gebhart/patrepeval huggingface dataset:
Sustained increase in hippocampal sharp-wave ripple activity during slow-wave sleep after learning (2008)

High-frequency oscillations, known as sharp-wave/ripple (SPW-R) complexes occurring in hippocampus during slow-wave sleep (SWS), have been proposed to promote synaptic plasticity necessary for memory consolidation. We recorded sleep for 3 h after rats were trained on an odor-reward association task. Learning resulted in an increased number SPW-Rs during the first hour of post-learning SWS. The magnitude of ripple events and their duration were also elevated for up to 2 h after the newly formed memory. Rats that did not learn the discrimination during the training session did not show any change in SPW-Rs. Successful retrieval from remote memory was likewise accompanied by an increase in SPW-R density and magnitude, relative to the previously recorded baseline, but the effects were much shorter lasting and did not include increases in ripple duration and amplitude. A short-lasting increase of ripple activity was also observed when rats were rewarded for performing a motor component of the task only. There were no increases in ripple activity after habituation to the experimental environment. These experiments show that the characteristics of hippocampal high-frequency oscillations during SWS are affected by prior behavioral experience. Associative learning induces robust and sustained (up to 2 h) changes in several SPW-R characteristics, while after retrieval from remote memory or performance of a well-trained procedural aspect of the task, only transient changes in ripple density were induced.
Direct measurement of chlorine penetration into biofilms during disinfection (1994)

Transient chlorine concentration profiles were measured in biofilms during disinfection by use of a microelectrode developed for this investigation. The electrode had a tip diameter of ca. 10 microm and was sensitive to chlorine in the micromolar range. The biofilms contained Pseudomonas aeruginosa and Klebsiella pneumoniae. Chlorine concentrations measured in biofilms were typically only 20% or less of the concentration in the bulk liquid. Complete equilibration with the bulk liquid did not occur during the incubation time of 1 to 2 h. The penetration depth of chlorine into the biofilm and rate of penetration varied depending on the measurement location, reflecting heterogeneity in the distribution of biomass and in local hydrodynamics. The shape of the chlorine profiles, the long equilibration times, and the dependence on the bulk chlorine concentration showed that the penetration was a function of simultaneous reaction and diffusion of chlorine in the biofilm matrix. Frozen cross sections of biofilms, stained with a redox dye and a DNA stain, showed that the area of chlorine penetration overlapped with nonrespiring zones near the biofilm-bulk fluid interface. These data indicate that the limited penetration of chlorine into the biofilm matrix is likely to be an important factor influencing the reduced efficacy of this biocide against biofilms as compared with its action against planktonic cells.
Paired-angle-rotation scanning optical coherence tomography forward-imaging probe (2006)

We report a novel forward-imaging optical coherence tomography (OCT), needle-probe paired-angle-rotation scanning OCT (PARS-OCT) probe. The probe uses two rotating angled gradient-index lenses to scan the output OCT probe beam over a wide angular arc (approximately 19 degrees half-angle) of the region forward of the probe. Among other advantages, this probe design is readily amenable to miniaturization and is capable of a variety of scan modes, including volumetric scans. To demonstrate the advantages of the probe design, we have constructed a prototype probe with an outer diameter of 1.65 mm and employed it to acquire four OCT images, with a 45 degrees angle between adjacent images, of the gill structure of a Xenopus laevis tadpole. The system sensitivity was measured to be 93 dB by using the prototype probe with an illumination power of 450 microW on the sample. Moreover, the axial and the lateral resolutions of the probe are 9.3 and 10.3-12.5 microm, respectively.
Open Angle Glaucoma (1987)

