gebhart/patrepeval huggingface dataset:
Hyperactive antifreeze protein in flounder species (2005)

The recent discovery of a large hyperactive antifreeze protein in the blood plasma of winter flounder has helped explain why this fish does not freeze in icy seawater. The previously known, smaller and much less active type I antifreeze proteins cannot by themselves protect the flounder down to the freezing point of seawater. The relationship between the large and small antifreezes has yet to be established, but they do share alanine-richness (> 60%) and extensive alpha-helicity. Here we have examined two other righteye flounder species for the presence of the hyperactive antifreeze, which may have escaped prior detection because of its lability. Such a protein is indeed present in the yellowtail flounder judging by its size, amino acid composition and N-terminal sequence, along with the previously characterized type I antifreeze proteins. An ortholog is also present in American plaice based on the above criteria and its high specific antifreeze activity. This protein was purified and shown to be almost fully alpha-helical, highly asymmetrical, and susceptible to denaturation at room temperature. It is the only detectable antifreeze protein in the blood plasma of the American plaice. Because this species appears to lack the smaller type I antifreeze proteins, the latter may have evolved by descent from the larger antifreeze.
Application of capillary electrophoresis, liquid chromatography, electrospray‐mass spectrometry and matrix‐assisted laser desorption/ionization ‐ time of flight ‐ mass spectrometry to the characterization of recombinant human erythropoietin (1998)

High performance capillary electrophoresis (HPCE), high performance liquid chromatography (HPLC), matrix-assisted laser desorption/ionization - time of flight - mass spectrometry (MALDI-TOF-MS), on-line CE-electrospray ionization-mass spectrometry (CE-ESI-MS) and on-line LC-ESI-MS have been employed to characterize a heterogeneous glycoprotein, recombinant human erythropoietin (rHuEPO) expressed from Chinese hamster ovary (CHO) cells. The analysis was demonstrated through two specific levels of detail: the intact protein and tryptic digests of the protein. Six glycoforms of rHuEPO were separated by HPCE; seventeen tryptic fragments in a total of 21 nonglycosylated and glycosylated peptides were characterized; the O-linked glycopeptides were analyzed directly by CE-ESI-MS and LC-ESI-MS. In particular, four glycans of O-acetylation of sialic acid were identified in the O-linked glycosylated fragments. The molecular weight of rHuEPO was accurately determined by MALDI-TOF-MS.
Autophagy in Neurodegenerative Diseases: From Mechanism to Therapeutic Approach (2015)

Autophagy is a lysosome-dependent intracellular degradation process that allows recycling of cytoplasmic constituents into bioenergetic and biosynthetic materials for maintenance of homeostasis. Since the function of autophagy is particularly important in various stress conditions, perturbation of autophagy can lead to cellular dysfunction and diseases. Accumulation of abnormal protein aggregates, a common cause of neurodegenerative diseases, can be reduced through autophagic degradation. Recent studies have revealed defects in autophagy in most cases of neurodegenerative disorders. Moreover, deregulated excessive autophagy can also cause neurodegeneration. Thus, healthy activation of autophagy is essential for therapeutic approaches in neurodegenerative diseases and many autophagy-regulating compounds are under development for therapeutic purposes. This review describes the overall role of autophagy in neurodegeneration, focusing on various therapeutic strategies for modulating specific stages of autophagy and on the current status of drug development.
Robotic Mobile System's Performance-Based MIMO-OFDM Technology (2009)

In this paper, a predistortion neural network (PDNN) architecture has been imposed to the Sniffer Mobile Robot (SNFRbot) that is based on spatial multiplexed wireless Orthogonal Frequency Division Multiplexing (OFDM) transmission technology. This proposal is used to improve the system performance by combating one of the main drawbacks that is encountered by OFDM technology; Peak-to-Average Power Ratio (PAPR). Simulation results show that using PDNN resulted in better PAPR performance than the previously published work that is based on linear coding, such as Low Density Parity Check (LDPC) codes and turbo encoding whether using flat fading channel or a Doppler spread channel.
Design of an Interferometric Spectrometer for Environmental Surveillance (1994)

