gebhart/patrepeval huggingface dataset:
Speech dereverberation via maximum-kurtosis subband adaptive filtering (2002)

This paper presents an efficient algorithm for high-quality speech capture in applications such as hands-free teleconferencing or voice recording by personal computers. We process the microphone signals by a subband adaptive filtering structure using a modulated complex lapped transform (MCLT), in which the subband filters are adapted to maximize the kurtosis of the linear prediction (LP) residual of the reconstructed speech. In this way, we attain good solutions to the problem of blind speech dereverberation. Experimental results with actual data, as well as with artificially difficult reverberant situations, show very good performance, both in terms of a significant reduction of the perceived reverberation, as well as improvement in spectral fidelity.
Human induced pluripotent stem cells are a novel source of neural progenitor cells (iNPCs) that migrate and integrate in the rodent spinal cord (2014)

Transplantation of human neural progenitor cells (NPCs) into the brain or spinal cord to replace lost cells, modulate the injury environment, or create a permissive milieu to protect and regenerate host neurons is a promising therapeutic strategy for neurological diseases. Deriving NPCs from human fetal tissue is feasible, although problematic issues include limited sources and ethical concerns. Here we describe a new and abundant source of NPCs derived from human induced pluripotent stem cells (iPSCs). A novel chopping technique was used to transform adherent iPSCs into free-floating spheres that were easy to maintain and were expandable (EZ spheres) (Ebert et al. [2013] Stem Cell Res 10:417-427). These EZ spheres could be differentiated towards NPC spheres with a spinal cord phenotype using a combination of all-trans retinoic acid (RA) and epidermal growth factor (EGF) and fibroblast growth factor-2 (FGF-2) mitogens. Suspension cultures of NPCs derived from human iPSCs or fetal tissue have similar characteristics, although they were not similar when grown as adherent cells. In addition, iPSC-derived NPCs (iNPCs) survived grafting into the spinal cord of athymic nude rats with no signs of overgrowth and with a very similar profile to human fetal-derived NPCs (fNPCs). These results suggest that human iNPCs behave like fNPCs and could thus be a valuable alternative for cellular regenerative therapies of neurological diseases.
Role of Disulfide Bonds in Acrp30/Adiponectin Structure and Signaling Specificity (2003)

Acrp30/adiponectin is an adipocyte-derived serum protein with important roles in regulation of lipid and glucose metabolism, but which of its isoforms are biologically active remains controversial. We addressed this issue by first characterizing the structure of each individual Acrp30 oligomer and the determinants responsible for multimer formation. Freeze etch electron microscopy showed the trimer to exhibit a ball-and- stick-like structure containing a large globular sphere, an extended collagen stalk, and a smaller sphere on the opposite end of the stalk. The hexamer consists of two adjacent trimeric globular domains and a single stalk composed of collagen domains from two trimers. Although not necessary for trimer formation or stability, two of the three monomers in an Acrp30 trimer are covalently linked by a disulfide bond between cysteine residues at position 22. In contrast, assembly of hexameric and higher molecular weight (HMW) forms of Acrp30 depends upon formation of Cys22-mediated disulfide bonds because their reduction with dithiothreitol or substitution of Cys22 with alanine led exclusively to trimers. HMW and hexamer isoforms of Acrp30 activated NF-kappaB in C2C12 cells, but trimers, either natural, formed by reduction of Acrp30 hexamer, or formed by the C22A mutant, did not. In contrast, incubation of isolated rat extensor digitorum longus with naturally formed Acrp30 trimers or trimeric C22A Acrp30 led to increased phosphorylation of AMP-activated protein kinase-alpha at Thr172 and its activation. Hexameric and HMW Acrp30 could not activate AMP-activated protein kinase. Thus, trimeric and HMW/hexameric Acrp30 activate different signal transduction pathways, and Acrp30 represents a novel example of the control of ligand signaling via changes in its oligomerization state.
Type I growth factor receptors: current status and future work. (1998)