As one entering his second decade in the care of glaucoma patients, and as one involved in glaucoma research, it seems a reasonable time to ask how effective our therapeutic approaches are. Glaucoma is somewhat unique in ophthalmic diseases with its chronic, relentless course and its customary need for truly unending medical therapies that, in fact, do not reverse the process, are difficult to administer, and may have significant morbidity. Perhaps only uveitis is a more discouraging disease, but even here there is always a chance, at least, for a remission. "Do I really have to use this medication the rest of my life?" the glaucoma patient asks. Unfortunately, the answer is usually<i>yes</i>, for although glaucoma may sometimes "burn out" in old age, it is also often the augury for the decline in other vital functions as well. Wise senior clinicians have pointed out that it is only in
Production of Recombinant Proteins (2004)

lodz.pl&amp;gt; increase of salt concentration, a process which enables the recovery of the protein fused with ELP from the solutions of high dilution degree such as medium of hydroponically grown plants or hairy root cultures. Recent developments and perspectives of the future application of in and ex situ production of recombinant proteins using plant bioreactors will be discussed.
Progesterone Receptor Isoform A But Not B Is Expressed in Endometriosis (2000)

We previously demonstrated that 17beta hydroxysteroid dehydrogenase type 2, the enzyme that inactivates estradiol to estrone, is expressed in luteal eutopic endometrium in response to progesterone but not in simultaneously biopsied peritoneal endometriotic tissue. This molecular evidence of progesterone resistance, together with the clinical observation of resistance of endometriosis to treatment with progestins, led us to determine the levels of progesterone receptor (PR) isoforms PR-A and PR-B in eutopic endometrial and extra-ovarian endometriotic tissues. It was proposed that progesterone action on target genes is mediated primarily by homodimers of PR-B, whereas the truncated variant PR-A acts as a repressor of PR-B function. Immunoprecipitation, followed by Western blot analysis, was performed to detect bands specific for PR-A and PR-B in paired samples of endometriotic and eutopic endometrial tissues simultaneously biopsed from 18 women undergoing laparoscopy during various phases of the menstrual cycle. PR-B was present in 17 of 18 eutopic endometrial samples, and its level increased in the preovulatory phase, as expected, whereas PR-A was detected in all samples (n = 18) with a similar, but less prominent, cyclic variation in its levels. In endometriotic samples, however, no detectable PR-B could be demonstrated, whereas PR-A was detected in all samples (n = 18), albeit in much lower levels and without any cyclic variation in contrast with the eutopic endometrium. Levels of PR-A and PR-B in endometriotic and eutopic endometrial tissues were determined and compared after normalization to total protein and estrogen receptor-alpha levels. Using RNase protection assay, we also demonstrated indirectly that only PR-A transcripts were present in endometriotic tissue samples (n = 8), whereas both PR-A and PR-B transcripts were readily detectable in all eutopic endometrial samples (n = 8). This was indicative that failure to detect PR-B protein in endometriotic tissues is due to the absence of PR-B transcripts. We conclude that progesterone resistance in endometriotic tissue from laboratory and clinical observations may be accounted for by the presence of the inhibitory PR isoform PR-A and the absence of the stimulatory isoform PR-B.
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers (2008)

The algorithm has been implemented in the web-accessible servers NetMHC-3.0: http://www.cbs.dtu.dk/services/NetMHC-3.0, and NetMHCpan-1.1: http://www.cbs.dtu.dk/services/NetMHCpan-1.1
Differential sensitivity of normal and Ha-ras-transformed C3H mouse embryo fibroblasts to tumor necrosis factor: induction of bcl-2, c-myc, and manganese superoxide dismutase in resistant cells. (1994)

In this study, we investigated the role of activated Ha-ras oncogene on the growth-regulatory properties of tumor necrosis factor (TNF) in C3H mouse embryo fibroblasts. TNF-resistant 10T1/2 cells transfected with an activated Ha-ras oncogene not only produced tumors in nude mice but also exhibited extreme sensitivity to cytolysis by TNF. TNF-induced cell death was mediated through apoptosis. The differential sensitivity of normal and Ha-ras transformed cells to TNF was not due to differences in the number of TNF receptors on their cell surface. However, TNF-resistant cells, but not sensitive cells, overexpressed bcl-2, c-myc, and manganese superoxide dismutase (MnSOD) mRNA following exposure to TNF. In addition, TNF treatment resulted in a marginal induction of p53 mRNA in both TNF-sensitive and resistant cells. These results suggest that TNF-induced cytotoxicity involves apoptosis and that TNF-induced over-expression of bcl-2, c-myc, and MnSOD genes is associated with TNF resistance in C3H mouse embryo fibroblasts.
Virus-Induced Silencing of a Plant Cellulose Synthase Gene (2000)

