gebhart/patrepeval huggingface dataset:
Activation of Protein Kinase C Augments Peptide Release from Rat Sensory Neurons (1996)

To determine whether protein kinase C (PKC) mediates release of peptides from sensory neurons, we examined the effects of altering PKC activity on resting and evoked release of substance P (SP) and calcitonin gene-related peptide (CGRP). Exposing rat sensory neurons in culture to 10 or 50 nM phorbol 12,13-dibutyrate (PDBu) significantly increased SP and CGRP release at least 10-fold above resting levels, whereas the inactive 4alpha-PDBu analogue at 100 nM had no effect on release. Furthermore, 100 nM bradykinin increased peptide release approximately fivefold. Down-regulation of PKC significantly attenuated the release of peptides evoked by either PDBu or bradykinin. PDBu at 1 nM or 1-oleoyl-2-acetyl-sn-glycerol at 50 microM did not alter resting release of peptides, but augmented potassium- and capsaicin-stimulated release of both SP and CGRP approximately twofold. This sensitizing action of PKC activators on peptide release was significantly reduced by PKC down-regulation or by pretreating cultures with 10 nM staurosporine. These results establish that activation of PKC is important in the regulation of peptide release from sensory neurons. The PKC-induced enhancement of peptide release may be a mechanism underlying the neuronal sensitization that produces hyperalgesia.
Plastin 3 Is a Protective Modifier of Autosomal Recessive Spinal Muscular Atrophy (2008)

Homozygous deletion of the survival motor neuron 1 gene (SMN1) causes spinal muscular atrophy (SMA), the most frequent genetic cause of early childhood lethality. In rare instances, however, individuals are asymptomatic despite carrying the same SMN1 mutations as their affected siblings, thereby suggesting the influence of modifier genes. We discovered that unaffected SMN1-deleted females exhibit significantly higher expression of plastin 3 (PLS3) than their SMA-affected counterparts. We demonstrated that PLS3 is important for axonogenesis through increasing the F-actin level. Overexpression of PLS3 rescued the axon length and outgrowth defects associated with SMN down-regulation in motor neurons of SMA mouse embryos and in zebrafish. Our study suggests that defects in axonogenesis are the major cause of SMA, thereby opening new therapeutic options for SMA and similar neuromuscular diseases.
Patterns of organization in auditory cortex (1985)

Previous work has described recently developed techniques that are contributing to advances in the study of the auditory system; some of these techniques have been used to make significant progress in this field. This paper includes a discussion of the tonotopic and binaural organizations of the auditory cortex (especially area AI), the neuronal connections between auditory cortical fields, the relationships between the functional maps and the connectivity patterns, the nature of binaural processing within AI, and the techniques used to assess the structural and functional properties of this portion of the central auditory pathway.
Long-Term Evaluation of HIV Antigen and Antibodies to p24 and gp41 in Patients with Hemophilia (1987)

To investigate the relation between human immunodeficiency virus (HIV) antigenemia and clinical manifestations of HIV infections, we studied 96 patients with hemophilia who were positive for HIV antibody, for a median of 34 months. Every 4 to 10 months a clinical and laboratory examination was performed and serum samples were tested for three HIV markers: HIV antigen, antibody to p24, and antibody to gp41. Twenty-two subjects (23 percent) were found to be positive for HIV antigen: 8 were positive upon entry and remained so (Group 1), and 14 became positive during the study, 4 to 26 months after HIV antibody appeared (seroconversion), 13 of whom remained positive for HIV antigen (Group 2). Most subjects positive for HIV antigen had low or undetectable titers of antibody to p24, whereas the antibody titer to gp41 remained high. In Group 2, patients with low p24 antibody titers had further decreases in their titers before or at the time HIV antigen appeared. Once present, HIV antigen persisted and tended to increase in concentration. In contrast to Group 3 (negative for HIV antigen, low anti-p24 titer) and 4 (negative for HIV antigen, high anti-p24 titer), the groups positive for HIV antigen had significantly higher incidences of acquired immunodeficiency syndrome (P = 0.05), immunodeficiency-related infections (P less than 0.001), and immune thrombocytopenia (P = 0.001), and had more severe disease as measured by the Walter Reed staging system (P less than 0.001). In this study, HIV antigen appeared to be a better predictive marker of HIV-related complications than the absolute T4+ count. These results suggest that HIV antigenemia indicates a poor clinical prognosis.
Pseudomembraneous enterocolitis: mechanism for restoring floral homeostasis. (1981)