This thesis describes the design of a field-portable spectrometer for spectral measurements in the visible and very near infrared from natural targets such as vegetation and the atmosphere. The instrument is a non-scanning version of the Fourier transform spectrometer (FTS) where the moving mirror is replaced by either a fixed, tilted mirror (holographic FTS, HFTS) or a fixed, Littrow-mounted grating (heterodyned holographic FTS, HHS, often referred to as spatially heterodyned spectrometer, SHS). This allows for a simpler and more rugged mechanical design than that of classical FTS instruments as well as a greatly reduced power consumption, all important advantages for a portable instrument for field use.
Diffusion of Oxygen Through Activated Sludge Flocs: Experimental Measurement, Modeling, and Implications for Simultaneous Nitrification and Denitrification (2007)

Diffusion of dissolved oxygen through activated sludge flocs was studied, as it represents a potential mechanism for simultaneous nitrification and denitrification in activated sludge systems. Dissolved oxygen profiles through six floc particles collected at different times from a full-scale activated sludge plant demonstrated that that the dissolved oxygen concentration declines through all floc particles. For larger floc particles (2-mm diameter and greater), the dissolved oxygen concentration reached near-zero values at depths depending on process operating conditions. A mathematical model based on diffusion of dissolved oxygen, organic substrate (methanol), ammonia, nitrite, and nitrate through a spherical floc and consumption of dissolved oxygen by heterotrophs and autotrophs accurately predicted the dissolved oxygen profile and required adjustment of only one model parameter--the concentration of heterotrophs. A different dissolved oxygen decline pattern was exhibited for the smaller floc particles characterized, with the dissolved oxygen reaching a non-zero plateau toward the center of the floc. This pattern was not reproduced with the mathematical model developed and suggests that additional mechanisms are responsible for the transport of dissolved oxygen into the center of these flocs. Implications of these results regarding the occurrence of simultaneous nitrification and denitrification include consideration of the factors that affect floc size and distribution (simultaneous nitrification and denitrification is maximized with larger floc particles), coupling of the International Water Association (London) activated models to predict activated sludge composition with diffusion models to consider intrafloc effects, and the effects of substrate diffusion on the apparent half-saturation constant for various substrates in activated sludge systems.
A Concise and Provably Informative Multi‐Scale Signature Based on Heat Diffusion (2009)

Abstract We propose a novel point signature based on the properties of the heat diffusion process on a shape. Our signature, called the Heat Kernel Signature (or HKS), is obtained by restricting the well‐known heat kernel to the temporal domain. Remarkably we show that under certain mild assumptions, HKS captures all of the information contained in the heat kernel, and characterizes the shape up to isometry. This means that the restriction to the temporal domain, on the one hand, makes HKS much more concise and easily commensurable, while on the other hand, it preserves all of the information about the intrinsic geometry of the shape. In addition, HKS inherits many useful properties from the heat kernel, which means, in particular, that it is stable under perturbations of the shape. Our signature also provides a natural and efficiently computable multi‐scale way to capture information about neighborhoods of a given point, which can be extremely useful in many applications. To demonstrate the practical relevance of our signature, we present several methods for non‐rigid multi‐scale matching based on the HKS and use it to detect repeated structure within the same shape and across a collection of shapes.
In Vivo Study of the Inflammatory Modulating Effects of Low‐level Laser Therapy on iNOS Expression Using Bioluminescence Imaging (2005)

This study was designed to demonstrate that bioluminescence imaging (BLI) can be used as a new tool to evaluate the effects of low-level laser therapy (LLLT) during in vivo inflammatory process. Here, the efficacy of LLLT in modulating inducible nitric oxide synthase (iNOS) expression using different therapeutic wavelengths was determined using transgenic animals with the luciferase gene under control of the iNOS gene expression. Thirty transgenic mice, FVB/N-Tg(iNOS-luc)Xen, were allocated randomly to one of four experimental groups treated with different wavelengths (lambda = 635, 785, 808 and 905 nm) or a control group (nontreated). Inflammation was induced by intra-articular injection of zymosan A in both knee joints. Laser treatment (25 mW cm(-2), 200 s, 5 J cm(-2)) was applied to the knees 15 min after inflammation induction. Measurements of iNOS expression were performed at various times (0, 3, 5, 7, 9 and 24 h) by measuring the bioluminescence signal using a highly sensitive charge-coupled device (CCD) camera. The results showed a significant increase in BLI signal after irradiation with 635 nm laser when compared to the nonirradiated animals and the other LLLT-treated groups, indicating wavelength dependence of LLLT effects on iNOS expression during the inflammatory process, and thus demonstrating an action spectrum of iNOS gene expression following LLLT in vivo that can be detected by BLI. Histological analysis was also performed and demonstrated the presence of fewer inflammatory cells in the synovial joints of mice irradiated with 635 nm compared with nonirradiated knee joints.
Differentially Expressed Genes in Metastatic Advanced Egyptian Bladder Cancer (2015)