Specific cDNA fragments corresponding to putative cellulose synthase genes (CesA) were inserted into potato virus X vectors for functional analysis in Nicotiana benthamiana by using virus-induced gene silencing. Plants infected with one group of cDNAs had much shorter internode lengths, small leaves, and a "dwarf" phenotype. Consistent with a loss of cell wall cellulose, abnormally large and in many cases spherical cells ballooned from the undersurfaces of leaves, particularly in regions adjacent to vascular tissues. Linkage analyses of wall polysaccharides prepared from infected leaves revealed a 25% decrease in cellulose content. Transcript levels for at least one member of the CesA cellulose synthase gene family were lower in infected plants. The decrease in cellulose content in cell walls was offset by an increase in homogalacturonan, in which the degree of esterification of carboxyl groups decreased from approximately 50 to approximately 33%. The results suggest that feedback loops interconnect the cellular machinery controlling cellulose and pectin biosynthesis. On the basis of the phenotypic features of the infected plants, changes in wall composition, and the reduced abundance of CesA mRNA, we concluded that the cDNA fragments silenced one or more cellulose synthase genes.
Recognition of misfolded proteins by Lon, a AAA + protease (2008)

Proteins unfold constantly in cells, especially under stress conditions. Degradation of denatured polypeptides by Lon and related ATP-dependent AAA(+) proteases helps prevent toxic aggregates formation and other deleterious consequences, but how these destructive enzymatic machines distinguish between damaged and properly folded proteins is poorly understood. Here, we show that Escherichia coli Lon recognizes specific sequences -- rich in aromatic residues -- that are accessible in unfolded polypeptides but hidden in most native structures. Denatured polypeptides lacking such sequences are poor substrates. Lon also unfolds and degrades stably folded proteins with accessible recognition tags. Thus, protein architecture and the positioning of appropriate targeting sequences allow Lon degradation to be dependent or independent of the folding status of a protein. Our results suggest that Lon can recognize multiple signals in unfolded polypeptides synergistically, resulting in nanomolar binding and a mechanism for discriminating irreversibly damaged proteins from transiently unfolded elements of structure.
Structure and function of type II DNA topoisomerases (1994)

Research Article| November 01 1994 Structure and function of type II DNA topoisomerases P M Watt; P M Watt 1Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, U.K. Search for other works by this author on: This Site PubMed Google Scholar I D Hickson I D Hickson 1Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8728 Print ISSN: 0264-6021 © 1994 The Biochemical Society, London1994 Biochem J (1994) 303 (3): 681–695. https://doi.org/10.1042/bj3030681 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation P M Watt, I D Hickson; Structure and function of type II DNA topoisomerases. Biochem J 1 November 1994; 303 (3): 681–695. doi: https://doi.org/10.1042/bj3030681 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1994 The Biochemical Society, London1994 Article PDF first page preview Close Modal You do not currently have access to this content.
Tumor Suppressor Genes: The Puzzle and the Promise (1989)

Tumor suppressor genes are wild-type alleles of genes that play regulatory roles in cell proliferation, differentiation, and other cellular and systemic processes. It is their loss or inactivation that is oncogenic. The first evidence of tumor suppressor genes appeared in the early 1970s, but only within the past few years has a wealth of new information illuminated the central importance of these genes. Two or more different suppressor genes may be inactivated in the same tumors, and the same suppressors may be inactive in different tumor types (for example, lung, breast, and colon). The suppressor genes already identified are involved in cell cycle control, signal transduction, angiogenesis, and development, indicating that they contribute to a broad array of normal and tumor-related functions. It is proposed that tumor suppressor genes provide a vast untapped resource for anticancer therapy.
LDPC codes for rank modulation in flash memories (2010)

