gebhart/patrepeval huggingface dataset:
Optimal discrimination and classification of neuronal action potential waveforms from multiunit, multichannel recordings using software-based linear filters (1994)

We describe advanced protocols for the discrimination and classification of neuronal spike waveforms within multichannel electrophysiological recordings. The programs are capable of detecting and classifying the spikes from multiple, simultaneously active neurons, even in situations where there is a high degree of spike waveform superposition on the recording channels. The protocols are based on the derivation of an optimal linear filter for each individual neuron. Each filter is tuned to selectively respond to the spike waveform generated by the corresponding neuron, and to attenuate noise and the spike waveforms from all other neurons. The protocol is essentially an extension of earlier work [1], [13], [18]. However, the protocols extend the power and utility of the original implementations in two significant respects. First, a general single-pass automatic template estimation algorithm was derived and implemented. Second, the filters were implemented within a software environment providing a greatly enhanced functional organization and user interface. The utility of the analysis approach was demonstrated on samples of multiunit electrophysiological recordings from the cricket abdominal nerve cord.
Macrophage-dependent stimulation of T cell-depleted spleen cells by Clostridium difficile toxin A and calcium ionophore (1990)

Clostridium difficile toxin A causes severe intestinal inflammation and fluid secretion in rabbit ileum and is chemotactic for neutrophils in vitro. The mechanism of intestinal injury produced by toxin A appears to involve direct epithelial cell damage as well as recruitment of an inflammatory cell response. The current study was undertaken to determine if toxin A can directly stimulate a proliferative response in lymphocytes. Highly purified toxin A, in the presence of the calcium ionophore, ionomycin, stimulated substantial [3H]thymidine incorporation by murine splenic lymphocytes, which was maximal at 10(-9) M toxin A and 800 ng/ml ionomycin. Removal of T cells with anti-Thy-1.2 antibody plus complement had no effect on the proliferative response induced by toxin A. However, [3H]thymidine incorporation in response to toxin A was significantly inhibited (P less than 0.001) by the removal of macrophages from splenocyte suspensions and was restored by the addition of peritoneal macrophages or cell-free supernatant from toxin A-treated macrophage cultures. Analysis of the toxin A-treated macrophage supernatants showed high levels of IL-1, but not IL-2 or IL-4. The combination of recombinant IL-1 plus ionomycin was found to stimulate [3H]thymidine incorporation by T cell-depleted splenic lymphocytes. These results suggest that toxin A stimulates the release of IL-1, and possibly other factors, from macrophages which can costimulate murine B lymphocytes.
Autoimmune responses against acetylcholine receptor: T and B cell collaboration and manipulation by synthetic peptides. (1997)

Myasthenia gravis (MG) and experimental autoimmune MG (EAMG) are induced by antibodies (Abs) against self acetylcholine receptor (AChR). We have mapped the T and B cell epitopes on AChR alpha subunit in human MG and in EAMG-susceptible (C57BL/6, B6) and nonsusceptible mouse strains. A T-cell epitope within residues alpha 146-162 (P14) of Torpedo californica (t)AChR plays an important role in EAMG pathogenesis of the auto Ab-induced disease. P14-specific T cell (P14Th) lines from tAChR-primed B6 mice activated, in vivo and in vitro, tAChR-primed B cells that secreted anti-AChR Abs directed against four other regions on the tAChR alpha-chain, but not against P14 itself. P14Th cells are pathogenic because they help B cells that make Abs against a conserved tAChR region (t alpha 122-150) involved in ACh binding. These Abs cross-react with region alpha 122-150 of mouse (m)AChR, thereby disrupting its normal physiological function. Thus, a T cell epitope not recognized by Abs plays an active role in B cell responses against other epitopes on the protein. We have found that in B6, the MHC region 62-76 of I-A beta(b) is involved in the presentation of P14 to T cells. Anti-peptide Abs, prepared in BALB/c, were found to inhibit in vitro the proliferation of P14-specific T-cells. Furthermore, this MHC peptide elicited Abs in B6 mice and we are investigating whether immunization of B6 with this peptide, before priming with tAChR, would suppress in vivo the T-cell response to the epitope in P14. Thus, these preliminary results would suggest that immunization with the MHC peptide might be employed for control of the autoimmune disease.
Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae (1998)

