gebhart/patrepeval huggingface dataset:
Assay Development for a Portable Fiberoptic Biosensor (1996)

The fiberoptic biosensor with tapered optical probes has been developed to perform rapid and sensitive fluoroimmunoassays. A number of assays for biologic analytes were developed using a laboratory breadboard device that employed a large, 514 nm argon ion laser. These assays, with limits of detection of 5-50 ng/ml for protein antigens, showed promise for clinical use because of their demonstrated lack of matrix effects from plasma, seru, or blood. However, such a large device was impractical for on-site diagnostics, so a new, portable, multichannel biosensor was developed. To test this new biosensor, which uses 635 nm laser diodes, the assays were converted to use the cyanine dye, Cy5. The detection antibodies were labeled with Cy5 and assays performed to detect the F1 antigen of Yersinia pestis and the protective antigen of Bacillus anthracis. The limit of detection was found to improve by a factor of 10 for each assay. The portable biosensor was then evaluated in a blind test containing F1 antigen spiked into 30 of 173 serum samples. One hundred percent detection was achieved for samples with 100 ng/ml or more F1 antigen, with a specificity of 88%.
Motion planning and dynamic control of a linked manipulator using modified magnetic fields (2002)

This work targets the navigation and control of multi-linked manipulators in tight, constrained spaces as are encountered in problems of robotic packaging or loading and unloading of pallets. The modified magnetic field algorithm was introduced by the authors (1996, 1997) for the specific purposes of generating motion plans for a robot moving in a complex and constrained workspace while veering around enclosing Cartesian space obstacle walls. The modified magnetic field method allows global convergence and collision constraint satisfaction while allowing the application of this method as a dynamic online plan generation and control technique in both Cartesian and configuration spaces. Methods for using the MMF for the online dynamic closed loop control of a robot arm in the presence of Cartesian obstacles and singular configurations are developed in this paper and results shown for a specific workspace configuration. This is done by extending the concept of the MMF through a detailed analysis of exactly what constitutes a desirable path in both Cartesian and configuration spaces. The dynamic control is performed in a hybrid manner to account for both, Cartesian as well as configuration space obstacles.
On the economic viability of network systems and architectures (2011)

Understanding the relationship between technology and economics is fundamental to making judicious policy and design decisions. Many technologies that are successful in meeting their technical goals often fail to get adopted due to economic factors. This holds true even for networked systems, e.g., the Internet, which witnessed failures in the adoption of QoS solutions, IPv6 migration etc., due to factors such as high costs, lack of demand, and weight of incumbency. To gain better insights into these issues, researchers need access to analytical frameworks that account for both technological and economic factors and provide useful design guidelines. This dissertation was motivated primarily by the need to undertake such a holistic, multidisciplinary approach towards creating such analytical frameworks. 
We focus on three important aspect related to deployment, adoption, and design of network systems and architectures. The Internet has been one of the most successful network technologies, serving both as a shared platform for easy deployment of new services and a driver for their adoption. But recent trends in convergence of voice, video, and data services, along with advances in virtualization technologies, raise questions as to whether deploying heterogeneous services on a shared network is right or not, especially given the operational complexity and costs involved. We develop a model to investigate the trade-offs between shared and dedicated infrastructures and identify the operational metrics that influence which infrastructure choice benefits more from resource reprovisioning. Closely related to the issue of network service deployment is that of its successful adoption, which serves as the second topic of this dissertation. An entrant’s success hinges not only on technical superiority but also on other factors, including its ability to win over an incumbent’s installed base by using gateways. Our model for adoption of competing technologies reveals several interesting behaviors, including the possibility for converters to reduce overall market penetration across both technologies and to prevent the convergence of the adoption process to a stable state. Lastly, we consider the issue of network platform design. The emergence and adoption of new technologies depend on the functional capabilities provided by the underlying network platform. Answering whether the minimalist design of Internet is still relevant as it evolves into an ecosystem of software services, require a cost-benefit analysis of choosing between a functionality-rich and a minimalist design. We develop a two-sided market model to show how this design choice crucially depends on the relationship between the cost of adding features to the platform and the benefits that application developers derive from them. The frameworks developed in this dissertation have the potential for application in many different network settings, and can spur further research on various topics in network economics.
Hypoxia-Inducible Factor 1 Mediates Upregulation of Telomerase (hTERT) (2004)