The present study identified some genes, that can be used as molecular biomarkers or target genes in Egyptian bladder cancer patients.
A 24.7dBm all-digital RF transmitter for multimode broadband applications in 40nm CMOS (2013)

Recently, digitizing RF circuits has attracted extensive attention by exploiting high speed transistors offered in nano-scale CMOS processes. The digitally-assisted or digital-intensive RF transceivers not only benefit from technology scaling in terms of power efficiency and die area, but also improve functional flexibility. The polar architecture is well recognized for digital RF transmitters [1,2,4,5], while the bandwidth expansion resulting from Cartesian-to-polar transformation makes it difficult to comply with high-speed wireless standards. Open-loop phase interpolation topology was employed in an outphasing transmitter [3], where 12dBm output power was demonstrated with 40MHz 802.11n signal. In this work, an all-digital RF transmitter with direct quadrature architecture is presented to address the need for broadband wireless connectivity.
Quality of Life in Persons with Human Immunodeficiency Virus Infection: Measurement by the Medical Outcomes Study Instrument (1992)

The MOS survey is a reliable measure of quality of life for patients with HIV infection. These patients tend to have low scores, suggesting validity of the survey. The MOS survey is extremely sensitive to the effect of symptoms, which suggests that it might be useful as a quality-of-life indicator for AIDS clinical drug trials.
Caprolactam (2011)

Abstract The article contains sections titled: 1. History 2. Physical Properties 3. Chemical Properties 4. Production 4.1. Processes via Cyclohexanone 4.1.1. Cyclohexanone Oxime 4.1.2. Beckmann Rearrangement to Caprolactam 4.1.3. Improvement of the Oximation Process 4.1.4. Gas‐Phase or Catalytic Rearrangement of Cyclohexanone Oxime 4.1.5. Modified Oximation and Beckmann Rearrangement 4.2. Photooximation 4.3. Production from Toluene 4.4. Recovery from Nylon‐6 Waste 4.5. Former Commercial Routes 4.6. New Routes in Development 4.7. Environmental Protection 5. Quality Specifications 6. Analysis 7. Storage and Transportation 8. Economic Aspects 9. Toxicology
Multiwavelength self-healing ring transparent networks (2002)

This paper describes the use of optical cross-connect nodes (as used in RACE project MWTN) for implementing multiwavelength unidirectional and bi-directional self-healing ring networks. A comparison of these two ring structures is presented in terms of the number of wavelength required to satisfy a uniform random traffic demand. Two protection strategies based on the electronic self-healing ring principles are applied to the wavelength division multiplexed (WDM) networks. It is shown how the bi-directional WDM rings can be protected against failure by means of spare wavelengths as well as spare fibres. The proposed network protection schemes are accomplished within the optical network with failure restoration transparent to the layers below. The ring networks described are also flexible and adaptable to changes in traffic patterns.
Gene silencing in alveolar type II cells using cell-specific promoter in vitro and in vivo (2004)

RNA interference (RNAi) is a sequence-specific post-transcriptional gene silencing process. Although it is widely used in the loss-of-function studies, none of the current RNAi technologies can achieve cell-specific gene silencing. The lack of cell specificity limits its usage in vivo. Here, we report a cell-specific RNAi system using an alveolar epithelial type II cell-specific promoter--the surfactant protein C (SP-C) promoter. We show that the SP-C-driven small hairpin RNAs specifically depress the expression of the exogenous reporter (enhanced green fluorescent protein) and endogenous genes (lamin A/C and annexin A2) in alveolar type II cells, but not other lung cells, using cell and organ culture in vitro as well as in vivo. The present study provides an efficient strategy in silencing a gene in one type of cell without interfering with other cell systems, and may have a significant impact on RNAi therapy.
Comparing Fifty Natural Languages and Twelve Genetic Languages Using Word Embedding Language Divergence (WELD) as a Quantitative Measure of Language Distance (2016)

