gebhart/patrepeval huggingface dataset:
Role of Electrical Activity in Horizontal Axon Growth in the Developing Cortex: A Time-Lapse Study Using Optogenetic Stimulation (2013)

During development, layer 2/3 neurons in the neocortex extend their axons horizontally, within the same layers, and stop growing at appropriate locations to form branches and synaptic connections. Firing and synaptic activity are thought to be involved in this process, but how neuronal activity regulates axonal growth is not clear. Here, we studied axonal growth of layer 2/3 neurons by exciting cell bodies or axonal processes in organotypic slice cultures of the rat cortex. For neuronal stimulation and morphological observation, plasmids encoding channelrhodopsin-2 (ChR2) and DsRed were coelectroporated into a small number of layer 2/3 cells. Firing activity induced by photostimulation (475 nm) was confirmed by whole-cell patch recording. Axonal growth was observed by time-lapse confocal microscopy, using a different excitation wavelength (560 nm), at 10-20-min intervals for several hours. During the first week in vitro, when spontaneous neuronal activity is low, DsRed- and ChR2-expressing axons grew at a constant rate. When high-frequency photostimulation (4 or 10 Hz) for 1 min was applied to the soma or axon, most axons paused in their growth. In contrast, lower-frequency stimulation did not elicit this pause behavior. Moreover, in the presence of tetrodotoxin, even high-frequency stimulation did not cause axonal growth to pause. These results indicate that increasing firing activity during development suppresses axon growth, suggesting the importance of neuronal activity for the formation of horizontal connections.
Cultured human retinal pigment epithelial cells express basic fibroblast growth factor and its receptor (1989)

Basic fibroblast growth factor (bFGF) has been implicated in the maintenance of neuronal differentiation, the induction of neovascularization and intravitreal proliferative diseases. We have found that human retinal pigment epithelial (RPE) cells grown in vitro transcribe the bFGF gene and synthesize a peptide that crossreacts with anti-bFGF antibodies. In culture, these cells appear to release activity with biological and biochemical properties similar to bFGF. RPE cells have specific bFGF receptors and proliferate in response to bFGF. Thus, it is possible that the RPE cell is an important source of retinal bFGF and may respond to bFGF in an autocrine manner.
Maintaining privacy on derived objects (2005)

Protecting privacy means to ensure users that access to their personal data complies with their preferences. However, information can be manipulated in order to derive new objects that may disclose part of the original information. Therefore, control of information flow is necessary for guaranteeing privacy protection since users should know and control not only who access their personal data, but also who access information derived from their data. Actually, current approaches for access control do not provide support for managing propagation of information and for representing user preferences.This paper proposes to extend the Flexible Authorization Framework (FAF) in order to automatically verify whether a subject is entitled to process personal data and derive the authorizations associated with the outcome of data processing. In order to control information flow, users may specify the range of authorizations that can be associated with objects derived from their data. The framework guarantees that every "valid" derived object does not disclose more information than users want and preserves the permissions that users want to maintain. To make the discussion more concrete, we illustrate the proposal with a bank case study.
Thymidine salvage in Pseudomonas stutzeri and Pseudomonas aeruginosa provided by heterologous expression of Escherichia coli thymidine kinase gene (1985)

Unlike enteric bacteria, Pseudomonas spp. generally lack thymidine phosphorylase and thymidine kinase activities, thus preventing their utilization of exogenous thymine or thymidine and precluding specific radioactive labeling of their DNA in vivo. To overcome this limitation, a DNA fragment encoding thymidine kinase (EC 2.7.1.21) from Escherichia coli was cloned into pKT230, a small, broad-host-range plasmid derived from plasmid RSF1010. From transformed E. coli colonies, the recombinant plasmid bearing the thymidine kinase gene was conjugally transferred to Pseudomonas stutzeri, Pseudomonas aeruginosa, Pseudomonas mendocina, Pseudomonas alcaligenes, and Pseudomonas pseudoalcaligenes. Thymidine kinase activity was expressed in all of these species, and all gained the ability to incorporate exogenous [2-14C]thymidine into their DNA. Thymidine incorporation into P. stutzeri was enhanced 12-fold more in mutants lacking thymidylate synthetase activity. These mutants produced higher levels of thymidine kinase and were thymidine auxotrophs; thymineless death resulted from removal of thymidine from a growing culture.
A series of six compact fungal transformation vectors containing polylinkers with multiple unique restriction sites (1993)

In comparison with transformation vectors available for use in E. coli or yeast, there has been relatively little development of vectors for use in filamentous fungi. For example, expression yeast vectors carrying polylinkers flanked by promoters and terminators are available for various uses but such vectors have not been in the public domain for researchers working with filamentous fungi.
An emerging role for bromodomain‐containing proteins in chromatin regulation and transcriptional control of adipogenesis (2010)