Previous characterization of the Saccharomyces cerevisiae Spt4, Spt5, and Spt6 proteins suggested that these proteins act as transcription factors that modify chromatin structure. In this work, we report new genetic and biochemical studies of Spt4, Spt5, and Spt6 that reveal a role for these factors in transcription elongation. We have isolated conditional mutations in SPT5 that can be suppressed in an allele-specific manner by mutations in the two largest subunits of RNA polymerase II (Pol II). Strikingly, one of these RNA Pol II mutants is defective for transcription elongation and the others cause phenotypes consistent with an elongation defect. In addition, we show that spt4, spt5, and spt6 mutants themselves have phenotypes suggesting defects in transcription elongation in vivo. Consistent with these findings, we show that Spt5 is physically associated with RNA Pol II in vivo, and have identified a region of sequence similarity between Spt5 and NusG, an Escherichia coli transcription elongation factor that binds directly to RNA polymerase. Finally, we show that Spt4 and Spt5 are tightly associated in a complex that does not contain Spt6. These results, taken together with the biochemical identification of a human Spt4-Spt5 complex as a transcription elongation factor (Wada et al. 1998), provide strong evidence that these factors are important for transcription elongation in vivo.
Increased IL-1β, IL-8, and IL-17 mRNA Expression in Blood Mononuclear Cells Observed in a Prospective Ischemic Stroke Study (1999)

A longitudinal study of patients with ischemic stroke revealed systemic increases of levels of IL-1beta, IL-8, and IL-17 that correlated with Scandinavian Stroke Scale scores. IL-8 levels were further increased in cerebrospinal fluid.
Therapeutic promise and challenges of targeting DLL4/NOTCH1 (2011)

DLL4-mediated NOTCH1 signaling represents an essential pathway for vascular development and has emerged as an attractive target for angiogenesis-based cancer therapies. However, newly reported toxicity findings raise safety concerns of chronic pathway blockade. Lessons learned from the development of γ-secretase inhibitors (GSIs) might offer insights into how to safely harness this important signaling pathway.
Adenovirus Hexon Protein Is a Potent Adjuvant for Activation of a Cellular Immune Response (2002)

The capacity of recombinant adenoviruses (rAd) to induce immunization against their transgene products has been well documented. In the present study, we evaluated the vaccinal adjuvant role of rAd independently of its vector function. BALB/c mice received one subcutaneous injection of a mixture of six lipopeptides (LP6) used as a model immunogen, along with AdE1 degrees (10(9) particles), a first-generation rAd empty vector. Although coinjected with a suboptimal dose of lipopeptides, AdE1 degrees significantly improved the effectiveness of the vaccination, even in the absence of booster immunization. In contrast to mice that received LP6 alone or LP6 plus a mock adjuvant, mice injected with AdE1 degrees plus LP6 developed both a polyspecific T-helper type 1 response and an effector CD8 T-cell response specific to at least two class I-restricted epitopes. The helper response was still observed when immunization was performed using LP6 plus a mixture of soluble capsid components released from detergent-disrupted virions. When mice were immunized with LP6 and each individual capsid component, i.e., hexon, penton base, or fiber, the results obtained suggested that hexon protein was responsible for the adjuvant effect exerted by disrupted Ad particles on the helper response to the immunogen. Our results thus have some important implications not only in vaccinology but also for gene therapy using rAd vectors.
A New Delay Additive for Hydraulic Fracturing Fluids (2007)

Abstract A new delay agent has been developed which has hybrid functionality versus previously-reported materials. It delays viscosity development in fracturing fluids based on guar derivatives crosslinked with a variety of common zirconate and titanate crosslinkers under a wide range of pH. The viscosity development can be optimized by adjusting the concentrations of polymer, crosslinker, and delay additive to give the desired profile for a given hydraulic fracturing application.
Prognostic Role of Neutrophil-to-Lymphocyte Ratio in Solid Tumors: A Systematic Review and Meta-Analysis (2014)

