gebhart/patrepeval huggingface dataset:
Safety and Efficacy Assessment of Chimeric Ribozyme to Proliferating Cell Nuclear Antigen to Prevent Recurrence of Proliferative Vitreoretinopathy (2007)

To our knowledge, this is the most recent, meticulously designed clinical trial in PVR.
A Web-based classification system of DNA-binding protein families (2001)

Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The family of DNA-binding proteins is one of the most populated and studied amongst the various genomes of bacteria, archaea and eukaryotes and the Web-based system presented here is an approach to their classification. The DnaProt resource is an annotated and searchable collection of protein sequences for the families of DNA-binding proteins. The database contains 3238 full-length sequences (retrieved from the SWISS-PROT database, release 38) that include, at least, a DNA-binding domain. Sequence entries are organized into families defined by PROSITE patterns, PRINTS motifs and de novo excised signatures. Combining global similarities and functional motifs into a single classification scheme, DNA-binding proteins are classified into 33 unique classes, which helps to reveal comprehensive family relationships. To maximize family information retrieval, DnaProt contains a collection of multiple alignments for each DNA-binding family while the recognized motifs can be used as diagnostically functional fingerprints. All available structural class representatives have been referenced. The resource was developed as a Web-based management system for online free access of customized data sets. Entries are fully hyperlinked to facilitate easy retrieval of the original records from the source databases while functional and phylogenetic annotation will be applied to newly sequenced genomes. The database is freely available for online search of a library containing specific patterns of the identified DNA-binding protein classes and retrieval of individual entries from our WWW server (http://kronos.biol.uoa.gr/~mariak/dbDNA.html).
CXCL8 enhances proliferation and growth and reduces apoptosis in endometrial stromal cells in an autocrine manner via a CXCR1-triggered PTEN/AKT signal pathway (2012)

This study suggests that CXCL8 and CXCR1 are involved in the pathogenesis of endometriosis by up-regulating proliferation and growth and restricting apoptosis in ESCs by activating the PTEN/Akt pathway and mediating the expression of survivin and Bcl-2.
IMMOBILIZING WILD MOUNTAIN LIONS (FELIS CONCOLOR) WITH KETAMINE HYDROCHLORIDE AND XYLAZINE HYDROCHLORIDE (1986)

A mixture of 120 mg ketamine hydrochloride (KHCL)/20 mg xylazine hydrochloride (XHCL)/ml was used to immobilize 37 wild mountain lions (Felis concolor) 46 times. Observations were recorded during 37 trials that included kittens, adult females, and adult males. Dosages were based on 11 mg KHCL and 1.8 mg XHCL/kg estimated body weight. Actual doses for 24 lions requiring a single injection for immobilization ranged from 4.7-15.8 mg KHCL/kg and 0.8-2.6 mg XHCL/kg. Induction, duration, and recovery times did not differ (P greater than 0.05) between the sex and age classes. Two kittens were overdosed with the drug combination, but the effects were not life threatening. Eleven other lions, nine of which were initially underdosed, required additional injections of the drug combination for safe handling. Immobilization was characterized initially by semi-consciousness, open eyelids, pupillary dilation, and muscle rigidity. Later, most lions appeared unconscious, muscles relaxed, and breathing slowed considerably. No convulsions or hypersalivation occurred. The KHCL/XHCL mixture given at approximately 11 mg KHCL and 1.8 mg XHCL/kg body weight proved useful for immobilizing wild mountain lions for research purposes. Suggestions for case of immobilized cats are included.
Three-Dimensional Cell Culture Matrices: State of the Art (2008)

Traditional methods of cell growth and manipulation on 2-dimensional (2D) surfaces have been shown to be insufficient for new challenges of cell biology and biochemistry, as well as in pharmaceutical assays. Advances in materials chemistry, materials fabrication and processing technologies, and developmental biology have led to the design of 3D cell culture matrices that better represent the geometry, chemistry, and signaling environment of natural extracellular matrix. In this review, we present the status of state-of-the-art 3D cell-growth techniques and scaffolds and analyze them from the perspective of materials properties, manufacturing, and functionality. Particular emphasis was placed on tissue engineering and in vitro modeling of human organs, where we see exceptionally strong potential for 3D scaffolds and cell-growth methods. We also outline key challenges in this field and most likely directions for future development of 3D cell culture over the period of 5-10 years.
Feudal Multi-Agent Hierarchies for Cooperative Reinforcement Learning (2019)