Hypoxia occurs during the development of the placenta in the first trimester and correlates with both trophoblast differentiation and the induction of telomerase activity through hTERT expression. We sought to determine the mechanism of regulation of hTERT expression during hypoxia. We show that hypoxia-inducible factor 1alpha (HIF-1alpha) and hTERT expression in the human placenta decrease with gestational age and that these are overexpressed in preeclamptic placenta, a major complication of pregnancy. Hypoxia not only transactivates the hTERT promoter activity but also enhances endogenous hTERT expression. The hTERT promoter region between -165 and +51 contains two HIF-1 consensus motifs, and in vitro reporter assays show that these are essential for hTERT transactivation by HIF-1. Introduction of an antisense oligonucleotide for HIF-1 diminishes hTERT expression during hypoxia, indicating that upregulation of hTERT by hypoxia is directly mediated through HIF-1. Our results provide persuasive evidence that the regulation of hTERT promoter activity by HIF-1 represents a mechanism for trophoblast growth during hypoxia and suggests that this may be a generalized response to hypoxia in various human disorders including resistance to cancer therapeutics by upregulating telomerase.
44.4: Invited Paper : The Organic Alternative to ITO (2008)

Abstract Orgacon™ products are based on the conducting polymer PEDOT/PSS and are very promising materials in cost‐effective R2R production of large area electronics. This paper will show both the progress in the surface resistance/VLT and progress in the stability (T/R.H. and light stability). A new generation of films, coating formulations and inks will be presented.
Transforming growth factor beta mimetics: discovery of 7-[4-(4-cyanophenyl)phenoxy]-heptanohydroxamic acid, a biaryl hydroxamate inhibitor of histone deacetylase. (2002)

Transforming growth factor beta (TGF-beta) is a multifunctional protein that has been shown to possess potent growth-inhibitory activity. To identify small molecular weight compounds with TGF-beta-like activities, high throughput screening was performed using mink lung epithelial cells stably transfected with a TGF-beta-responsive plasminogen activator inhibitor 1 promoter/luciferase construct. Biaryl hydroxamate compounds were identified that demonstrated TGF-beta-like activities. 7-[4-(4-cyanophenyl)phenoxy]-heptanohydroxamic acid (A-161906) demonstrated complete TGF-beta-like agonist activity in the plasminogen activator inhibitor 1/luciferase construct. A-161906 inhibited the proliferation of multiple cell lines in a concentration-dependent manner. Cells were growth arrested at the G1-S checkpoint similar to TGF-beta. Consistent with the G1-S arrest, A-161906 induced the expression of the cyclin-dependent kinase inhibitor p21waf1/cip1. A-161906 produced many cellular effects similar to that of TGF-beta but did not displace labeled TGF-beta from its receptors. Cells with mutations in either of the TGF-beta receptors I or II were growth-arrested by A-161906. Therefore, the site of action of A-161906 appears to be distal to the receptors and possibly involved with the signaling events controlled by TGF-beta. The TGF-beta mimetic effect of A-161906 can be partially, if not entirely, explained by its activity as a histone deacetylase (HDAC) inhibitor. A-161906 demonstrated potent HDAC-inhibitory activity (IC50 = 9 nM). A-161906 is a novel small molecular weight compound (< 400 MW) having TGF-beta mimetic activity as a result of its potent HDAC-inhibitory activity. These results and those of others demonstrate the importance of HDACs in regulation of the TGF-beta signaling pathway(s).
Novel lentiviral vectors for gene therapy of sickle cell disease combining gene addition and gene silencing strategies (2023)

Sickle cell disease (SCD) is due to a mutation in the β-globin gene causing production of the toxic sickle hemoglobin (HbS; α<sub>2</sub>β<sup>S</sup> <sub>2</sub>). Transplantation of autologous hematopoietic stem and progenitor cells (HSPCs) transduced with lentiviral vectors (LVs) expressing an anti-sickling β-globin (βAS) is a promising treatment; however, it is only partially effective, and patients still present elevated HbS levels. Here, we developed a bifunctional LV expressing βAS3-globin and an artificial microRNA (amiRNA) specifically downregulating β<sup>S</sup>-globin expression with the aim of reducing HbS levels and favoring βAS3 incorporation into Hb tetramers. Efficient transduction of SCD HSPCs by the bifunctional LV led to a substantial decrease of β<sup>S</sup>-globin transcripts in HSPC-derived erythroid cells, a significant reduction of HbS<sup>+</sup> red cells, and effective correction of the sickling phenotype, outperforming βAS gene addition and <i>BCL11A</i> gene silencing strategies. The bifunctional LV showed a standard integration profile, and neither HSPC viability, engraftment, and multilineage differentiation nor the erythroid transcriptome and miRNAome were affected by the treatment, confirming the safety of this therapeutic strategy. In conclusion, the combination of gene addition and gene silencing strategies can improve the efficacy of current LV-based therapeutic approaches without increasing the mutagenic vector load, thus representing a novel treatment for SCD.
Endoscopic retrograde cholangiopancreatography using a single-balloon enteroscope in patients with altered Roux-en-Y anatomy (2010)