A high NLR is associated with an adverse OS in many solid tumors. The NLR is a readily available and inexpensive biomarker, and its addition to established prognostic scores for clinical decision making warrants further investigation.
Hypoglycemic effect of aqueous extract of seabuckthorn (Hippophae rhamnoides L.) seed residues in streptozotocin‐induced diabetic rats (2009)

An extract of seabuckthorn (Hippophae rhamnoides L.) seed residues has been shown to possess hypoglycemic and hypolipidemic properties in normal mice. The present study investigated the effects of an aqueous extract of seabuckthorn seed residues (ASSR) on serum glucose, lipid profiles and antioxidant parameters in streptozotocin-induced diabetic rats. Male Sprague-Dawley rats were divided into four groups: a normal control group; diabetic control group; diabetic groups supplemented with 5 mg/kg body weight glibenclamide (reference drug) and 400 mg/kg body weight ASSR. Diabetes in rats was induced by intraperitoneal injection of streptozotocin (45 mg/kg body weight). Vehicle (distilled water), glibenclamide and ASSR were administered orally to normal and diabetic rats once a day lasting for 4 weeks. The data showed that administration of ASSR significantly lowered the serum glucose, triglyceride and nitric oxide levels in diabetic rats. Moreover, ASSR treatment also increased serum superoxide dismutase activity and glutathione level markedly. These results show that ASSR has hypoglycemic, hypotriglyceridemic and antioxidant effects in streptozotocin-induced diabetic rats, suggesting that ASSR supplementation can be useful in preventing diabetic complications associated with hyperlipidemia and oxidative stress.
Simple Hydrazone Building Blocks for Complicated Functional Materials (2014)

CONSPECTUS: The ability to selectively and effectively control various molecular processes via specific stimuli is a hallmark of the complexity of biological systems. The development of synthetic structures that can mimic such processes, even on the fundamental level, is one of the main goals of supramolecular chemistry. Having this in mind, there has been a foray of research in the past two decades aimed at developing molecular architectures, whose properties can be modulated using external inputs. In most cases, reversible conformational, configurational, or translational motions, as well as bond formation or cleavage reactions have been used in such modulations, which are usually initiated using inputs including, irradiation, metalation, or changes in pH. This research activity has led to the development of a diverse array of impressive adaptive systems that have been used in showcasing the potential of molecular switches and machines. That being said, there are still numerous obstacles to be tackled in the field, ranging from difficulties in getting molecular switches to communicate and work together to complications in integrating and interfacing them with surfaces and bulk materials. Addressing these challenges will necessitate the development of creative new approaches in the field, the improvement of the currently available materials, and the discovery of new molecular switches. This Account will describe how our quest to design new molecular switches has led us to the development of structurally simple systems that can be used for complicated functions. Our focus on the modular and tunable hydrazone functional group was instigated by the desire to simplify the structure and design of molecular switches in order to circumvent multistep synthesis. We hypothesized that by avoiding this synthetic bottleneck, which is one of the factors that hinder fast progress in the field, we can expedite the development and deployment of our adaptive materials. It should be noted though that designing structurally simple switches cannot be an end goal by itself! Therefore, we showed that our molecules can be used in applications that are beyond a simple molecular switching event (i.e., the control of the photophysical properties of liquid crystals and multistep switching cascades). While focusing on these switches, we discovered that the hydrazones can be easily transformed, using straightforward one-step reactions, into visible light activated azo switches, and two different families of fluorophores that can be used in sensing applications. These findings demonstrate that our approach of developing simple systems for sophisticated functions is not limited to the field of molecular switches and machines but can also encompass other adaptive materials.
Fast aggregation of colloidal silica (1990)