Transcriptional co-activators, co-repressors and chromatin remodeling machines are essential elements in the transcriptional programs directed by the master adipogenic transcription factor PPARgamma. Many of these components have orthologs in other organisms, where they play roles in development and pattern formation, suggesting new links between cell fate decision-making and adipogenesis. This review focuses on bromodomain-containing protein complexes recently shown to play a critical role in adipogenesis. Deeper understanding of these pathways is likely to have major impact on treatment of obesity-associated diseases, including metabolic syndrome, cardiovascular disease and Type 2 diabetes. The research effort is urgent because the obesity epidemic is serious; the medical community is ill prepared to cope with the anticipated excess morbidity and mortality associated with diet-induced obesity.
Effects of Anabolic-Androgenic Steroids on Muscular Strength (1991)

Anabolic steroids may slightly enhance muscle strength in previously trained athletes. No firm conclusion is possible concerning the efficacy of anabolic steroids in enhancing overall athletic performance. Results for the low steroid dosages studied in the published reports cannot be generalized to steroid-using athletes taking megadose regimens.
Rapid Synthesis of Crystalline Gallium Nitride from Solid Precursors at Atmospheric Pressure (1999)

Highly crystalline hexagonal gallium nitride (GaN) can be formed in a rapid ambient pressure metathesis reaction between GaI3, Li3N, and NH4Cl. An ideal ratio of GaI3:Li3N:NH4Cl produces highly crystalline GaN (Figure, bottom) while a nonideal ratio produces amorphous GaN (Figure, top). After washing, the phase-pure GaN formed exhibits photoluminescence at 3.38 eV consistent with its known band gap and micrometer-sized crystallites.
Automated Repair Service Bureau: Second-Generation Mechanized Loop Testing System-A Distributed Microprocessor Application (1982)

The Mechanized Loop Testing (MLT) system is that part of the Automated Repair Service Bureau that provides automatic acquisition and analysis of electrical test data for customer telephone loops. The MLT-2 system is a second-generation MLT that has as its basic architectural features communication, loop access, and loop test distributed as closely as possible to the point of testing. Architectural components include a wire center-based Loop Testing System (LTS) and a centrally located Data Communication Network (DCN). Each LTS contains communication, access, and test capabilities, and is logically connected by the DCN to each controlling minicomputer (up to 12). The LTS and DCN are each composed of multiple microprocessor-based circuits. The architecture of MLT-2 is presented. Particular attention is given to the subjects of partitioning both hardware and software, to the development of change-tolerant software, and to intrasystem communication capabilities powerful enough to support a large number of distributed processors. In addition, special measurement techniques employed by MLT-2 that take advantage of analog and digital large-scale integration technology are discussed. Operational scenarios are included for an appreciation of how the MLT-2 system works.
Structural characterization of the oligosaccharides of a human monoclonal anti-lipopolysaccharide immunoglobulin M (1998)

The oligosaccharide side chains of a human anti-lipopolysaccharide IgM produced by a human-human-mouse heterohybridoma were analyzed at each of its five conserved N-glycosylation sites. This antibody also has a potential sixth N-glycosylation site in the variable region of its heavy chain which is not glycosylated. The oligosaccharides were released by digestion with various endo- and exoglycosidases and analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and fluorophore-assisted carbohydrate electrophoresis. The antibody has various complex- and hybrid-type oligosaccharide structures at Asn 171, various sialylated complex-type oligosaccharides at Asn 332 and 395, and high-mannose-type oligosaccharides at Asn 402 and 563. Of note is the presence in this human IgM of oligosaccharides containing N-glycolylneuraminic acid and N-acetylneuraminic acid in the ratio of 98:2 as determined using anion-exchange chromatography. Furthermore, we observed oligosaccharide structures containing Gal alpha (1,3)Gal that have not been reported as components of human glycoproteins.
Evaluation of a community‐based cancer support group (1993)

Abstract Stimulated by patient need and encouraged by results from randomized studies in academic centers, many community organizations have initiated cancer support groups in order to improve the psychosocial adjustment of people coping with cancer. For a variety of reasons, little research has been done to evaluate these community support groups. The efficacy of cancer support groups, which has been demonstrated in academic centers, therefore awaits demonstration in community settings. This paper provides process and outcome data from 77 people with cancer who completed an 8‐week support group facilitated by licensed and trained mental health professionals in a local community cancer support organization. Similar to the experience of others, participants were primarily female, of European descent, well‐educated, and relatively young (mean age 50 years, S.D. = 12). As predicted, their self‐reported quality of life (as measured by the Functional Living Index—Cancer) improved significantly, paired t = − 2.06, p &lt; 0.05. Five‐point ratings (poor, fair, good, very good, excellent) were assigned either ‘very good’ or ‘excellent’ for the overall group (90%) and facilitator (87%). More detailed ratings of group and facilitator qualities were consistently and strikingly positive. While facilitators were rated positively and appreciated for their presence, peer support exceeded facilitator skill/input as the primary ingredient noted by participants to be the most helpful aspect of the group. Community‐based cancer support groups appear to provide measurable benefit to participants who complete the group. The benefit is consistent with that demonstrated in randomized studies and emphasizes improvement in coping stimulated by mutual support in a safe environment.
Mixed messages: modulation of inflammation and immune responses by prostaglandins and thromboxanes (2001)