The type 1 family of growth factor receptors consists of the epidermal growth factor receptor (EGFR), and ErbB-2, ErbB-3 and ErbB-4. Six ligands are known to bind directly to EGFR, none (at present) to ErbB-2, and a family of ligands collectively called the neuregulins bind to both ErbB-3 and ErbB-4. It is now apparent that the receptors function in various heterodimeric pairs, depending on their concentrations, the concentrations of particular ligands in the environment and some intrinsic degree of dimer selectivity. Overexpression of EGFR, ErbB-2 and ErbB-3 has been found commonly in solid human tumours. ErbB-4 has not yet been examined. The EGFR is also activated by various mutations in brain tumours and possibly in other tumour types. These changes appear to be one of the causes of malignant transformation. They may also provide information regarding the course of disease and response to current treatments. Finally, they are targets for a variety of new forms of treatment being developed in the laboratory, in preclinical models and in a few cases in clinical trials.
Activation of Protein Kinase C by Phorbol 12-Myristate 13-Acetate suppresses the growth of lung cancer cells through KLF6 induction (2009)

Phorbol 12-myristate 13-acetate (PMA) modulates cell proliferation and survival by activating several intracellular signaling pathways. Protein kinase C (PKC) plays a key role in PMA-induced growth arrest of non-small cell lung cancer (NSCLC) cells. Kruppel-like transcription factor 6 (KLF6), which is associated with negative control of cell proliferation, is downregulated in many cancers, including NSCLC. In this study, we found that KLF6 is downregulated in 17 lung cancer cell lines and in cells representing early stages of lung cancer development. Moreover, PMA induced cell growth arrest through KLF6 induction in H358 NSCLC cells. The increase in KLF6 by PMA was associated with upregulation of the cyclin-dependent kinase inhibitors (CDKIs) p21(WAF1/CIP1) and p27(KIP1). In addition, inhibition of PKC or JNK activation decreased PMA-induced KLF6 induction and activation of PKC alone by Bryostatin-1 and Thymeleatoxin increased KLF6 levels. Moreover, siRNA-mediated knockdown of KLF6 reduced PMA-induced cell growth inhibition concomitantly with decreased expression of both p21(WAF1/CIP1) and p27(KIP1), and in accordance, overexpression of KLF6 alone upregulated both CDKIs protein levels. Our results demonstrate the induction of the tumor suppressor KLF6 following PKC activation and its importance for PMA-mediated cancer cell growth arrest.
Role of Cyclooxygenase 2 in Acute Spinal Cord Injury (1998)

Cyclooxygenase, or prostaglandin G/H synthase, is the rate-limiting step in the production of prostaglandins. A new isoform, cyclooxygenase-2 (COX-2), has been cloned that is induced during inflammation in leukocytes and by synaptic activity in neurons. The objectives of this study are to determine the nature of COX-2 expression in normal and traumatized rat spinal cord, and to determine the effects of selective COX-2 inhibition on functional recovery following spinal cord injury. Using a weight-drop model of spinal cord injury, COX-2 mRNA expression was studied with in situ hybridization. COX-2 protein expression was examined by immunohistochemistry and Western analysis. Finally, using the highly selective COX-2 inhibitor, 1-[(4-methylsufonyl)phenyl]-3-tri-fluro-methyl-5-[(4-flur o)phenyl]prazole (SC58125), the effect of COX-2 inhibition on functional outcome following a spinal cord injury was determined. COX-2 was expressed in the normal adult rat spinal cord. COX-2 mRNA and protein production were increased following injury with increases in COX-2 mRNA production detectable at 2 h following injury. Increased levels of COX-2 protein were detectable for at least 48 h following traumatic spinal cord injury. Selective inhibition of COX-2 activity with SC58125 resulted in improved mean Basso, Beattie, and Bresnahan scores in animals with 12.5- and 25-g/cm spinal cord injuries; however, the effect was significant only for the 12.5g/cm injury group (p=0.0001 vs. p=0.0643 in the 25-g/cm group). These data demonstrate that COX-2 mRNA and protein expression are induced by spinal cord injury, and that selective inhibition of COX-2 improves functional outcome following experimental spinal cord injury.
The impact of molecular biology on neuroscience (1999)

How our brains work is one of the major unsolved problems of biology. This paper describes some of the techniques of molecular biology that are already being used to study the brains of animals. Mainly as a result of the human genome project many new techniques will soon become available which could decisively influence the progress of neuroscience. I suggest that neuroscientists should tell molecular biologists what their difficulties are, in the hope that this will stimulate the production of useful new biological tools.
Bunch: a clustering tool for the recovery and maintenance of software system structures (1999)