The aggregation kinetics of colloidal silica is highly dependent on conditions such as the pH and salt concentration. In this paper we investigate the aggregation of colloidal silica under conditions that promote rapid growth, contrasting our findings with earlier investigations of the slow growth of silica. A number of interesting effects are observed, including power-law growth of the mean aggregate radius, dependence of the aggregation rate on concentration and the chemical nature of the salt used, a reduced aggregate fractal dimension, fragmentation of the fast aggregates under changing solution conditions, and shear-induced restructuring of aggregates. Finally, we present evidence that the fractal dimension of aggregates is not strongly universal, but depends weakly on such factors as the solution concentration. We conclude that although the diffusion-limited cluster-cluster aggregation model gives a good first-order description of rapid aggregation, real systems exhibit richer behavior that is not given to such a facile interpretation.
Conclusion (2012)

This chapter contains sections titled: A Hot and Cold Running Genius Science Must Slow Its Speed
ChemInform Abstract: Applications of Lewis Acids for the Efficient Syntheses of Diltiazem, Cephems, and Taxoids (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Transmission-Line Properties of Parallel Strips Separated by a Dielectric Sheet (1965)

A transmission line is made of a symmetrical pair of strip conductors, or a single strip and a ground plane, on opposite faces of a sheet of dielectric material. There is computed, to a close approximation, the relations among the dielectric constant of the sheet, the effective dielectric constant of the sheet and the empty space, the shape ratio, and the wave resistance, for the entire range of possible values. These relations are summarized in a graphical chart covering the range of practical interest. The computation is based on conformal mapping of the dielectric boundary on coordinates such that its effect can be most closely evaluated by simple principles. All relations are approximated in terms of ordinary functions (exponential and hyperbolic). Of particular interest is the effective filling fraction of the dielectric material, which depends mainly on the shape ratio and only slightly on the dielectric constant. Explicit formulas are given for analysis or synthesis.
Structures of a New Type of Indoloditerpene, Petromindole, and a New Asterriquinone Derivative, PM-53, from the Ascostromata of Petromyces muricatus. (1997)

A new typw of indoloditerpene, petromindole (1), and a new asterriquinone derivative, PM-53 (2), were isolated from the ascostromata of Petromyces muricatus, along with bisindolylbenzenoids, petromurins A (3)-D (6). The structure of 1 was suggested by spectroscopic data and confirmed by an X-ray crystallographic analysis, while that of 2 was determined by analyses of the various NMR spectra.
Deletion of an Amino-Terminal Sequence Stabilizes β-Catenin In Vivo and Promotes Hyperphosphorylation of the Adenomatous Polyposis Coli Tumor Suppressor Protein (1996)

Regulation of cell adhesion and cell signaling by beta-catenin occurs through a mechanism likely involving the targeted degradation of the protein. Deletional analysis was used to generate a beta-catenin refractory to rapid turnover and to examine its effects on complexes containing either cadherin or the adenomatous polyposis coli (APC) protein. The results show that amino-terminal deletion of beta-catenin results in a protein with increased stability that acts in a dominant fashion with respect to wild-type beta-catenin. Constitutive expression in AtT20 cells of a beta-catenin lacking 89 N-terminal amino acids (deltaN89beta-catenin) resulted in severely reduced levels of the more labile wild-type beta-catenin. The mutant beta-catenin was expressed at endogenous levels but displaced the vast majority of wild-type beta-catenin associated with N-cadherin. The deltaN89beta-catenin accumulated on the APC protein to a level 10-fold over that of wild-type beta-catenin and recruited a kinase into the APC complex. The kinase was highly active toward APC in vitro and promoted a sodium dodecyl sulfate gel band shift that was also evident for endogenous APC from cells expressing the mutant beta-catenin. Unlike wild-type beta-catenin, which partitions solely as part of a high-molecular-weight complex, the deltaN89 mutant protein also fractionated as a stable monomer, indicating that it had escaped the requirement to associate with other proteins. That similar N-terminal mutants of beta-catenin have been implicated in cellular transformation suggests that their abnormal association with APC may, in part, be responsible for this phenotype.
Long-Term Treatment with Eicosapentaenoic Acid Augments Both Nitric Oxide-Mediated and Non-Nitric Oxide-Mediated Endothelium-Dependent Forearm Vasodilatation in Patients with Coronary Artery Disease (1999)

