters take very small or very large values. Our results help in understanding the hyperparameter space that leads to an efficient heuristic method of searching for hyperparameter values with small generalization errors. The analysis also indicates that if complete model selection using the gaussian kernel has been conducted, there is no need to consider linear SVM.
The boron hydrides and related compounds (1948)

The first page of this article is displayed as the abstract.
Revisiting the Sequential Programming Model for Multi-Core (2007)

Single-threaded programming is already considered a complicated task. The move to multi-threaded programming only increases the complexity and cost involved in software development due to rewriting legacy code, training of the programmer, increased debugging of the program, and efforts to avoid race conditions, deadlocks, and other problems associated with parallel programming. To address these costs, other approaches, such as automatic thread extraction, have been explored. Unfortunately, the amount of parallelism that has been automatically extracted is generally insufficient to keep many cores busy. This paper argues that this lack of parallelism is not an intrinsic limitation of the sequential programming model, but rather occurs for two reasons. First, there exists no framework for automatic thread extraction that brings together key existing state-of-the-art compiler and hardware techniques. This paper shows that such a framework can yield scalable parallelization on several SPEC CINT2000 benchmarks. Second, existing sequential programming languages force programmers to define a single legal program outcome, rather than allowing for a range of legal outcomes. This paper shows that natural extensions to the sequential programming model enable parallelization for the remainder of the SPEC CINT2000 suite. Our experience demonstrates that, by changing only 60 source code lines, all of the C benchmarks in the SPEC CINT2000 suite were parallelizable by automatic thread extraction. This process, constrained by the limits of modern optimizing compilers, yielded a speedup of 454% on these applications.
<i>N,N</i>-Dimethylamination of Acid Chlorides with Dmf (2000)

Abstract A solution of acid chlorides 3a-g in DMF solvent was refluxed to give N,N-dimethylamides 4a-f and 5g in excellent yields.
Optical and Electronic Packaging Processes for Silicon Photonic Systems (2015)

Fiber optic interconnection processes and hybrid integration of electronic devices for high speed Si photonic systems are presented. Thermal effects arising from these hybrid integration processes are also investigated. An overview of ePIXfab which offers affordable access to an advanced Si photonic foundry service is also presented. This includes the presentation of fundamental photonic packaging design rules which can greatly reduce the time and cost associated with the development of complex Si photonic devices.
A radiative transfer framework for rendering materials with anisotropic structure (2010)

The radiative transfer framework that underlies all current rendering of volumes is limited to scattering media whose properties are invariant to rotation. Many systems allow for "anisotropic scattering," in the sense that scattered intensity depends on the scattering angle, but the standard equation assumes that the structure of the medium is isotropic. This limitation impedes physics-based rendering of volume models of cloth, hair, skin, and other important volumetric or translucent materials that do have anisotropic structure. This paper presents an end-to-end formulation of physics-based volume rendering of anisotropic scattering structures, allowing these materials to become full participants in global illumination simulations. We begin with a generalized radiative transfer equation, derived from scattering by oriented non-spherical particles. Within this framework, we propose a new volume scattering model analogous to the well-known family of microfacet surface reflection models; we derive an anisotropic diffusion approximation, including the weak form required for finite element solution and a way to compute the diffusion matrix from the parameters of the scattering model; and we also derive a new anisotropic dipole BSSRDF for anisotropic translucent materials. We demonstrate results from Monte Carlo, finite element, and dipole simulations. All these contributions are readily implemented in existing rendering systems for volumes and translucent materials, and they all reduce to the standard practice in the isotropic case.
Protective Effect of Melatonin and Catalase in Bovine Neutrophil-induced Model of Mammary Cell Damage (2002)

