gebhart/patrepeval huggingface dataset:
cAMP phosphodiesterase inhibitors potentiate effects of prostacyclin analogs in hypoxic pulmonary vascular remodeling (2004)

We investigated the effects of prostacyclin analogs and isoform-selective phosphodiesterase (PDE) inhibitors, alone and in combination, on pulmonary vascular remodeling in vitro and in vivo. Vascular smooth muscle cells (VSMC) isolated from pulmonary (proximal and distal) and systemic circulations demonstrated subtle variations in expression of PDE isoform mRNA. However, using biochemical assays, we found PDE3 and PDE4 isoforms to be responsible for the majority of cAMP hydrolysis in all VSMC. In growth assays, the prostacyclin analogs cicaprost and iloprost inhibited mitogen-induced proliferation of VSMC in a cAMP-dependent manner. In addition, isoform-selective antagonists of PDEs 1, 3, or 4 inhibited VSMC proliferation, an effect that synergized with the effect of prostacyclin analogs. The inhibitory effects were greater in cells isolated from pulmonary circulation. In an in situ perfused rat lung preparation, administration of prostacyclin analogs or the PDE inhibitors vinpocetine (PDE1), cilostamide (PDE3), or rolipram (PDE4), but not EHNA (PDE2), attenuated acute hypoxic vasoconstriction (HPV). Combinations of agents led to a greater reduction in HPV. Furthermore, during exposure to hypoxia for 13 days, Wistar rats were treated with iloprost, rolipram, cilostamide, or combinations of these agents. Compared with normoxic controls, hypoxic animals developed pulmonary hypertension and distal pulmonary artery muscularization. These parameters were attenuated by iloprost+cilostamide, iloprost+rolipram, and cilostamide+rolipram but were not significantly affected by single agents. Together, these findings provide a greater understanding of the role of cAMP PDEs in VSMC proliferation and provide rationale for combined use of prostacylcin analogs plus PDE3/4 inhibitors in treatment of pulmonary vascular remodeling.
Luminometric Studies of Yeast Response to Complex Environmental Calcium Variations Demonstrate Sensing of External Calcium Ion Changes (2022)

The response of yeast to sharp environmental increases in calcium concentration has been extensively studied. However, systematic studies of the response under more general changes are still lacking. Only limited exploration of cellular responses has been conducted where calcium concentration is decreased. This article describes a set of luminometric experiments that monitor the cytosolic calcium concentration under changing external concentration conditions. As a decrease in external calcium concentrations requires the use of large sample volumes, the experiments require the use of equipment adapted for this purpose. We describe the modification of commercial luminometric equipment to make the exploration possible. We explore the yeast cellular behavior when an increase in external calcium concentration is followed by a decrease in external calcium concentration. We compare these results with those from the case of a double pulse of concentration increase. Results from the experiment show that the first, concentration increasing pulse produces the well-known sharp increase in cytosolic calcium followed by calcium sequestration to return to a cytosolic concentration near its initial condition. Surprisingly, the calcium decrease step shows similar results with a cytosolic increase followed by a return to lower levels. The results suggest the presence of a calcium sensing mechanism regulating calcium influx from external sources. This mechanism would produce channel opening as a response to any changes in external concentration, be it an enhancement or a depletion.
Routing Control Plane Security Capabilities (2007)

The document lists the security capabilities needed for the routing
control plane of an IP infrastructure to support the practices defined
in Operational Security Current Practices. In particular this includes
capabilities for route filtering, for authentication of routing
protocol packets, and for ensuring resource availability for control
functions.
Inference and Gradient Measurement for Backpropagation in Photonic Neural Networks (2022)

We experimentally demonstrate in situ backpropagation in a programmable nanophotonic interferometer network, achieving inference accuracies matching digital implementations. Error gradients are computed by simultaneously measuring optical interference at intermediate network components, eliminating expensive digital computations.
Proteomic analysis of cholangiocarcinoma cell line (2004)