Over an 18-year period 16 patients with pseudomembraneous enterocolitis were treated by restoration of floral homeostasis by administration of fecal enemas when standard accepted forms of therapy had failed to resolve the disease. Thirteen of the patients responded dramatically, with decreases in diarrhea, temperature, white blood cell counts, and a rapid convalesence. Of the three patients who died, two did not have the pseudomembrane at death, and one had involvement of the small bowel. No ill effects from the fecal enemas were noted. The observation of the pseudomembrane involving only the right half of the colon in a patient with a diverting transverse colostomy indicates that the disease is a contact mucositis.
Deep Compression: Compressing Deep Neural Networks with Pruning, Trained Quantization and Huffman Coding (2015)

Neural networks are both computationally intensive and memory intensive, making them difficult to deploy on embedded systems with limited hardware resources. To address this limitation, we introduce "deep compression", a three stage pipeline: pruning, trained quantization and Huffman coding, that work together to reduce the storage requirement of neural networks by 35x to 49x without affecting their accuracy. Our method first prunes the network by learning only the important connections. Next, we quantize the weights to enforce weight sharing, finally, we apply Huffman coding. After the first two steps we retrain the network to fine tune the remaining connections and the quantized centroids. Pruning, reduces the number of connections by 9x to 13x; Quantization then reduces the number of bits that represent each connection from 32 to 5. On the ImageNet dataset, our method reduced the storage required by AlexNet by 35x, from 240MB to 6.9MB, without loss of accuracy. Our method reduced the size of VGG-16 by 49x from 552MB to 11.3MB, again with no loss of accuracy. This allows fitting the model into on-chip SRAM cache rather than off-chip DRAM memory. Our compression method also facilitates the use of complex neural networks in mobile applications where application size and download bandwidth are constrained. Benchmarked on CPU, GPU and mobile GPU, compressed network has 3x to 4x layerwise speedup and 3x to 7x better energy efficiency.
Assessment of Cytotoxicity Using Electric Cell−Substrate Impedance Sensing:  Concentration and Time Response Function Approach (2002)

This paper describes a simple and convenient method to measure the concentration and time response function f (C,t) of cells exposed to a toxicant by electric cell-substrate impedance sensing. Attachment and spreading of fibroblastic V79 cells cultured on small gold electrodes precoated with fibronectin were detected as electrical resistance changes. With this method, chemical cytotoxicity was easily screened by observing the response function of attached cells in the presence of inhibitor. The cytotoxicities of three test models, cadmium chloride, sodium arsenate, and benzalkonium chloride, were quantified by measuring the percentage inhibition as a function of the inhibitor concentration. The half-inhibition concentration, the required concentration to achieve 50% inhibition, derived from the response function agreed well with the results obtained using the standard neutral red assay.
Sub-Nyquist acquisition and constrained reconstruction in time resolved angiography (2011)

In 1980 DSA provided a real time series of digitally processed angiographic images that facilitated and reduced the risk of angiographic procedures. This technique has become an enabling technology for interventional radiology. Initially it was hoped that intravenous DSA could eliminate the need for arterial injections. However the 2D nature of the images resulted in overlap of vessels and repeat injections were often required. Ultimately the use of smaller arterial catheters and reduced iodine injections resulted in significant reduction in complications. During the next two decades time resolved MR DSA angiographic methods were developed that produced time series of 3D images. These 4D displays were initially limited by tradeoffs in temporal and spatial resolution when acquisitions obeying the Nyquist criteria were employed. Then substantial progress was made in the implementation of undersampled non-Cartesian acquisitions such as VIPR and constrained reconstruction methods such as HYPR, which removed this tradeoff and restored SNR usually lost by accelerated techniques. Recently, undersampled acquisition and constrained reconstruction have been applied to generate time series of 3D x-ray DSA volumes reconstructed using rotational C-arm acquisition completing a 30 year evolution from DSA to 4D DSA. These 4D DSA volumes provide a flexible series of roadmaps for interventional procedures and solve the problem of vessel overlap for intravenous angiography. Full time-dependent behavior can be visualized in three dimensions. When a biplane system is used, 4D fluoroscopy is also possible, enabling the interventionalist to track devices in vascular structures from any angle without moving the C-arm gantrys. Constrained reconstruction methods have proved useful in a broad range of medical imaging applications, where substantial acquisition accelerations and dose reductions have been reported.
High speed, scalable, and accurate implementation of packet fair queueing algorithms in ATM networks (2002)