The effect of several antioxidants and a proteinase inhibitor on bovine neutrophil-induced mammary epithelial cell damage was investigated using an in vitro model of co-culturing bovine neutrophils and MAC-T cells, a mammary epithelial cell line. Epithelial cell damages were evaluated by measuring lactate dehydrogenase activity in culture media and by morphological observations of cells after acridine orange staining. Activation of neutrophils with Escherichia coli lipopolysaccharide and phorbol 12-myristate 13-acetate caused superoxide and gelatinase release in media. Activated neutrophils damaged the epithelial cells, as demonstrated by an increase in lactate dehydrogenase release and the observation of morphological changes. The addition of melatonin or catalase reduced neutrophil-induced cytotoxicity in a dose-dependent manner, whereas superoxide dismutase and aprotinin had no effect on cytotoxicity. Melatonin has been reported to scavenge hydroxyl radical and peroxynitrite, whereas catalase and superoxide dismutase scavenge hydrogen peroxide and superoxide, respectively. Our results suggest that hydroxyl radicals released by activated bovine neutrophils cause damage to mammary epithelial cells and that antioxidants may be useful to protect the mammary tissue during bovine mastitis.
Nongenomic Glucocorticoid Inhibition via Endocannabinoid Release in the Hypothalamus: A Fast Feedback Mechanism (2003)

Glucocorticoid negative feedback in the brain controls stress, feeding, and neural-immune interactions by regulating the hypothalamic-pituitary-adrenal axis, but the mechanisms of inhibition of hypothalamic neurosecretory cells have never been elucidated. Using whole-cell patch-clamp recordings in an acute hypothalamic slice preparation, we demonstrate a rapid suppression of excitatory glutamatergic synaptic inputs to parvocellular neurosecretory neurons of the hypothalamic paraventricular nucleus (PVN) by the glucocorticoids dexamethasone and corticosterone. The effect was maintained with dexamethasone conjugated to bovine serum albumin and was not seen with direct intracellular glucocorticoid perfusion via the patch pipette, suggesting actions at a membrane receptor. The presynaptic inhibition of glutamate release by glucocorticoids was blocked by postsynaptic inhibition of G-protein activity with intracellular GDP-beta-S application, implicating a postsynaptic G-protein-coupled receptor and the release of a retrograde messenger. The glucocorticoid effect was not blocked by the nitric oxide synthesis antagonist N(G)-nitro-L-arginine methyl ester hydrochloride or by hemoglobin but was blocked completely by the CB1 cannabinoid receptor antagonists AM251 [N-(piperidin-1-yl)-5-(4-iodophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide] and AM281 [1-(2,4-dichlorophenyl)-5-(4-iodophenyl)-4-methyl-N-4-morpholinyl-1H-pyrazole-3-carboxamide] and mimicked and occluded by the cannabinoid receptor agonist WIN55,212-2 [(beta)-(+)-[2,3-dihydro-5-methyl-3-(4-morpholinylmethyl)pyrrolo[1,2,3-de]-1,4-benzoxazin-6-yl]-1-naphthalenylmethanone mesylate], indicating that it was mediated by retrograde endocannabinoid release. Several peptidergic subtypes of parvocellular neuron, identified by single-cell reverse transcripton-PCR analysis, were subject to rapid inhibitory glucocorticoid regulation, including corticotropin-releasing hormone-, thyrotropin-releasing hormone-, vasopressin-, and oxytocin-expressing neurons. Therefore, our findings reveal a mechanism of rapid glucocorticoid feedback inhibition of hypothalamic hormone secretion via endocannabinoid release in the PVN and provide a link between the actions of glucocorticoids and cannabinoids in the hypothalamus that regulate stress and energy homeostasis.
Performance of Organic light-emitting diode by various surface treatments of indium tin oxide (2002)

We have done various treatments of indium tin oxide (ITO) surface for organic light-emitting diodes (OLEDs), and investigated the surface states by different surface treatments using atomic force microscopy (AFM) and Auger electron spectroscopy (AES). We have fabricated OLEDs deposited by ultra-high vacuum molecular beam deposition system and studied the characteristics of the OLEDs. We have observed the dramatical improvement of the performance of OLEDs fabricated on ITO substrates treated by plasma treatment reduces the carbon comtamination of ITO surfaces and increases the work function of ITO.
Modulation of the immune response by systemic targeting of antigens to lymph nodes. (2001)