We introduce a new measure of distance between languages based on word embedding, called word embedding language divergence (WELD). WELD is defined as divergence between unified similarity distribution of words between languages. Using such a measure, we perform language comparison for fifty natural languages and twelve genetic languages. Our natural language dataset is a collection of sentence-aligned parallel corpora from bible translations for fifty languages spanning a variety of language families. Although we use parallel corpora, which guarantees having the same content in all languages, interestingly in many cases languages within the same family cluster together. In addition to natural languages, we perform language comparison for the coding regions in the genomes of 12 different organisms (4 plants, 6 animals, and two human subjects). Our result confirms a significant high-level difference in the genetic language model of humans/animals versus plants. The proposed method is a step toward defining a quantitative measure of similarity between languages, with applications in languages classification, genre identification, dialect identification, and evaluation of translations.
Muscle-specific Calpain, p94, Responsible for Limb Girdle Muscular Dystrophy Type 2A, Associates with Connectin through IS2, a p94-specific Sequence (1995)

p94, a muscle-specific member of calpain family, is unique in that it undergoes rapid and exhaustive autolysis with a half-life of less than 1 h resulting in its disappearance from muscle. Recently, p94 was shown to be responsible for limb girdle muscular dystrophy type 2A. To elucidate the muscular proteolytic system mediated by p94 and to solve the mystery of its unusually rapid autolysis, we searched for p94-binding proteins by the two-hybrid system. Although calpain small subunit plays a crucial role for regulation of ubiquitous calpains, it did not associate with p94. After a screening of skeletal muscle library, connectin (or titin), a gigantic filamentous protein spanning the M- to Z-lines of muscle sarcomere, was found to bind to p94 through a p94-specific region, IS2. The connectin-insoluble fraction of washed myofibrils contained full-length intact p94, suggesting that connectin regulates p94 activity.
Molecular characterization of a novel human PDZ domain protein with homology to INAD from Drosophila melanogaster (1997)

PDZ domains are thought to act as protein-binding modules mediating the clustering of membrane and membrane-associated proteins. The INAD protein has been shown to interact via a PDZ domain with the calcium channel TRP which contributes to capacitative calcium entry into Drosophila photoreceptor cells. We have cloned the cDNA of a human INAD-Like protein (hINADL) of 1524 amino acids in length containing at least five PDZ domains. Additionally, two truncated versions hINADL(delta304) and hINADL(delta853) were identified. hInadl transcripts of differing size are expressed in various tissues including brain, where transcripts are abundant in the cerebellum.
The NMDA Receptor (1995)

2) Agonists and competitive antagonists: structure, activity and molecular modelling studies 3) Non-competitive antagonists of N-methyl-D-aspartate 4) Molecular pharmacology of NMDA receptors 5) Molecular biology of NMDA receptors 6) Anatomical, pharmacological, and molecular diversity of native NMDA receptor subtypes 7) The NMDA receptor, its channel, and its modulation by glycine 8) The time-course of NMDA receptor-mediated synaptic currents 9) Activation of NMDA receptors 10) NMDA receptors and their interactions with other excitatory amino acid receptors in synaptic transmission in the mammalian central nervous system 11) The importance of NMDA receptors in the processing of spinal primary afferent input patterns 12 ) The role of NMDA receptors in synaptic integration and the organization of motor patterns 13) NMDA receptors and long-term potentiation in the hippocampus 14) NMDA receptors and developmental plasticity in visual neocortex 15) The role of NMDA receptors in learning and memory 16) Clinical implications of NMDA receptors 17) The NMDA receptor in epilepsy 18) NMDA receptors, neuronal development, and neurodegeneration 19) Competitive NMDA antagonists as drugs 20) Non-competitive NMDA antagonists as drugs 1) The NMDA receptor concept: origins and development
An Antidiabetic Thiazolidinedione Is a High Affinity Ligand for Peroxisome Proliferator-activated Receptor γ (PPARγ) (1995)