Software systems are typically modified in order to extend or change their functionality, improve their performance, port them to different platforms, and so on. For developers, it is crucial to understand the structure of a system before attempting to modify it. The structure of a system, however, may not be apparent to new developers, because the design documentation is non-existent or, worse, inconsistent with the implementation. This problem could be alleviated if developers were somehow able to produce high-level system decomposition descriptions from the low-level structures present in the source code. We have developed a clustering tool called Bunch that creates a system decomposition automatically by treating clustering as an optimization problem. The paper describes the extensions made to Bunch in response to feedback we received from users. The most important extension, in terms of the quality of results and execution efficiency, is a feature that enables the integration of designer knowledge about the system structure into an otherwise fully automatic clustering process. We use a case study to show how our new features simplified the task of extracting the subsystem structure of a medium size program, while exposing an interesting design flaw in the process.
Electroporation Gene Therapy Preclinical and Clinical Trials for Melanoma (2010)

In vivo electroporation (EP) is a versatile delivery method for gene transfer which can be applied to any accessible tissue. Delivery of plasmid DNA encoding therapeutic genes or cDNAs with in vivo EP has been tested extensively in preclinical melanoma models. Direct delivery to the tumor has been shown to generate a direct antitumor effect. Delivery to alternative sites may generate additional therapeutic options, for example the production of cancer vaccines, the reduction of tumor angiogenesis, or the induction of tumor cell apoptosis. Several of the preclinical therapies tested have a demonstrated therapeutic effect against melanomas. Two immunotherapies have advanced to melanoma clinical trials. Delivery of a plasmid DNA encoding interleukin-12 (IL-12) or interleukin-2 (IL-2) using electroporation was demonstrated to be a safe with no grade 3 or 4 toxicities reported. Delivery of IL-12 with electroporation resulted in significant necrosis of melanoma cells in the majority of treated tumors and significant lymphocytic infiltrate in biopsies from patients in several cohorts. In addition, clinical evidence of responses in untreated lesions suggested the induction of a systemic response following therapy. This review discusses preclinically tested electroporation gene therapies for melanoma with clinical potential and the conversion of these therapies to clinical trials.
Regional Mu Opioid Receptor Regulation of Sensory and Affective Dimensions of Pain (2001)

The endogenous opioid system is involved in stress responses, in the regulation of the experience of pain, and in the action of analgesic opiate drugs. We examined the function of the opioid system and μ-opioid receptors in the brains of healthy human subjects undergoing sustained pain. Sustained pain induced the regional release of endogenous opioids interacting with μ-opioid receptors in a number of cortical and subcortical brain regions. The activation of the μ-opioid receptor system was associated with reductions in the sensory and affective ratings of the pain experience, with distinct neuroanatomical involvements. These data demonstrate the central role of the μ-opioid receptors and their endogenous ligands in the regulation of sensory and affective components of the pain experience.
Down-Regulation of S100A11, a Calcium-Binding Protein, in Human Endometrium May Cause Reproductive Failure (2012)

Endometrial S100A11 is a crucial intermediator in EGF-stimulated embryo adhesion, endometrium receptivity, and immunotolerance via affecting Ca2+ uptake and release from intracellular Ca2+ stores. Down-regulation of S100A11 may cause reproductive failure.
The Addition of Explicit Congestion Notification (ECN) to IP (2001)