Factors that determine the immunogenicity of an antigen in vivo are still largely unknown. Direct administration of antigens into lymphatic organs appears to enhance immune response. We hypothesized that systemically targeting antigens to lymphatic tissue in vivo might modulate immunity. To test this hypothesis, we measured the humoral immune response elicited by bacteriophage vaccination. We show that the responses against a lymph node-targeted phage are significantly higher than those against control untargeted phage; the effect is specific because it is inhibited by coadministration of the cognate synthetic peptides displayed. Our data suggest that systemic targeting of antigens to lymph nodes through the circulation modulates humoral immune response. This strategy may have broad applications in the development of vaccines, production of antibodies, and immunotherapy.
LILRB2 Interaction with HLA Class I Correlates with Control of HIV-1 Infection (2014)

Natural progression of HIV-1 infection depends on genetic variation in the human major histocompatibility complex (MHC) class I locus, and the CD8+ T cell response is thought to be a primary mechanism of this effect. However, polymorphism within the MHC may also alter innate immune activity against human immunodeficiency virus type 1 (HIV-1) by changing interactions of human leukocyte antigen (HLA) class I molecules with leukocyte immunoglobulin-like receptors (LILR), a group of immunoregulatory receptors mainly expressed on myelomonocytic cells including dendritic cells (DCs). We used previously characterized HLA allotype-specific binding capacities of LILRB1 and LILRB2 as well as data from a large cohort of HIV-1-infected individuals (N = 5126) to test whether LILR-HLA class I interactions influence viral load in HIV-1 infection. Our analyses in persons of European descent, the largest ethnic group examined, show that the effect of HLA-B alleles on HIV-1 control correlates with the binding strength between corresponding HLA-B allotypes and LILRB2 (p = 10(-2)). Moreover, overall binding strength of LILRB2 to classical HLA class I allotypes, defined by the HLA-A/B/C genotypes in each patient, positively associates with viral replication in the absence of therapy in patients of both European (p = 10(-11)-10(-9)) and African (p = 10(-5)-10(-3)) descent. This effect appears to be driven by variations in LILRB2 binding affinities to HLA-B and is independent of individual class I allelic effects that are not related to the LILRB2 function. Correspondingly, in vitro experiments suggest that strong LILRB2-HLA binding negatively affects antigen-presenting properties of DCs. Thus, we propose an impact of LILRB2 on HIV-1 disease outcomes through altered regulation of DCs by LILRB2-HLA engagement.
Bifunctional μ/δ Opioid Peptides: Variation of the Type and Length of the Linker Connecting the Two Components (2011)

On the basis of evidence that opioid compounds with a mixed μ agonist/δ antagonist profile may produce an antinociceptive effect with low propensity to induce side effects, bifunctional opioid peptides containing the μ agonist H-Dmt-d-Arg-Phe-Lys-NH(2) ([Dmt(1) ]DALDA; Dmt = 2',6'-dimethyltyrosine) connected tail-to-tail via various α,ω-diaminoalkyl- or diaminocyclohexane linkers to the δ antagonists H-Tyr-TicΨ[CH(2) -NH]Cha-Phe-OH (TICP[Ψ]; Cha = cyclohexylalanine, Tic = 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid), H-Dmt-Tic-OH or H-Bcp-Tic-OH (Bcp = 4'-[N-((4'-phenyl)phenethyl)carboxamido]phenylalanine) were synthesized and pharmacologically characterized in vitro. Bifunctional [Dmt(1) ]DALDA→NH-(CH(2) )(n) -NH←TICP[Ψ] compounds (n = -12) showed decreasing μ and δ receptor binding affinities with increasing linker length. As expected, several of the bifunctional peptides were μ agonist/δ antagonists with low nanomolar μ and δ receptor binding affinities. However, compounds with unexpected opioid activity profiles, including a μ partial agonist/δ partial agonist, μ antagonist/δ antagonists and μ agonist/δ agonists, were also identified. These results indicate that the binding affinities and intrinsic efficacies of these bifunctional compounds at both receptors depend on the length and type of the linker connecting the μ and δ components. An important recommendation emerging from this study is that the in vitro activity profiles of bifunctional compounds containing an agonist and an antagonist component connected via a linker need to be determined prior to their pharmacological evaluation in vivo.