The fluid generalized processor sharing (GPS) algorithm has desirable properties for integrated services networks and many packet fair queueing (PFQ) algorithms have been proposed to approximate GPS. However, there have been few high speed implementations of PFQ algorithms that can support large number of sessions with diverse rate requirements and at the same time maintain all the important properties of GPS. The implementation cost of a PFQ algorithm is determined by two components: (1) computation of the system virtual time function and (2) maintaining the relative ordering of the packets via their timestamps in a priority queue mechanism. While most of the recently proposed PFQ algorithms reduce the complexity of computing the system virtual time function, the complexity of maintaining the priority queue, and therefore the overall complexity of implementing PFQ, is still a function of the number of active sessions. In addition, while reducing the algorithmic or asymptotic complexity has been the focus of most analysis, to run at high speed, it is also important to reduce the complexity of basic operations. In this paper, we develop techniques to reduce both types of complexities. In particular, we present a novel grouping architecture for implementing PFQ with an algorithmic complexity that is a function of the number of distinct rates supported, but independent of the number of sessions in the system.
Evidence for several higher order structural elements in ribosomal RNA. (1989)

Comparative analysis of small subunit ribosomal RNA sequences suggests the existence of two new higher order interactions: (i) a double-helical structure involving positions 505-507 and 524-526 (Escherichia coli numbering) and (ii) an interaction between the region of position 130 and the helix located approximately between positions 180 and 195. In the first of these, one of the strands of the helix exists in the bulge loop, and the other strand exists in the terminal loop of a previously recognized compound helix involving positions 500-545. Therefore, the new structure formally represents a pseudoknot. In the second, the insertion/deletion of a nucleotide in the vicinity of position 130 correlates with the length of the helix in the 180-195 region, the latter having a 3-base-pair stalk when the base in question is deleted and a stalk of approximately 10 pairs when it is inserted.
Association of p120, a tyrosine kinase substrate, with E-cadherin/catenin complexes. (1995)

p120 was originally identified as a substrate of pp60src and several receptor tyrosine kinases, but its function is not known. Recent studies revealed that this protein shows homology to a group of proteins, beta-catenin/Armadillo and plakoglobin (gamma-catenin), which are associated with the cell adhesion molecules cadherins. In this study, we examined whether p120 is associated with E-cadherin using the human carcinoma cell line HT29, as well as other cell lines, which express both of these proteins. When proteins that copurified with E-cadherin were analyzed, not only alpha-catenin, beta-catenin, and plakoglobin but also p120 were detected. Conversely, immunoprecipitates of p120 contained E-cadherin and all the catenins, although a large subpopulation of p120 was not associated with E-cadherin. Analysis of these immunoprecipitates suggests that 20% or less of the extractable E-cadherin is associated with p120. When p120 immunoprecipitation was performed with cell lysates depleted of E-cadherin, beta-catenin was no longer coprecipitated, and the amount of plakoglobin copurified was greatly reduced. This finding suggests that there are various forms of p120 complexes, including p120/E-cadherin/beta-catenin and p120/E-cadherin/plakoglobin complexes; this association profile contrasts with the mutually exclusive association of beta-catenin and plakoglobin with cadherins. When the COOH-terminal catenin binding site was truncated from E-cadherin, not only beta-catenin but also p120 did not coprecipitate with this mutated E-cadherin. Immunocytological studies showed that p120 colocalized with E-cadherin at cell-cell contact sites, even after non-ionic detergent extraction. Treatment of cells with hepatocyte growth factor/scatter factor altered the level of tyrosine phosphorylation of p120 as well as of beta-catenin and plakoglobin. These results suggest that p120 associates with E-cadherin at its COOH-terminal region, but the mechanism for this association differs from that for the association of beta-catenin and plakoglobin with E-cadherin, and thus, that p120, whose function could be modulated by growth factors, may play a unique role in regulation of the cadherin-catenin adhesion system.
Discovery of Chiral Catalysts through Ligand Diversity: Ti‐Catalyzed Enantioselective Addition of TMSCN to meso Epoxides (1996)