We investigate how reinforcement learning agents can learn to cooperate. Drawing inspiration from human societies, in which successful coordination of many individuals is often facilitated by hierarchical organisation, we introduce Feudal Multi-agent Hierarchies (FMH). In this framework, a 'manager' agent, which is tasked with maximising the environmentally-determined reward function, learns to communicate subgoals to multiple, simultaneously-operating, 'worker' agents. Workers, which are rewarded for achieving managerial subgoals, take concurrent actions in the world. We outline the structure of FMH and demonstrate its potential for decentralised learning and control. We find that, given an adequate set of subgoals from which to choose, FMH performs, and particularly scales, substantially better than cooperative approaches that use a shared reward function.
Natural Control in Manufacturing (1989)

This paper reviews certain theoretical results in robot task planning and control obtained with the support of NSF Research Initiation Grant DMC-8505160. The “natural control” paradigm is reviewed and detailed attention is focused upon the specific task of robot navigation in a cluttered environment. The paper concludes with some comments concerning the problems which remain before this approach to robot command and control can be made practicable in a real manufacturing environment. A summary of formal results presented in the paper now follows. The class of “navigation functions” simultaneously encodes the task of navigating amidst obstacles and automatically generates correct feedback control laws for this purpose as well. We show that the topology of navigation tasks precludes any stronger class of controllers (with respect to convergence properties). On the other hand we demonstrate that a member of this class must exist for any environment. Finally, we construct controllers for an increasingly realistic catalogue of environments by recourse to “deformation” of the true environment into a computationally simpler but topologically equivalent model.
Intra-individual Change Over Time in DNA Methylation With Familial Clustering (2008)

These data indicate that methylation changes over time and suggest that methylation maintenance may be under genetic control.
Behavioral Modeling and Performance Evaluation of Microelectrofluidics-Based PCR Systems Using SystemC (2004)

Composite microsystems that incorporate microelectromechanical and microelectrofluidic devices are emerging as the next generation of system-on-a-chip (SOC). We present a performance comparison between two types of microelectrofluidic systems (MEFS): continuous-flow systems and droplet-based systems. The comparison is based on a specific microelectrofluidic application-a polymerase chain reaction (PCR) system. The behavioral modeling, simulation, and performance evaluation are based on a SystemC design environment. The performance comparison includes the system throughput, system-correction capacity, system-processing capacity, and system-design complexity. By using our system-performance evaluation environment, we demonstrated that the droplet-based MEFS provides higher performance, as well as lower design and integration complexity.
An Extracellular Proteolytic Cascade Promotes Neuronal Degeneration in the Mouse Hippocampus (1997)

Mice lacking the serine protease tissue plasminogen activator (tPA) are resistant to excitotoxin-mediated hippocampal neuronal degeneration. We have used genetic and cellular analyses to study the role of tPA in neuronal cell death. Mice deficient for the zymogen plasminogen, a known substrate for tPA, are also resistant to excitotoxins, implicating an extracellular proteolytic cascade in degeneration. The two known components of this cascade, tPA and plasminogen, are both synthesized in the mouse hippocampus. tPA mRNA and protein are present in neurons and microglia, whereas plasminogen mRNA and protein are found exclusively in neurons. tPA-deficient mice exhibit attenuated microglial activation as a reaction to neuronal injury. In contrast, the microglial response of plasminogen-deficient mice was comparable to that of wild-type mice, suggesting a tPA-mediated, plasminogen-independent pathway for activation of microglia. Infusion of inhibitors of the extracellular tPA/plasmin proteolytic cascade into the hippocampus protects neurons against excitotoxic injury, suggesting a novel strategy for intervening in neuronal degeneration.
Factors Influencing Poor Outcomes in Synthetic Tissue‐Engineered Tracheal Replacement (2019)