Long-term treatment with eicosapentaenoic acid (EPA) is known to improve impaired endothelium-dependent relaxations of atherosclerotic blood vessels in animals and humans. However, it remains to be determined which mechanisms are involved in this beneficial effect of EPA. In this study, we investigated our hypothesis that EPA improves both nitric oxide (NO)-mediated and non-NO-mediated endothelium-dependent vasodilatation in patients with coronary artery disease. The study included eight patients with documented coronary artery disease. The forearm vascular responses to the endothelium-dependent vasodilator acetylcholine and substance P were examined before and after intraarterial infusion of NG-monomethyl-L-arginine (L-NMMA). Same measurements were repeated after the treatment with EPA (1,800 mg/day) for 6 weeks. The long-term treatment with EPA augmented forearm blood-flow response to both acetylcholine and substance P. Furthermore, acute administration of L-NMMA significantly inhibited the EPA-induced augmented response to acetylcholine but not that to substance P. The forearm vascular response to sodium nitroprusside was unchanged by the EPA treatment. These results indicate that long-term treatment with EPA augments both NO-dependent and non-NO-dependent endothelium-dependent forearm vasodilatation in patients with coronary artery disease. Thus the beneficial effects of EPA appear to extend to non-NO-dependent mechanism(s).
Multivariate Analysis and Visualization of Splicing Correlations in Single-Gene Transcriptomes (2007)

Patterns of splicing correlations are revealed, which span a broad range of interaction order and change in development. The methods have a broad scope of applicability, beyond the single gene--including, for example, multiple gene interactions in the complete transcriptome.
Induced Multilineage Differentiation of Chicken Embryonic Germ Cells via Embryoid Body Formation (2009)

Although the pluripotent and proliferative capacity of embryonic germ (EG) cells is thought to be equivalent to that of embryonic stem (ES) cells, there has been far less attention focused on the potential use of EG cells for applications in developing novel strategies of tissue transplantation in the treatment of degenerative diseases. In this study, EG cells were derived from primordial germ cells (PGCs) of genital ridges of 4-day-old chicken embryos. These cells satisfied the criteria previously used for defining chicken EG cells by using the expression of markers characteristic to ES cells. When injected subcutaneously, chicken EG cells could form teratomas that enable differentiation into a wide range of tissue types of all three primary cell lineages including neural cells, cartilage, forming bone, adipocytes, blood vessels, smooth muscle, and secretory epithelia in the recipients. Furthermore, cells in embryoid bodies (EBs) expressed lineage-specific markers of three germ layers and could be induced to differentiate into more advanced stages of various committed cell types, including dopamine and cholinergic neurons, astrocytes, oligodendrocytes, adipocytes, and hepatocytes, which were demonstrated by immunocytochemical staining or RT-PCR analysis. These findings support the multilineage differentiation capability of chicken pluripotent EG cells, thus confirming the presumption that chicken embryos may be used as a potential model for better understanding the mechanisms of tissue-specific differentiation and regeneration that will help to devise strategies based on the transplantation of stem cell-derived tissues for restoring function to damaged or diseased tissues.
Reliable quantum computers (1998)

The new field of quantum error correction has developed spectacularly since its origin less than two years ago. Encoded quantum information can be protected from errors that arise due to uncontrolled interactions with the environment. Recovery from errors can work effectively even if occasional mistakes occur during the recovery procedure. Furthermore, encoded quantum information can be processed without serious propagation of errors. Hence, an arbitrarily long quantum computation can be performed reliably, provided that the average probability of error per quantum gate is less than a certain critical value, the accuracy threshold. A quantum computer storing about 10⁶ qubits, with a probability of error per quantum gate of order 10⁻⁶, would be a formidable factoring engine. Even a smaller less–accurate quantum computer would be able to perform many useful tasks. &#13;\n&#13;\nThis paper is based on a talk presented at the ITP Conference on Quantum Coherence and Decoherence, 15 to 18 December 1996.