Single-balloon ERCP is feasible in patients with complex postsurgical Roux-en-Y anastomosis, allows diagnostic evaluation and therapeutic intervention in patients with pancreaticobiliary disease, and is a useful salvage technique in the majority of patients in whom ERCP using colonoscopies has failed.
Conformational isomerism leads to supramolecular isomerism and nanoscale inclusion in 2D extended framework solids based on C-methylcalix[4]resorcinarene (2001)

Co-crystallization of C-methylcalix[4]resorcinarene 1 with 4,4′-bipyridine 2 in the presence of m-xylene results in the formation of a 2D brick framework, 3c·2(m-xylene), that possesses nanoscale cavities that host four aromatics as guests in which 1 adopts a ‘T-shaped’ conformation.
Síndrome de Peutz-Jeghers complicado: Reporte de un caso (2008)

El Síndrome de Peutz-Jeghers (SPJ), es una patología poco frecuente, hereditaria, autosómica dominante, caracterizada por la pigmentación de la mucosa oral y de la piel plantar y palmar, junto a una poliposis gastrointestinal de tipo hamartomatoso. En su crecimiento dicho pólipos pueden llegar a complicarse y causar intususcepción, obstrucción y hemorragias intestinales. La mutación genética asociada a éste síndrome es en el cromosoma 19p, en el gen STK 11, y en la enzima LKB 1, que disminuye su función de supresión de tumores. Hay un aumento de la enzima Cox-2, pudiendo llegar a asociarse a una mayor incidencia de cáncer gastrointestinal y extraintestinal, por lo que es importante una pesquisa precoz de los pólipos. El objetivo de este trabajo, es reportar un caso de Íleo mecánico a nivel del yeyuno proximal como una complicación aguda de una poliposis de larga evolución por SPJ, que consultó en nuestro Servicio de Urgencia y que requirió de una laparotomía exploradora
Pre-treatment with dissolved air flotation considering an integrated process design (2001)

The raw water from Lake Zegrzynski is difficult to treat and requires a high chemical dosing rate of coagulant for the reduction of organic matter in order to comply with EU standards. The high degree of reduction calls for an efficient coagulant, but also an optimal chemistry such as correct dosing amount and an optimal flocculation-pH. The paper describes different removal efficiencies of organic matter, particularly with respect to pH in flocculation. During the warm season, the raw water can also suffer from large amounts of plankton that are difficult to remove to a satisfactory degree. In a two-step chemical treatment concept, with Dissolved Air Flotation (DAF) and the pulsator process, the plankton content in the final outlet water is reduced to very low levels. It follows that eventual peaks of plankton in the raw water cannot be detected in the final outlet water. Ozone is added for removal of taste and odour originating from the presence of plankton. In the pre-treatment step prior to the ozonation, a great deal of the organic matter is removed, which reduces the necessary ozone dosage. The Municipal Water Company of Warsaw City has decided to consider an additional pre-treatment step to the existing water treatment plant at Wieliszew. For that purpose, and bearing in mind an integrated process design, the company has performed pilot-scale experiments with DAF installed prior to a process line identical with the existing full-scale plant. The experimental flow is about 10 m3/h.
FURTHER SEROLOGICAL AND RFLP ANALYSIS OF THE MRL‐+/+ AND MRL‐lpr/lpr MICE (1988)