Virtually every organism has evolved mechanisms by which, upon stimulation, lipids are released from plasma membranes and metabolized into mediators capable of changing cellular physiology. As these lipids are present at the first site exposed to external challenge, they provide an ideal substrate for the synthesis of defensive mediators and homeostatic regulators. One such group of lipid mediators is the prostanoids, including the prostaglandins (PGs) and thromboxanes (TXs).

Soon after their initial isolation and characterization, the ability of prostanoids to influence inflammation and immune responses was recognized. For example, administration of prostanoids, either alone or in combination, could reproduce the cardinal signs of inflammation. Because they could induce inflammatory changes when injected into tissue and were present at high levels in inflamed lesions, prostanoids were initially categorized as proinflammatory mediators. As our understanding of prostanoid physiology has evolved, it has become clear that these mediators can act to both promote and inhibit inflammation. Thus, it is more accurate to envision these molecules as part of a complex regulatory network that modulates the actions of immune cells and the surrounding microenvironment. Their overall impact in an individual inflammatory response will depend on several factors, including the level of immune cell activation, the presence of other mediators, and the physiological state of the organism.

Our ability to dissect the role of prostanoids in complex inflammatory responses has been substantially advanced by the recent development of mouse lines with targeted mutations of genes encoding enzymes and receptors in the prostanoid pathway. In this review we will develop the concept that prostanoids are both effectors and regulators of inflammation, emphasizing new information provided by these mouse models.
Estimation of parameters in nonlinear systems using balanced synchronization (2008)

Using synchronization between observations and a model with undetermined parameters is a natural way to complete the specification of the model. The quality of the synchronization, a cost function to be minimized, typically is evaluated by a least squares difference between the data time series and the model time series. If the coupling between the data and the model is too strong, this cost function is small for any data and any model and the variation of the cost function with respect to the parameters of interest is too small to permit selection of an optimal value of the parameters. We introduce two methods for balancing the competing desires of a small cost function for the quality of the synchronization and the numerical ability to determine parameters accurately. One method of "balanced" synchronization adds to the synchronization cost function a requirement that the conditional Lyapunov exponent of the model system, conditioned on being driven by the data remain negative but small in magnitude. The other method allows the coupling between the data and the model to vary in time according to the error in synchronization. This method succeeds because the data and the model exhibit generalized synchronization in the region where the parameters of the model are well determined. Examples are explored which have deterministic chaos with and without noise in the data signal.
Pharmacologic inhibition of JAK-STAT signaling promotes hair growth (2015)

Several forms of hair loss in humans are characterized by the inability of hair follicles to enter the growth phase (anagen) of the hair cycle after being arrested in the resting phase (telogen). Current pharmacologic therapies have been largely unsuccessful in targeting pathways that can be selectively modulated to induce entry into anagen. We show that topical treatment of mouse and human skin with small-molecule inhibitors of the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway results in rapid onset of anagen and subsequent hair growth. We show that JAK inhibition regulates the activation of key hair follicle populations such as the hair germ and improves the inductivity of cultured human dermal papilla cells by controlling a molecular signature enriched in intact, fully inductive dermal papillae. Our findings open new avenues for exploration of JAK-STAT inhibition for promotion of hair growth and highlight the role of this pathway in regulating the activation of hair follicle stem cells.
Identification and Characterization of a New Bocavirus Species in Gorillas (2010)

A novel parvovirus, provisionally named Gorilla Bocavirus species 1 (GBoV1), was identified in four stool samples from Western gorillas (Gorilla gorilla) with acute enteritis. The complete genomic sequence of the new parvovirus revealed three open reading frames (ORFs) with an organization similar to that of known bocaviruses. Phylogenetic analysis using complete capsid and non structural (NS) gene sequence suggested that the new parvovirus is most closely related to human bocaviruses (HBoV). However, the NS ORF is more similar in length to the NS ORF found in canine minute virus and bovine parvovirus than in HBoV. Comparative genetic analysis using GBoV and HBoV genomes enabled characterization of unique splice donor and acceptor sites that appear to be highly conserved among all four HBoV species, and provided evidence for expression of two different NS proteins in all primate bocaviruses. GBoV is the first non-human primate bocavirus identified and provides new insights into the genetic diversity and evolution of this highly prevalent and recently discovered group of parvoviruses.
Memory Capacities for Synaptic and Structural Plasticity (2009)