Thiazolidinedione derivatives are antidiabetic agents that increase the insulin sensitivity of target tissues in animal models of non-insulin-dependent diabetes mellitus. In vitro, thiazolidinediones promote adipocyte differentiation of preadipocyte and mesenchymal stem cell lines; however, the molecular basis for this adipogenic effect has remained unclear. Here, we report that thiazolidinediones are potent and selective activators of peroxisome proliferator-activated receptor gamma (PPAR gamma), a member of the nuclear receptor superfamily recently shown to function in adipogenesis. The most potent of these agents, BRL49653, binds to PPAR gamma with a Kd of approximately 40 nM. Treatment of pluripotent C3H10T1/2 stem cells with BRL49653 results in efficient differentiation to adipocytes. These data are the first demonstration of a high affinity PPAR ligand and provide strong evidence that PPAR gamma is a molecular target for the adipogenic effects of thiazolidinediones. Furthermore, these data raise the intriguing possibility that PPAR gamma is a target for the therapeutic actions of this class of compounds.
NF-kappaB activation in CD27 signaling: involvement of TNF receptor-associated factors in its signaling and identification of functional region of CD27. (1998)

CD27 belongs to TNF receptor family, and it is unique in this family for its disulfide-linked homodimerization of 55-kDa monomers. In the present study we demonstrate that overexpression of CD27 in 293 cells induces a low level of NF-kappaB activation, and the ligation of the receptor by its corresponding ligand (CD70) augments this signal dramatically. Either TNF receptor-associated factor-2 (TRAF2) or TRAF3 binds to the CD27 molecule from the coimmunoprecipitation experiment. This NF-kappaB activation signal is inhibited by dominant negative TRAF2 or intact TRAF3, indicating that TRAF2 and TRAF3 works as a mediator and an inhibitor, respectively. The activated NF-kappaB complex contains at least two components, p50 and p65, but not p52. All these phenomena have also been observed in the TNF receptor type II, CD30 and CD40 signaling system, indicating that this receptor family uses the common or similar molecules for this signal. Finally, we identified the 13-amino acid alignment in the cytoplasmic region of the CD27 molecule (residues 238-250 amino acids), which is critical for the NF-kappaB activation signal and also for its association with TRAFs. This amino acid alignment contains the EEEG sequence, which is essential for interaction of CD30 or CD40 with TRAFs (TRAF1 and TRAF2, but not TRAF3), and also contains the PIQED sequence, which is similar to PXQXT that is known to be necessary for interaction of TNF receptor II and CD30 with TRAFs (TRAF1, 2, and 3).
Monotelechelic Poly(oxa)norbornenes by Ring-Opening Metathesis Polymerization Using Direct End-Capping and Cross-Metathesis (2009)

Two different methodologies for the synthesis of monotelechelic poly(oxa)norbornenes prepared by living ring-opening metathesis polymerization (ROMP) are presented. The first method, termed direct end-capping, is carried out by adding an internal cis-olefin terminating agent (TA) to the reaction mixture immediately after the completion of the living ROMP reaction. The second method relies on cross metathesis (CM) between a methylene-terminated poly(oxa)norbornene and a cis-olefin TA mediated by the ruthenium olefin metathesis catalyst (H(2)IMes)(Cl)(2)Ru(CH-o-OiPrC(6)H(4)) (H(2)IMes = 1,3-dimesitylimidazolidine-2-ylidene). TAs containing various functional groups, including alcohols, acetates, bromides, a-bromoesters, thioacetates, N-hydroxysuccinimidyl esters and Boc-amines, as well as fluorescein and biotin groups, were synthesized and tested. The direct end-capping method typically resulted in >90% end-functionalization efficiency, while the CM method was nearly as effective for TAs without polar functional groups or significant steric bulk. End-functionalization efficiency values were determined by (1)H NMR spectroscopy.
Local tuning of organic light-emitting diode color by dye droplet application (1998)

We have demonstrated that fluorescent dyes may be introduced into previously fabricated polymer thin films by local application of a dye-containing droplet. The UV fluorescence spectra of the films and the spectra of organic light-emitting diodes made from these films can be successfully tuned by this method. The technique has been implemented by ink-jet printing of the dye droplet.