During their ageing, MRL-lpr/lpr mice (H-2k) suffer from progressive lymph node enlargement, associated with the development of several acute autoimmune lesions. The primary effect and location of the lpr mutation is unknown. However, a minority of the lymphoid cells of some MRL-+/+, as well as MRL-lpr/lpr mice, express 'alien' H-2d antigenic specificities. In the course of the investigation of the origin of the latter, we have carried out the genotyping of the MHC of several MRL-+/+ and MRL-lpr/lpr mice using the Southern blotting technique and employing a variety of MHC class I and class II probes, and restriction enzymes known to discriminate between the d and the k haplotypes. None of the results obtained so far suggests the contribution of genuine H-2d genes to the MHC of the MRL-+/+ and MRL-lpr/lpr mouse strains. Alternative hypotheses for the generation of the 'alien' epitopes are discussed.
Induction of CD8+ T‐lymphocyte responses to a secreted antigen of Mycobacterium tuberculosis by an attenuated vaccinia virus (2001)

Protective immunity against Mycobacterium tuberculosis infection requires the activation of mycobacterium-specific CD8+ T cells, as well as CD4+ T cells. Therefore, optimizing strategies that stimulate CD8+ T cells recognizing dominant mycobacterial antigens, including secreted proteins, may lead to the development of more effective vaccines against tuberculosis. To generate a viral vaccine that is safe in humans, the early secreted protein, MPT64, was expressed in the attenuated vaccinia virus (VV) strain, modified vaccinia virus Ankara (MVA-64). The immunogenicity of MVA-64 was compared with that of the Western Reserve strain of VV (VVWR-64). The replication-defective MVA-64 was as efficient as VVWR-64 in inducing specific antibodies and cytolytic T-cell responses to a defined H-2-Db-restricted epitope on MTP-64. In addition, priming with MPT64-expressing plasmid DNA (DNA-64), and boosting with either MVA-64 or VVWR-64, markedly enhanced MPT64-specific cytolytic and IFN-gamma-producing CD8+ T-cell responses. These findings suggest that MVA may be a suitable vaccine carrier for stimulating mycobacterium-specific CD8+ T-cell responses and may be particularly relevant for developing vaccines for use in regions endemic for tuberculosis and HIV infection.
Radial Confinement of Light in an Ultracold Anisotropic Medium (2005)

We demonstrate radial confinement and waveguiding of light in an ultracold anisotropic gas. The waveguiding medium is a laser cooled ensemble of rubidium atoms confined in a trap of large aspect ratio. A recoil induced resonance (RIR) is used to create strong dispersion and large gain in this ensemble. The combination of the anisotropic trap and the RIR give rise to a spatially varying group refractive index resulting in a slow-light optical waveguide. Waveguided pulses of light experience strong gain (approximately 50), low group velocities (c approximately 1500 m/s), and long group delays (delta approximately 7 micros) due to the enhanced path length.
Thermal activation of the purified rat hepatic glucocorticoid receptor. Evidence for a two-step mechanism. (1985)

Thermal "activation" or "transformation" of rat hepatic [6,7-3H]triamcinolone acetonide (TA)-receptor complexes purified in the unactivated state to near homogeneity (Grandics, P., Miller, A., Schmidt, T. J., Mittman, D., and Litwack, G. (1984) J. Biol. Chem. 259, 3173-3180) has been further investigated. The data generated in reconstitution experiments demonstrate that warming (25 degrees C for 30 min) of the purified unactivated complexes promotes their activation as judged by an increase in DNA-cellulose binding, but to a lower extent than that observed after warming of glucocorticoid-receptor complexes in crude cytosols. However, maximal DNA-cellulose binding capacity can be detected in reconstituted systems (also heated at 25 degrees C for 30 min) consisting of purified unactivated [3H]TA-receptor complexes and a cytoplasmic "stimulator(s)." This cytoplasmic factor(s), which does not copurify with the receptor, is heat-stable (90 degrees C for 30 min), excluded from Sephadex G-25, and trypsin-sensitive and stimulates DNA-cellulose binding in a dose-dependent manner. The ability of Na2MoO4 to block thermal activation of the highly purified receptor complexes suggests that this transition metal anion interacts directly with the receptor protein itself. The fact that the cytoplasmic stimulator(s) enhances DNA-cellulose binding of the [3H]TA-receptor complexes without increasing the proportion of those complexes eluted in the activated (low salt) position from DEAE-cellulose is consistent with a proposed two-step model of in vitro activation. During the Na2MoO4-sensitive Step 1, elevated temperature (25 degrees C for 30 min) may directly alter the conformation of the purified receptor complexes (i.e. subunit dissociation or disaggregation), resulting in the appropriate shift in the elution profile of the [3H]TA-receptor complexes on DEAE-cellulose but only in a minimal (approximately 2-3-fold) increase in the binding of these complexes to DNA-cellulose. During the Na2MoO4-insensitive and temperature-independent Step 2, a heat-stable cytoplasmic protein(s) may interact with these thermally activated [3H]TA-receptor complexes and enhance their ability to bind to DNA-cellulose without further increasing the percentage of those complexes which elute from DEAE-cellulose in the activated position. In crude cytosols these two steps would presumably occur simultaneously, and addition of Na2MoO4 prior to warming would block Step 1 and hence Step 2 would not occur.
Organic Pseudo-CMOS Circuits for Low-Voltage Large-Gain High-Speed Operation (2011)