Cholangiocarcinoma (CCA), a malignant tumor derived from bile duct epithelium, occurs with a higher incidence in tropical countries, such as Thailand. Distinguishing CCA from hepatocellular carcinoma (HCC) of the liver often requires the use of histochemistry, so molecular markers for diagnosis and prognosis are still required. In this study, the two-dimensional (2-D) protein map of a Thai human bile duct epithelial carcinoma cell line (HuCCA-1) has been compared to human hepatocellular carcinoma cell lines (HepG2 and HCC-S102) and a human breast epithelial cancer cell line (MCF-7). Our results show that HuCCA-1 expressed a unique pattern of proteins. Forty-three major proteins were identified by matching to the map of MCF-7, and by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and electrospray ionization-tandem MS (ESI-MS/MS). Cytokeratins CK8 and CK18 were overexpressed in both HuCCA-1 and HCC, while CK7 and CK19 were only expressed in HuCCA-1. Four specific proteins with MW/pI 57.2/5.21 (U1, vimentin), 42.2/6.20 (U2), 43.2/6.20 (U3, EF-TU), and 42.2/6.40 (U4, unidentified) were absent from HepG2. U2 showed high expression in HuCCA-1, while U1 and U4 showed high expression in HCC-S102. U2 could be separated in 2 proteins, U2/1 (alpha-enolase) and U2/2 (not identified) by using IPG pH 4-7. Galectin-3 showed high expression level in HuCCA-1 by 1-DE immunodetection, and gave only one spot with MW 32.9 kDa and pI 8.29 on 2-DE immunoblotting, Thus, certain proteins, namely CK7, CK19, U2/2 and galectin-3, may be good markers useful for differential diagnosis of cholangiocarcinoma compared to hepatocellular carcinoma.
Secure and privacy-enhanced e-mail system based on the concept of proxies (2014)

Security and privacy on the Internet and especially the e-mail, is becoming more and more important and crucial for the user. The requirements for the protection of e-mail include issues like tracking and privacy intrusions by hackers and commercial advertisers, intrusions by casual observers, and even spying by government agencies. In an expanding email use in the digital world, Internet and mobile, the quantity and sensitivity of personal information has also tremendously expanded. Therefore, protection of data and transactions and privacy of user information is key and of interest for many users. Based on such motives, in this paper we present the design and current implementation of our secure and privacy-enhanced e-mail system. The system provides protection of e-mails, privacy of locations from which the e-mail system is accessed, and authentication of legitimate users. Differently from existing standard approaches, which are based on adding security extensions to e-mail clients, our system is based on the concept of proxy servers that provide security and privacy of users and their e-mails. It uses all required standards: S/MIME for formatting of secure letters, strong cryptographic algorithms, PKI protocols and certificates. We already have the first implementation and an instance of the system is very easy to install and to use.
Carbon loading in airway macrophages to traffic-derived particulate matter air pollution (2015)

Background and aims Epidemiological studies indicate that the health outcomes of exposure to urban air pollution are driven by exposure to elemental carbon (EC) emitted from traffic-related fuel combustion. One possible method for assessing chronic exposure to EC in individual subjects consists of estimating the amount of carbonaceous particles present in alveolar macrophages (AM)s. However, a number of issues remain to be solved regarding this biomarker. We studied the reproducibility and the kinetics of this biomarker by making repeated measurements over one year in healthy subjects, with some of them having moved from a highly polluted area (PM10 > 30 μg/m ) to a moderately polluted area (PM10 20-30 μg/m ).
Distributing MPEG movies over the Internet using programmable networks (2003)

Distributing video over the Internet is an increasingly important application. Nevertheless, the real-time and high bandwidth requirements of video make video distribution over today's Internet a challenge. Adaptive approaches can be used to respond to changes in bandwidth availability while limiting the effect of such changes on perceptual quality and resource consumption. Nevertheless, most existing adaptation mechanisms have limited scalability and do not effectively exploit the heterogeneity of the Internet. In this paper, we describe the design and implementation of a MPEG video broadcasting service based on active networks. In an active network, routers can be programmed to make routing decisions based on local conditions. Because decisions are made locally, adaptation reacts rapidly to changing conditions and is unaffected by conditions elsewhere in the network. Programmability allows the adaptation policy to be tuned to the structure of the transmitted data, and to the properties of local clients. We use the PLAN-P domain-specific language for programming active routers; this language provides high-level abstractions and safety guarantees that allow complex protocols to be developed rapidly and reliably. Our experiments show that our approach to video distribution permits the decoding of up to 9 times as many frames in a heavily loaded network as distribution using standard routers.
In Situ -Forming Gels for Ophthalmic Drug Delivery (1994)