Abstract For corrigendum see DOI: 10.1002/anie.199619951
Novel Potent and Selective Central 5-HT3 Receptor Ligands Provided with Different Intrinsic Efficacy. 2. Molecular Basis of the Intrinsic Efficacy of Arylpiperazine Derivatives at the Central 5-HT3 Receptors (1999)

Novel 5-HT3 receptor ligands were designed and synthesized with the aim of obtaining deeper insight into the molecular basis of the intrinsic efficacy of arylpiperazines interacting with the central 5-HT3 receptor. The newly synthesized compounds and some previously published compounds belonging to the same class of heteroarylpiperazines were tested for their potential ability to displace [3H]granisetron from rat cortical membranes. These 5-HT3 receptor binding studies revealed subnanomolar affinity in several of the compounds under study. The most active ligands were quipazine derivatives bearing a phenyl group in the 4-position and various oxygenated alkyl side chains in the 3-position of the quinoline nucleus. Qualitative and theoretical quantitative structure-affinity relationship studies were carried out, and the interaction model for the 5-HT3 ligands related to quipazine with their receptor, proposed in part 1 of the present work, was updated to incorporate the latest data. The potential 5-HT3 agonist/antagonist activity of 12 selected compounds was assessed in vitro on the 5-HT3 receptor-dependent [14C]guanidinium uptake in NG 108-15 cells. Their intrinsic efficacy ranged from the 5-HT3 full agonist properties of compounds 7a and 8h, i to those of partial agonists 10a,d and antagonists 8b,d,e, and 9c, d,h,i. The comparison between these functional data and those relative to the previously described compounds suggested that in this class of 5-HT3 ligands the intrinsic efficacy is modulated in a rather subtle manner by the steric features of the heteroaryl moiety.
Non-viral approaches to gene therapy (1995)

There have been rapid advances in the development of non-viral techniques for gene transfer. Although viruses are highly evolved to infect mammalian cells, they have several limitations. The general theme is to mimic the advantageous components of viral systems whilst separating them from their limiting functions. The systems described here are broadly divided into true non-viral techniques and viral-assisted technologies. The merits and limitations of each method are presented, and examples of their application to current developments in gene therapy are discussed. At present no preferred technique has emerged as a clear favourite for non-viral delivery. Further refinement of the technology with particular emphasis on achieving long-term gene expression is required before initiating clinical trials of non-viral gene delivery.
Nucleotide sequences of the envelope genes of two isolates of feline leukemia virus subgroup B (1984)

We determined the nucleotide sequences of the envelope genes of the Snyder-Theilen and Gardner-Arnstein isolates of feline leukemia virus subgroup B. Comparison of the deduced amino acid sequences of the envelope gene products revealed regions of sequence divergence, which we relate to structural features of the viral protein. We also examined nucleotide sequences within the long terminal repeats of these related isolates of feline leukemia virus subgroup B.
High-Efficiency Single-Quantum-Well Green and Yellow-Green Light-Emitting Diodes on Semipolar (20\bar21) GaN Substrates (2010)

We demonstrate high-efficiency green and yellow-green single-quantum-well light-emitting diodes (LEDs) grown on semipolar (2021) GaN substrates by metal organic chemical vapor deposition. The output power and external quantum efficiency at a driving current of 20 mA under a pulsed condition with a 10% duty cycle are 9.9 mW and 20.4% for the green LED and 5.7 mW and 12.6% for the yellow-green LED, respectively. The electroluminescence linewidth narrowing, which is related to the band-filling effect caused by potential fluctuations, is not observed.
Documenting Chinese tourists' motivation patterns (2015)