This document specifies the incorporation of ECN (Explicit Congestion Notification) to TCP and IP, including ECN&amp;apos;s use of two bits in the IP header. We begin by describing TCP&amp;apos;s use of packet drops as an indication of congestion. Next we explain that with the addition of active queue management (e.g., RED) to the Internet infrastructure, where routers detect congestion before the queue overflows, routers are no longer limited to packet drops as an indication of congestion. Routers can instead set the Congestion Experienced (CE) codepoint in the IP header of packets from ECN-capable transports. We describe when the CE codepoint is to be set in routers, and describe Ramakrishnan, Floyd, Black Proposed Standard [Page 1] draft-ietf-tsvwg-ecn-04 Addition of ECN to IP June 2001 modifications needed to TCP to make it ECN-capable. Modifications to other transport protocols (e.g., unreliable unicast or multicast, reliable multicast, other reliable unicast transport protocols) could be considered as those protocols are developed and advance through the standards process. We also describe in this document the issues involving the use of ECN within IP tunnels, and within IPsec tunnels in particular. One of the guiding principles for this document is that, to the extent possible, the mechanisms specified here be incrementally deployable. One challenge to the principle of incremental deployment has been the prior existence of some IP tunnels that were not compatible with the use of ECN. As ECN becomes deployed, noncompatible IP tunnels will have to be upgraded to conform to this document. This document is intended to obsolete RFC 2481, &amp;quot;A Proposal to add Explicit Congestion Notification (ECN) to IP&amp;quot;, which defined ECN as an Experimental Protocol for the Internet Communit...
Physical and Genetic Interactions of Cytosolic Malate Dehydrogenase with Other Gluconeogenic Enzymes (2003)

A truncated form (deltanMDH2) of yeast cytosolic malate dehydrogenase (MDH2) lacking 12 residues on the amino terminus was found to be inadequate for gluconeogenic function in vivo because the mutant enzyme fails to restore growth of a Deltamdh2 strain on minimal medium with ethanol or acetate as the carbon source. The DeltanMDH2 enzyme was also previously found to be refractory to the rapid glucose-induced inactivation and degradation observed for authentic MDH2. In contrast, kinetic properties measured for purified forms of MDH2 and deltanMDH2 enzymes are very similar. Yeast two-hybrid assays indicate weak interactions between MDH2 and yeast phosphoenolpyruvate carboxykinase (PCK1) and between MDH2 and fructose-1,6-bisphosphatase (FBP1). These interactions are not observed for deltanMDH2, suggesting that differences in cellular function between authentic and truncated forms of MDH2 may be related to their ability to interact with other gluconeogenic enzymes. Additional evidence was obtained for interaction of MDH2 with PCK1 using Hummel-Dreyer gel filtration chromatography, and for interactions of MDH2 with PCK1 and with FBP1 using surface plasmon resonance. Experiments with the latter technique demonstrated a much lower affinity for interaction of deltanMDH2 with PCK1 and no interaction between deltanMDH2 and FBP1. These results suggest that the interactions of MDH2 with other gluconeogenic enzymes are dependent on the amino terminus of the enzyme, and that these interactions are important for gluconeogenic function in vivo.
An artificial neural network model of certain aspects of fighter pilot cognition (2002)

The purpose of the research described was to model the representation of the major cognitive states and decision making processes of a fighter pilot during the intercept phase of a two-versus-two air combat engagement against a single group of adversary aircraft. A highlight of the research was the integration of an artificial neural network (ANN) model into a hybrid structure containing conventional symbolic logic and algorithmic elements. A conceptual framework was developed within which to define the situational awareness (SA) construct. The key design goal for the ANN was to achieve a depth of learning that transcends associative mapping and internalizes the multivariate, nonlinear relationships characteristic of an air combat engagement. An air combat simulation was created to illustrate the model's performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Human Serum Does Not Contain a High Affinity Estrogen-Binding Glycoprotein Different from Sex Hormone-Binding Globulin* (1989)

The mannoglycoprotein fraction obtained by Concanavalin-A chromatography of human serum binds both androgens and estrogens with high affinity. Sex hormone-binding globulin (SHBG) is a component of this fraction that binds both steroids, but the fraction may contain another component that binds only estrogen. We used several chromatographic methods to ascertain whether the estradiol-binding properties of the mannoglycoprotein fraction could be attributed to SHBG or to SHBG and the putative estrogen-binding protein. DEAE-trisacryl, chromatofocusing, and anti-SHBG-immunoglobulin Sepharose chromatography resulted in coelution of the androgen- and estrogen-binding activities. SHBG purified by ligand affinity chromatography as well as immunoaffinity-purified SHBG had estradiol-binding properties similar to those of the crude mannoglycoprotein preparation. These data strongly suggest that 1) SHBG is the only estradiol-binding protein in the mannoglycoprotein fraction obtained by Concanavalin-A chromatography of human serum, and 2) the putative estradiol-binding protein of serum is most likely SHBG.
In Vitro and In Vivo Properties of Adenovirus Vectors with Increased Affinity to CD46 (2008)