Poor bioavailability of ophthalmic solutions caused by dilution and drainage from the eye can be overcome by using in situ-forming ophthalmic drug delivery systems prepared from polymers that exhibit reversible phase transitions. Joshi et al. (1), have demonstrated that aqueous compositions that reversibly gel in response to simultaneous variations in at least two physical parameters, such as temperature, pH, and ionic strength, can be formed by appropriate combinations of macromolecular polymers which exhibit reversible gelation properties. In the present study, the rheological characterization of such a system, prepared by a combination of Carbopol (C) and methyl cellulose (MC), was carried out at two different pH (4.0 and 7.4) and temperatures (25 and 37 degrees C) by rotational cone and plate viscometry. The shear stress (tau) vs. shear rate (D) flow curves of the aqueous polymer solutions indicated a pseudoplastic behavior, with a yield point. An increase in pH from 4.0 to 7.4, or temperature from 25 to 37 degrees C, resulted in an increase in viscosity (eta), tau, and yield point, the magnitude of changes being highest when both the parameters were altered simultaneously. An increase in concentration of either C or MC, or an increase in MC molecular weight results in an increase in eta, tau, and yield point. Among the compositions studied, a solution containing 1.5% MC 0.3% C was found to have low eta, and formed a strong gel under simulated physiological conditions. Such a system can be formulated as drug containing liquid suitable for administration by instillation into the eye, which upon exposure to physiological conditions will shift to the gel (semi-solid) phase, thus increasing the precorneal residence time of the delivery system and enhancing ocular bioavailability.
Proteomic analysis of excretory/secretory products released by Teladorsagia circumcincta larvae early post‐infection (2008)

Teladorsagia circumcincta is an important parasitic nematode of domestic small ruminants. Drug resistance in this species is common so alternative methods of control are required. As animals develop immunity to T. circumcincta, vaccination is a valid option. Little is known about the antigens that play a role in stimulating immunity at this host/parasite interface. As responses generated between 1 and 5 dpi are known to affect development of these nematodes in their gastric niche, we focused on proteins released during the early stages of infection. To identify molecules potentially involved in immunity, we undertook a proteomics analysis of proteins released from larvae harvested at 1-, 3- and 5-days post-infection (dpi). This analysis produced peptide sequence data that was used to search information available in T. circumcincta expressed sequence tag (EST) databases and enabled identification of a number of excretory/secretory (ES) proteins. Immunoblots were performed to assess the relative molecular weight of ES antigens that were targets of local IgA responses in mucus from sheep rendered immune to infection. ELISA was performed to assess antigen-specific mucus IgA levels in individual sheep. These experiments provided preliminary evidence that the proteins identified in the larval secretome were subject to these antibody responses.
A Commercially Viable 193 nm Single Layer Resist Platform. (1997)

We report on our recent investigations on the formulation and processing of 193 nm single layer photoresists based on alternating copolymers of cycloolefins with malefic anhydride. Resists formulated with cycloolefin copolymers are compatible with 0.262N tetramethylammonium developers, have excellent adhesion, sensitivity, etch resistance and thermal flow properties. The effect of polymer structure and composition, dissolution inhibitor structure and loading as well as the effect of the photoacid generator on the resist dissolution properties was investigated. Based on the results high contrast formulations were evaluated on a GCA XLS (NA=0.53, 4X reduction optics) deep-UV stepper to exhibit 0.27μm L/S pair resolution with excellent photosensitivity.Based on the dissolution properties and a spectroscopic examination of the resist, we have designed materials that show <0.17μm L/S pair resolution with 193 nm exposures on a ISI tool (NA=0.60, 10x reduction optics). In this paper, the formulation methodology will be detailed and the most recent results upon both with 248 and 193nm irradiation will be described.
Repeatedly Regenerating Mechanically Robust Polymer Brushes from Persistent Initiator Coating (PIC) (2022)