Researchers and destination marketers are aware of the need to understand the motives of Chinese tourists. Using exploratory factor analysis the study investigated the cross-cultural applicability of the Travel Career Pattern approach to motivation (Pearce & Lee, 2005) for an extensive Chinese sample. The demographic factors of age and travel experience and their links to the motivational factors were analyzed and interpreted. Solid support for the original motive factors and their alignment in patterns of core, mid-level, and lesser importance were established. The subtle nuances in the Chinese tourists' motivational patterns and the way some motives were reconstituted arguably reflected culturally specific ways of thought and the evolution of Chinese travel patterns. The specific roles of age and travel experience variables were influential in shaping the motivation patterns. These directions in building the travel career approach to motivation offer promise for further analysis and refinement in many contexts.
이온 강도가 다른 용액내에서 이탄표면의 (泥炭表面) 하전특성 (荷電特性 ) (1987)

The distribution of the surface charges in two kinds of peats and their physico-chemical properties have a been studied by means of the potentiometric titration and by ion adsorption in different strength of electrolytes. The organic matter contents were 43.3% and 53.7% in Yeong Yang peat and Peong Tack peat, respectively. Their X-ray diffractograms showed that quartz was dominant in both peats, and illite, kaolinite, hydrated-halloysite and feldspars were contained in a trace. Total acidic group contents was 1.257me/g in Poeng Tack peat that was a little more than of Peong Yang heat were pKa values of Yeong Yang and Poeng Tack peat were 13.1 and 12.65, respectively. The titration curves at different ionic strength of electrolytes crossed at pH 3.9 and 4.4 in Yeong Yang peat, and pH 3.8 and 4.0 in Peong Tack peat. The pH ranges of suspensions when the net surfacecharge of the peats varied from poaitive. to negative value were pH 4.55∼5.20 (NaCl) and pH 3.95∼5.70 (CaCl₂) in Yeong Fang peat, and pH 4.15∼5.40 (NaCl) and pH 3.80∼4.15(CaCl₂) in Peong Tack peat. Therefore it is apparent that the zero point of charge of these peats was about pH 4.0.
Base Excision Repair (2013)

Base excision repair (BER) corrects DNA damage from oxidation, deamination and alkylation. Such base lesions cause little distortion to the DNA helix structure. BER is initiated by a DNA glycosylase that recognizes and removes the damaged base, leaving an abasic site that is further processed by short-patch repair or long-patch repair that largely uses different proteins to complete BER. At least 11 distinct mammalian DNA glycosylases are known, each recognizing a few related lesions, frequently with some overlap in specificities. Impressively, the damaged bases are rapidly identified in a vast excess of normal bases, without a supply of energy. BER protects against cancer, aging, and neurodegeneration and takes place both in nuclei and mitochondria. More recently, an important role of uracil-DNA glycosylase UNG2 in adaptive immunity was revealed. Furthermore, other DNA glycosylases may have important roles in epigenetics, thus expanding the repertoire of BER proteins.
Structural Studies of Adeno-Associated Virus Serotype 8 Capsid Transitions Associated with Endosomal Trafficking (2011)

The single-stranded DNA (ssDNA) parvoviruses enter host cells through receptor-mediated endocytosis, and infection depends on processing in the early to late endosome as well as in the lysosome prior to nuclear entry for replication. However, the mechanisms of capsid endosomal processing, including the effects of low pH, are poorly understood. To gain insight into the structural transitions required for this essential step in infection, the crystal structures of empty and green fluorescent protein (GFP) gene-packaged adeno-associated virus serotype 8 (AAV8) have been determined at pH values of 6.0, 5.5, and 4.0 and then at pH 7.5 after incubation at pH 4.0, mimicking the conditions encountered during endocytic trafficking. While the capsid viral protein (VP) topologies of all the structures were similar, significant amino acid side chain conformational rearrangements were observed on (i) the interior surface of the capsid under the icosahedral 3-fold axis near ordered nucleic acid density that was lost concomitant with the conformational change as pH was reduced and (ii) the exterior capsid surface close to the icosahedral 2-fold depression. The 3-fold change is consistent with DNA release from an ordering interaction on the inside surface of the capsid at low pH values and suggests transitions that likely trigger the capsid for genome uncoating. The surface change results in disruption of VP-VP interface interactions and a decrease in buried surface area between VP monomers. This disruption points to capsid destabilization which may (i) release VP1 amino acids for its phospholipase A2 function for endosomal escape and nuclear localization signals for nuclear targeting and (ii) trigger genome uncoating.