In our ovine model, clinically applied synthetic tissue-engineered tracheas demonstrated infectious, inflammatory, and mechanical failures with a lack of epithelialization and neovascularization.
Variable rate speech coding for multiple access wireless networks (2002)

Variable-rate speech coding is a key component of certain multiple access schemes for wireless networks. Such coding methods exploit the silent intervals in a conversation and the statistical variability of active speech, to enhance network capacity for a given speech quality. Voice activity detection schemes distinguish active speech from background noise. Variable-rate coding algorithms are based on source or network control of rate. A source-controlled variable-rate speech coding algorithm, named variable rate phonetic segmentation (VRPS), is described. In VRPS the rate and coding strategy are based on phonetic classification of speech segments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Chronic blockade of nitric oxide synthesis in the rat produces systemic hypertension and glomerular damage. (1992)

Tonic basal release of nitric oxide (NO) by vascular endothelial cells controls blood pressure (BP) in the basal state. In these studies we investigated the effects of chronic inhibition of basal NO synthesis in the rat for a 2-mo period. Significant systemic hypertension developed in chronically NO-blocked rats compared to controls. Marked renal vasoconstriction was also observed with elevations in glomerular blood pressure (PGC) and reductions in the glomerular capillary ultrafiltration coefficient (Kf). Chronically NO-blocked rats also develop proteinuria and glomerular sclerotic injury compared to controls. These studies therefore describe a new model of systemic hypertension with glomerular capillary hypertension and renal disease due to chronic blockade of endogenous NO synthesis. These observations highlight the importance of the endogenous NO system in control of normal vascular tone and suggest that hypertensive states may result from relative NO deficiency.
Use of the polymerase chain reaction to monitor the effectiveness of ex vivo tumor cell purging (1991)

The polymerase chain reaction (PCR) was used to detect residual malignant disease before and after ex vivo purging with monoclonal antibodies and complement or immunomagnetic treatment of BM samples contaminated with known numbers of t(14;18)-carrying tumor cells. Sensitivity of the PCR was demonstrated by detecting a specific t(14;18) amplification product in DNA extracted from a preparation consisting of one tumor cell among 10(5) normal cells. When BM contaminated with 1% to 5% t(14;18)-carrying cells from the B-cell lymphoma line SU-DHL-4 was subjected to two rounds of anti-B-cell pool of antibodies and complement (Ab-C) treatment a 3- to 4-log reduction of the pretreatment PCR signal was observed. A similar log-cell kill was detected using an independent clonogenic assay confirming the utility of the PCR approach. BM contaminated with a second B-cell lymphoma cell line, OCI-Ly8, was more resistant because a third cycle of Ab-C treatment was required to obtain a similar reduction in the PCR signal. A similar 4 logs of tumor cell removal was obtained using anti-B-cell antibodies conjugated to magnetic beads. These studies demonstrate that the t(14;18) PCR can be used to detect levels of tumor cells as low as 0.001%. This approach can be used to determine the effectiveness of BM purging in patients undergoing autologous BM transplantation as well as to assess the biologic role of minimal marrow disease.
Green Roots: Photosynthesis and Photoautotrophy in an Underground Plant Organ (1993)

The potential for photosynthetic and photoautotrophic growth was studied in hairy root cultures of Asteraceae and Solanaceae species. Upon transfer to light, initially heterotrophic root cultures of Acmella oppositifolia and Datura innoxia greened rapidly, differentiated chloroplasts, and developed light-dependent CO2 fixation in the cortical cells. Photosynthetic potential was expressed in root cultures of all the Asteraceae genera examined (Acmella, Artemisia, Rudbeckia, Stevia, and Tagetes). Hairy roots of A. oppositifolia and D. innoxia were further adapted to photoautotrophy by growing in the presence of light and added CO2 (1-5%) and by direct or sequential transfers into media containing progressively lower sugar concentrations. The transition to photoautotrophy was accompanied by an increase in CO2 fixation and in the specific activity of 1,5-ribulose-bisphosphate carboxylase/ oxygenase (Rubisco). During the adaptation of A. oppositifolia roots to photoautotrophy, the ratio of Rubisco to phosphoenolpyruvate carboxylase increased significantly, approaching that found in the leaves. The levels and patterns of alkaloids and polyacetylenes produced by Solanaceae and Asteraceae hairy roots, respectively, were dramatically altered in photomixotrophic and photoautotrophic cultures. Photoautotrophic roots of A. oppositifolia have been mainitained in vitro for over 2 years.
BONE MARROW–DERIVED DENDRITIC CELLS, INFECTION WITH HUMAN IMMUNODEFICIENCY VIRUS, AND IMMUNOPATHOLOGY (1997)