Neural associative networks with plastic synapses have been proposed as computational models of brain functions and also for applications such as pattern recognition and information retrieval. To guide biological models and optimize technical applications, several definitions of memory capacity have been used to measure the efficiency of associative memory. Here we explain why the currently used performance measures bias the comparison between models and cannot serve as a theoretical benchmark. We introduce fair measures for information-theoretic capacity in associative memory that also provide a theoretical benchmark. In neural networks, two types of manipulating synapses can be discerned: synaptic plasticity, the change in strength of existing synapses, and structural plasticity, the creation and pruning of synapses. One of the new types of memory capacity we introduce permits quantifying how structural plasticity can increase the network efficiency by compressing the network structure, for example, by pruning unused synapses. Specifically, we analyze operating regimes in the Willshaw model in which structural plasticity can compress the network structure and push performance to the theoretical benchmark. The amount C of information stored in each synapse can scale with the logarithm of the network size rather than being constant, as in classical Willshaw and Hopfield nets (< or = ln 2 approximately 0.7). Further, the review contains novel technical material: a capacity analysis of the Willshaw model that rigorously controls for the level of retrieval quality, an analysis for memories with a nonconstant number of active units (where C < or = 1/e ln 2 approximately 0.53), and the analysis of the computational complexity of associative memories with and without network compression.
Single cell trapping and DNA damage analysis using microwell arrays (2010)

With a direct link to cancer, aging, and heritable diseases as well as a critical role in cancer treatment, the importance of DNA damage is well-established. The intense interest in DNA damage in applications ranging from epidemiology to drug development drives an urgent need for robust, high throughput, and inexpensive tools for objective, quantitative DNA damage analysis. We have developed a simple method for high throughput DNA damage measurements that provides information on multiple lesions and pathways. Our method utilizes single cells captured by gravity into a microwell array with DNA damage revealed morphologically by gel electrophoresis. Spatial encoding enables simultaneous assays of multiple experimental conditions performed in parallel with fully automated analysis. This method also enables novel functionalities, including multiplexed labeling for parallel single cell assays, as well as DNA damage measurement in cell aggregates. We have also developed 24- and 96-well versions, which are applicable to high throughput screening. Using this platform, we have quantified DNA repair capacities of individuals with different genetic backgrounds, and compared the efficacy of potential cancer chemotherapeutics as inhibitors of a critical DNA repair enzyme, human AP endonuclease. This platform enables high throughput assessment of multiple DNA repair pathways and subpathways in parallel, thus enabling new strategies for drug discovery, genotoxicity testing, and environmental health.
Dynamic expression changes in vivo of adhesion and costimulatory molecules determine load and pattern of lymphoma liver metastasis. (1996)

Although intradermal primary tumor growth and spontaneous liver metastasis of ESbL-lacZ lymphoma in syngeneic DBA/2 mice are progressive and malignant, they are characterized by a transient plateau period with a constant tumor diameter and a low number of metastasized cells in the liver. This period, which was shown to be immune dependent, was followed by a second expansion phase characterized by a preferential localization of tumor cells in the periportal areas of liver lobules (mosaic phenotype). To elucidate possible mechanisms leading to the plateau period as well as for the mosaic-like metastasis pattern, we investigated, using flow cytometry analysis, alterations in costimulatory and adhesion molecule expression in liver sinusoidal cells as well as in tumor cells isolated directly ex vivo throughout the kinetics of metastasis. In tumor and sinusoidal cells, we found up-regulation in the expression of MHC class II and B7 molecules during the plateau period. These molecules, which facilitate cell-mediated immune responses, were again down-regulated during the final exponential tumor growth and metastasis. In the final expansion phase, in which the mosaic phenotype of liver metastasis is seen, we detected a significant increase of leukocyte function-associated antigen-1/intercellular adhesion molecule-1 expression in both tumor and sinusoidal cells, suggesting tumor cell-sinusoidal cell interactions. vascular cell adhesion molecule-1/very late activated antigen-4 did not show any modification during the whole metastatic process. In vivo application of monoclonal antibodies directed to leukocyte function-associated antigen-1 and intercellular adhesion molecule-1 appeared to block the spread of metastasis, while no effect was seen with monoclonal antibodies directed to vascular cell adhesion molecule-1 and very late activated antigen-4. This study reveals in situ expression changes of cell surface molecules in tumor and host cells during metastasis. The changes seen during the plateau phase and during the second expansion phase differ, suggesting associations with mechanisms of immune control and tumor immune evasion, respectively.
Silencing of Rieske iron–sulfur protein using chemically synthesised siRNA as a potential biopesticide against Plutella xylostella (2011)

This is the first demonstration of the potential use of chemically synthesised siRNA in the development of new biopesticides as a mitochondrial electron transport inhibitor.