Abstract In this study, a novel surface initiated polymerization (SIP) method was developed from organic‐inorganic hybrid persistent initiator coating (PIC) that embeds initiator molecules into inorganic silica sol‐gel layer. Comparing with traditional silane initiator surface that prepared by chemical vapor deposition (CVD) method, the PIC can effectively improve the mechanical stability of initiator that was able to endure ten‐thousand times of friction cycles. Besides, it allows polymer grafting from sub‐surface and so the grafted brushes, poly 3‐sulfopropyl methacrylate potassium salt (pSPMA) on the PIC were also much more wear‐resisting than those prepared by the traditional ways. More importantly, the PIC could still trigger new polymerization reaction when the grafted brushes were worn off. In addition, the PIC is universal and can be covered on different substrates including glass, metals and plastics, etc. to realize functionalization of these materials. The approach may pave technological way for the application of surface grafted polymer brushes.
Superadiabatic Combustion with Reciprocating Flow in Porous Media. (1996)

Superadiabatic combustion with reciprocating flow in a porous medium has been investigated through experiments and a numerical calculation. In the system, an extremely low-heat-content gas flows into the porous medium, where the flow direction reverses regularly. By means of the reciprocating flow system, the combustion gas enthalpy is effectively regenerated into an enthalpy increase in the mixture through the porous medium, which provides heat storage. The results have shown that the maximum temperature is about 10 times higher than the theoretical one of an ordinary flame in free space. The heating value of the mixture is 128 kJ/M3, which is equivalent to the temperature increase of about 98 K. Furthermore, through an asymptotic analysis, it is revealed that the maximum temperature is dependent on the overall activation energy, the pre-exponential factor, the Reynolds number and the heating value.
Longterm Changes in Creatinine Clearance after Laparoscopic Renal Surgery (2008)

Ischemia causes acute renal damage, which is apparently reversible in patients without evidence of medical renal disease. Patients with known medical renal disease have substantial longterm changes in renal function associated with unilateral renal ischemia. Considering the insensitivity of creatinine-based renal function metrics, only eliminating ischemic time will realize the goal of maximal nephron preservation, particularly in patients with preexisting medical renal disease.
Intracavity dispersion measurement in modelocked fibre laser (1993)

It has previously been shown that the minimum pulse width obtainable in modelocked fibre lasers depends primarily on the total cavity dispersion. The Letter compares measurements of the dispersion in figure eight lasers, taken directly by wavelength tuning and indirectly by the sideband spectrum. The dispersions of the different component fibres, including the gain fibre, are deduced from these in situ measurements.
Variational Inference using Implicit Distributions (2017)

Generative adversarial networks (GANs) have given us a great tool to fit implicit generative models to data. Implicit distributions are ones we can sample from easily, and take derivatives of samples with respect to model parameters. These models are highly expressive and we argue they can prove just as useful for variational inference (VI) as they are for generative modelling. Several papers have proposed GAN-like algorithms for inference, however, connections to the theory of VI are not always well understood. This paper provides a unifying review of existing algorithms establishing connections between variational autoencoders, adversarially learned inference, operator VI, GAN-based image reconstruction, and more. Secondly, the paper provides a framework for building new algorithms: depending on the way the variational bound is expressed we introduce prior-contrastive and joint-contrastive methods, and show practical inference algorithms based on either density ratio estimation or denoising.
New candidate loci identified by array‐CGH in a cohort of 100 children presenting with syndromic obesity (2014)