Dendritic cells (DC) exposed to HIV-1 show nonproductive infection that may become productive as they mature. The distribution of DC within genital mucosa and their susceptibility to infection particularly with clade E viruses could be reflected in the ease of heterosexual transmission. Carriage of virus and viral antigen by DC into lymph nodes may allow clustering and activation of T cells and production of protective immune responses. However, secondary infection of activated T cells from infected DC could cause dissemination of virus and loss of infected DC and T cells. In asymptomatic infection, fewer dendritic cells with reduced capacity to stimulate CD4 T cell proliferation are found before evidence of T cell abnormalities, and these early changes in antigen-presenting cells may result in a decline in the production of CD4 memory T cells. However, DC fuel ongoing production of antibody to HIV-1. Signaling by DC to T cells may thus underlie two major features of early HIV infection--loss in CD4+ memory T cells and persistence of antibody production. In AIDS, infected dendritic and epithelial cells within the thymus may affect maturation and contribute to loss of the "naive" T cell population. Further loss of memory T cells may occur through syncytium formation with infected DC. Finally, in AIDS patients, there is a failure in the development and the function of DC from CD34+ stem cells. In conclusion, the infection of dendritic cells, loss in their numbers, and changed signaling to T cells may shape the pattern of immunity during infection with HIV-1. Conversely, treatments that reverse the defect in antigen presentation by DC may improve cell-mediated immunity.
A Calmodulin-Related Protein That Suppresses Posttranscriptional Gene Silencing in Plants (2000)

Posttranscriptional gene silencing (PTGS) is an ancient eukaryotic regulatory mechanism in which a particular RNA sequence is targeted and destroyed. The helper component-proteinase (HC-Pro) of plant potyviruses suppresses PTGS in plants. Using a yeast two-hybrid system, we identified a calmodulin-related protein (termed rgs-CaM) that interacts with HC-Pro. Here we report that rgs-CaM, like HC-Pro itself, suppresses gene silencing. Our work is the first report identifying a cellular suppressor of PTGS.
A multiplexed optofluidic biomolecular sensor for low mass detection (2009)

Optical techniques have proven to be well suited for in situ biomolecular sensing because they enable high fidelity measurements in aqueous environments, are minimally affected by background solution pH or ionic strength, and facilitate label-free detection. Recently, there has been significant interest in developing new classes of optically resonant biosensors possessing very high quality-factors. This high quality-factor enables them to resolve the presence of very small amounts of bound mass and leads to very low limits of detection. A drawback of these devices is that the majority of the resonant electromagnetic energy is confined within the solid light-guiding structure thus limiting the degree to which it overlaps with the bound matter. This in turn lowers the ultimate device sensitivity, or the change in output signal in response to changes in bound mass. Here we present a novel optofluidic biosensor platform that incorporates a unique one-dimensional photonic crystal resonator array which enables significantly stronger light-matter interaction. We show here how this, coupled with the ability of planar photonic crystals to spatially localize the optical field to mode volumes on the order of a wavelength cubed, enables a limit of detection on the order of 63 ag total bound mass (estimated using a polyelectrolyte growth model) and a device sensitivity an order of magnitude better than similar devices. The multiplexing capabilities of our sensor are demonstrated by the individual and concurrent detection of interleukins 4, 6 and 8 using a sandwich assay.
Mirvetuximab Soravtansine (IMGN853), a Folate Receptor Alpha–Targeting Antibody-Drug Conjugate, Potentiates the Activity of Standard of Care Therapeutics in Ovarian Cancer Models (2016)