Gene transfer vectors containing adenovirus (Ad) serotype 35 (Ad35) fibers have shown promise for cancer and stem cell gene therapy. In this study, we attempted to improve the in vitro and in vivo infection properties of these vectors by increasing their affinity to the Ad35 fiber receptor CD46. We constructed Ad vectors containing either the wild-type Ad35 fiber knob (Ad5/35) or Ad35 knob mutants with 4-fold- and 60-fold-higher affinity to CD46 (Ad5/35+ and Ad5/35++, respectively). In in vitro studies with cell lines, the higher affinities of Ad5/35+ and Ad5/35++ to CD46 did not translate into correspondingly higher transduction efficiencies, regardless of the CD46 receptor density present on cells. However, in vivo, in a mouse model with preestablished CD46(high) liver metastases, intravenous injection of Ad5/35++ resulted in more-efficient tumor cell transduction. We conclude that Ad5/35 vectors with increased affinity to CD46 have an advantage in competing with non-CD46-mediated sequestration of vector particles after intravenous injection.
Anaesthetic Management of Chemodectoma Excision (2007)

Carotid body tumours (CBTs) or chemodectoma are rare non- chromaffin paragangliomas arising from the chemoreceptor cells found at the carotid bifurcation. About 1000 cases have been reported in the literature
Studies of Heterocyclic Compounds. IV. : Ultraviolet Spectra of 2-(2-Furyl)vinylbenzenes and 2-(2-Furyl)vinylfurans (1968)

Ultraviolet spectra of 2-(2-furyl)vinylbenzenes and 2-(2-furyl)vinylfurans were measured, and relationship between the absorption maxima of these derivatives and the Hammett rule was examined. It was found that substituted 4-[2-(5-nitro-2-furyl)vinyl]-benzenes, 2-(4-substituted phenyl)-3-(5-nitro-2-furyl)acrylic acids, and 2-substituted 5-[2-(5-nitro-2-furyl)vinyl]furans followed the Hammetts rule but not 2-(5-substituted 2-furyl)vinylbenzenes.
Resolving file conflicts in the Ficus file system (1994)

Abstract Ficus is a flexible replication facility with optimisticconcurrency control designed to span a wide range
Multiplex Sensing of Protease and Kinase Enzyme Activity via Orthogonal Coupling of Quantum Dot–Peptide Conjugates (2011)

Nanoparticle-based labels are emerging as simpler and more sensitive alternatives to traditional fluorescent small molecules and radioactive reporters in biomarker assays. The determination of biomarker levels is a recommended clinical practice for the assessment of many diseases, and detection of multiple analytes in a single assay, known as multiplexing, can increase predictive accuracy. While multiplexed detection can also simplify assay procedures and reduce systematic variability, combining multiple assays into a single procedure can lead to complications such as substrate cross-reactivity, signal overlap, and loss of sensitivity. By combining the specificity of biomolecular interactions with the tunability of quantum dot optical properties, we have developed a detection system capable of simultaneous evaluation of the activity of two critical enzyme classes, proteases and kinases. We avoid cross-reactivity and signal overlap by synthesizing enzyme-specific peptide sequences with orthogonal terminal functionalization for attachment to quantum dots with distinct emission spectra. Enzyme activity is reported via binding of either gold nanoparticle-peptide conjugates or FRET acceptor dye-labeled antibodies, which mediate changes in quantum dot emission spectra. To the best of our knowledge, this is the first demonstration of the multiplexed sensing of the activity of two different classes of enzymes via a nanoparticle-based activity assay. Using the quantum dot-based assay described herein, we were able to detect the protease activity of urokinase-type plasminogen activator at concentrations ≥ 50 ng/mL and the kinase activity of human epidermal growth factor receptor 2 at concentrations ≥ 7.5 nM, levels that are clinically relevant for determination of breast cancer prognosis. The modular nature of this assay design allows for the detection of different classes of enzymes simultaneously and represents a generic platform for high-throughput enzyme screening in rapid disease diagnosis and drug discovery.