Syndromic obesity is defined by the association of obesity with one or more feature(s) including developmental delay, dysmorphic traits, and/or congenital malformations. Over 25 syndromic forms of obesity have been identified. However, most cases remain of unknown etiology. The aim of this study was to identify new candidate loci associated with syndromic obesity to find new candidate genes and to better understand molecular mechanisms involved in this pathology. We performed oligonucleotide microarray-based comparative genomic hybridization in a cohort of 100 children presenting with syndromic obesity of unknown etiology, after exhaustive clinical, biological, and molecular studies. Chromosomal copy number variations were detected in 42% of the children in our cohort, with 23% of patients with potentially pathogenic copy number variants. Our results support that chromosomal rearrangements are frequently associated with syndromic obesity with a variety of contributory genes having relevance to either obesity or developmental delay. A list of inherited or apparently de novo duplications and deletions including their enclosed genes and not previously linked to syndromic obesity was established. Proteins encoded by several of these genes are involved in lipid metabolism (ACOXL, MSMO1, MVD, and PDZK1) linked with nervous system function (BDH1 and LINGO2), neutral lipid storage (PLIN2), energy homeostasis and metabolic processes (CDH13, CNTNAP2, CPPED1, NDUFA4, PTGS2, and SOCS6).
Synthesis of nitrogen-doped graphene by co-segregation method (2011)

We report a facile strategy to grow nitrogen-doped graphene using embedded nitrogen and carbon in metal substrate via co-segregation method. As the doping is concurrently done in the co-segregation process of carbon and nitrogen species, N atoms can be substitutionally doped into the graphene lattice. This approach has great advantages for achieving a precise control of doping degree and location, which allows for growing various heterojunctions at desired location. In principle, this method can scale up to various elements doping of graphene, such as P- and BN- doped graphene.
High-Rate Algae Ponds for Wastewater Treatment and Protein Production (1982)

High-rate algal ponds (HRAP) under proper climatic conditions can produce annually over 150 tonnes of dry biomass per hectare of which 60 percent is photoautotrophic algae. This result in production of approximately 150 ton/ha-yr of oxygen, in addition 15 ton/ha-yr of nitrogen and 3 ton/ha-hr of phosphorus are removed by incorporation into the biomass which contain between 45 to 50 percent proteins. High quality effluent is produced following physico-chemical separation of the suspended biomass by alum flocculation and flotation.
Motor coordination difficulties in a municipality group and in a clinical sample of poor readers (2005)

The purpose of the study was to investigate incidence, severity and types of motor problems in two groups of poor readers compared to good reading controls. A group of children with severe dyslexia referred to specialist evaluation, a teacher selected municipality sample comprising the 5% poorest readers, and a control group consisting of the 5% best readers were all assessed applying a norm-based, standardized measure by Henderson and Sugden 1992; (The Movement Assessment Battery for Children. Kent: The Psychological Corporation). The three groups were compared with regard to total motor impairment scores as well as motor function within the areas of manual dexterity, ball-skills and balance. More than 50% of the children in both groups of poor readers showed definite motor coordination difficulties at or below the 5th centile, for which motor intervention is recommended. Children in both groups showed difficulties within the sub-area of manual dexterity in particular and also performed significantly worse than controls within the sub-area of balance, but not in ball-skills. The high incidence of motor coordination problems in the two groups of poor readers indicates that all children with reading difficulties should be screened for possible motor difficulties.
Farnesol as a Regulator of HMG-CoA Reductase Degradation: Characterization and Role of Farnesyl Pyrophosphatase (1997)

We have recently reported that the isoprenoid compound farnesol accelerates degradation of the cholesterologenic enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, when added to cultured cells. We have thus proposed that farnesol is a required nonsterol regulator of this degradation event (T. E. Meigs, D. S. Roseman, and R. D. Simoni, 1996, J. Biol. Chem. 271, 7916-7922). In this report, we have studied the enzyme farnesyl pyrophosphatase (FPPase) in Chinese hamster ovary cells. We demonstrate that FPPase activity increases under conditions of increased metabolic flow through the isoprenoid pathway. Also, we show that a nonhydrolyzable analog of farnesyl pyrophosphate, an isoprenoid (phosphinylmethyl)phosphonate, inhibits FPPase in vitro, and when added to cells this inhibitor blocks the mevalonate-dependent, sterol-induced degradation of HMG-CoA reductase. Furthermore, exogenous farnesol overcomes the effect of this inhibitor. These results suggest an isoprenoid-mediated regulatory mechanism governing intracellular farnesol production and support the hypothesis that farnesol is a nonsterol regulator of reductase degradation.