Elevated folate receptor alpha (FRα) expression is characteristic of epithelial ovarian cancer (EOC), thus establishing this receptor as a candidate target for the development of novel therapeutics to treat this disease. Mirvetuximab soravtansine (IMGN853) is an antibody-drug conjugate (ADC) that targets FRα for tumor-directed delivery of the maytansinoid DM4, a potent agent that induces mitotic arrest by suppressing microtubule dynamics. Here, combinations of IMGN853 with approved therapeutics were evaluated in preclinical models of EOC. Combinations of IMGN853 with carboplatin or doxorubicin resulted in synergistic antiproliferative effects in the IGROV-1 ovarian cancer cell line in vitro. IMGN853 potentiated the cytotoxic activity of carboplatin via growth arrest and augmented DNA damage; cell cycle perturbations were also observed in cells treated with the IMGN853/doxorubicin combination. These benefits translated into improved antitumor activity in patient-derived xenograft models in vivo in both the platinum-sensitive (IMGN853/carboplatin) and platinum-resistant (IMGN853/pegylated liposomal doxorubicin) settings. IMGN853 co-treatment also improved the in vivo efficacy of bevacizumab in platinum-resistant EOC models, with combination regimens causing significant regressions and complete responses in the majority of tumor-bearing mice. Histological analysis of OV-90 ovarian xenograft tumors revealed that concurrent administration of IMGN853 and bevacizumab caused rapid disruption of tumor microvasculature and extensive necrosis, underscoring the superior bioactivity profile of the combination regimen. Overall, these demonstrations of combinatorial benefit conferred by the addition of the first FRα-targeting ADC to established therapies provide a compelling framework for the potential application of IMGN853 in the treatment of patients with advanced ovarian cancer.
The antinociceptive effects of intraplantar injections of 2‐arachidonoyl glycerol are mediated by cannabinoid CB2receptors (2006)

Locally injected 2-AG and URB602 decreased pain behaviour in a dose-dependent manner in an inflammatory model of pain. The antinociceptive effect of 2-AG was mediated by the CB(2) receptor.
Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker (2011)

Hematopoietic tissues in acute myeloid leukemia (AML) patients contain both leukemia stem cells (LSC) and residual normal hematopoietic stem cells (HSC). The ability to prospectively separate residual HSC from LSC would enable important scientific and clinical investigation including the possibility of purged autologous hematopoietic cell transplants. We report here the identification of TIM3 as an AML stem cell surface marker more highly expressed on multiple specimens of AML LSC than on normal bone marrow HSC. TIM3 expression was detected in all cytogenetic subgroups of AML, but was significantly higher in AML-associated with core binding factor translocations or mutations in CEBPA. By assessing engraftment in NOD/SCID/IL2Rγ-null mice, we determined that HSC function resides predominantly in the TIM3-negative fraction of normal bone marrow, whereas LSC function from multiple AML specimens resides predominantly in the TIM3-positive compartment. Significantly, differential TIM3 expression enabled the prospective separation of HSC from LSC in the majority of AML specimens with detectable residual HSC function.
In vivo autofluorescence spectroscopy of oral premalignant and malignant lesions: Distortion of fluorescence intensity by submucous fibrosis (2003)

Autofluorescence spectroscopy can be used to diagnose EH, ED, and SCC lesions in non-OSF patients but not in OSF patients.
Materials aspects of copper interconnection technology for semiconductor applications (2001)

Metallisations, which form key components on semiconductor devices and circuits, have gone through many changes since the first discoveries of these devices. Metallisation applications include contacts to semiconductor surfaces, gate on metal oxide semiconductor devices, and interconnections, each defining its own criteria for the application of a given metal or metallisation scheme. This paper focusses only on the interconnection application. A brief examination of the desired properties of an interconnection metal, especially Cu, and a discussion of the materials aspect of this application has been carried out, including whether copper satisfies the needs of today and will satisfy them in the future.