Pseudo-CMOS inverters operating at 2 V and comprising four p-type organic transistors with ultrahigh gain are fabricated using self-assembled monolayer gate dielectrics. The inverter gain is as large as 302 at an operation voltage of 2 V, whereas the minimum operation voltage is as small as 0.5 V. The oscillation frequency of a five-stage ring oscillator comprising pseudo-CMOS inverters is 4.27 kHz at 2 V, corresponding to 23.4 μs of propagation delay per stage. This is the fastest among organic circuits operating at low voltage. Pseudo-CMOS amplifier circuits show a large gain of 240 for a 3.0-mV input voltage.
Safety pharmacology of sibutramine mesylate, an anti-obesity drug (2005)

Sibutramine mesylate is a new anti-obesity drug. It is a crystalline salt of sibutramine developed to improve the solubility of sibutramine hydrochloride. Methanesulfonic acid was used as a salt-forming acid instead of hydrochloric acid, resulting in a greatly improved solubility of 1000 mg/mL in water. Sibutramine mesylate was administered orally to ICR mice, Sprague-Dawley rats, and beagle dogs at dose levels of 1.15, 3.45, and 11.50 mg/kg to measure its effects on the central nervous system (CNS), general behaviour, cardiovascular-respiratory system and the other organ systems. Following administration of sibutramine mesylate, spontaneous locomotor activity was significantly increased from 120 min to 24 hours at 3.45 mg/kg and from 30 min to 24 hours at 11.50 mg/kg. Furthermore, there were a decrease in hexobarbital-induced sleep time, an increase in respiratory rate at 120 min, increases in intestinal transport capacity and gastric pH at 11.50 mg/kg, and decreases in gastric volume and total acidity at 3.45 and 11.50 mg/kg. However sibutramine mesylate caused no effects on general behaviour, motor coordination, body temperature, analgesia, convulsion, blood pressure, heart rate, electrocardiogram, cardiac functions of the isolated rat heart, isolated smooth muscles and renal function. Based on the above results, it was concluded that sibutramine mesylate caused effects on the spontaneous locomotor activity, hexobarbital-induced sleep time, respiration, gastrointestinal transport, and gastric secretion at a dose level of 3.45 mg/kg or greater but caused no effects on other general pharmacological reactions.
Non-satellite based field communications system for battlefield deployments (2012)

Many wireless systems used by military ground personnel are satellite based. This paper explores a hybrid system that benefits from both satellite and terrestrial wireless technologies while overcoming the limitations of each. We present the architecture, describe the merits, and then explain the essence of the system: IP Flow mobility. After introducing this concept, we describe some of the important aspects that specifically relate to mobility and security.
Two-in-One Spider Silk Protein with Combined Mechanical Features in All-Aqueous Spun Fibers (2023)

Major ampullate (MA) spider silk reveals outstanding mechanical properties in terms of a unique combination of high tensile strength and extensibility, unmatched by most other known native or synthetic fiber materials. MA silk contains at least two spider silk proteins (spidroins), and here, a novel two-in-one (TIO) spidroin was engineered, resembling amino acid sequences of such two of the European garden spider. The combination of mechanical and chemical features of both underlying proteins facilitated the hierarchical self-assembly into β-sheet-rich superstructures. Due to the presence of native terminal dimerization domains, highly concentrated aqueous spinning dopes could be prepared from recombinant TIO spidroins. Subsequently, fibers were spun in a biomimetic, aqueous wet-spinning process, yielding mechanical properties at least twice as high as fibers spun from individual spidroins or blends. The presented processing route holds great potential for future applications using ecological green high-performance fibers.