An LDPC code is proposed for flash memories based on rank modulation. In contrast to previous approaches, this enables the use of long ECCs with fixed-length modulation codes. For ECC design, the rank modulation scheme is treated as part of an equivalent channel. A probabilistic model of the equivalent channel is derived and a simple high-SNR approximation is given. LDPC codes over integer rings and finite fields are designed for the approximate channel and a low-complexity symbol-flipping verification-based (SFVB) message-passing decoding algorithm is proposed to take advantage of the channel structure. Density evolution (DE) is used to calculate decoding thresholds and simulations are used to compare the low-complexity decoder with sum-product decoding.
Is Alzheimer's disease an apolipoprotein E amyloidosis? (1995)

The presence of the apolipoprotein E4 allele has been identified as a major risk factor for late-onset Alzheimer's disease. Apolipoprotein E has also been found immunohistochemically in Alzheimer's disease lesions. We biochemically isolated amyloid beta from senile plaques and found that a carboxyl-terminal fragment (residues 216-299) of apolipoprotein E co-purified. In vitro this fragment from recombinant apolipoprotein E could form amyloid-like fibrils, which were Congo-red positive. Thus senile plaques may contain both amyloid beta and apolipoprotein E amyloid fibrils.
Control of sway using vibrotactile feedback of body tilt in patients with moderate and severe postural control deficits (2005)

We evaluated the effect of the vibrotactile display of body tilt upon the postural stability of vestibulopathic subjects during standing. Two groups were studied: those with moderate and with severe deficits as defined by postural stability test scores. They were studied under conditions of distorted sensory input, and during anterior-posterior perturbations. Seventeen subjects, with uni- or bilateral vestibular deficits, as determined by electronystagmography and vertical axis rotation, were tested using Equitest computerized dynamic posturography (CDP). Based on their performance on the CDP they were divided into two groups having either moderate (nine subjects) or severe (eight subjects) postural control deficits. Their anterior-posterior (A/P) body motion at the waist was measured with a micromechanical rate gyroscope and a linear accelerometer. The resulting tilt estimate was displayed by a vibrotactile array attached to the torso. The vibration served as a tilt feedback to the subject. The subject's performance was evaluated using the root-mean-square (RMS) of both the A/P body motion and center-of-pressure (CoP) estimates. Sensory distortions were introduced using the Equitest Sensory Organization Tests (SOT). These tests are designed to distort A/P sensory inputs while standing. The SOT 5 distorts proprioceptive information about ankle joint movement, while the subject stands eyes-closed on a moving support platform that measures foot pressure. The SOT 6 adds distorted visual information about body movement instead of testing with eyes closed. Perturbations were introduced using the Equitest Motor Control Tests (MCT). These move the support platform forward or backward with small, medium and large displacements in the horizontal plane while measuring subjects' foot pressure responses. We used the medium and large backward tests. Vibrotactile display of body tilt reduced the subjects' A/P sway and improved their balance. The finding was more evident for those subjects with severe deficits than those moderate ones. This trend was found for both SOT 5 and 6, as well as the medium and large MCT. Additionally, during the MCT, the peak deflection and mean recovery time also decreased significantly.
Universal rules and idiosyncratic features in tRNA identity (1998)

Correct expression of the genetic code at translation is directly correlated with tRNA identity. This survey describes the molecular signals in tRNAs that trigger specific aminoacylations. For most tRNAs, determinants are located at the two distal extremities: the anticodon loop and the amino acid accepting stem. In a few tRNAs, however, major identity signals are found in the core of the molecule. Identity elements have different strengths, often depend more on k cat effects than on K m effects and exhibit additive, cooperative or anti-cooperative interplay. Most determinants are in direct contact with cognate synthetases, and chemical groups on bases or ribose moieties that make functional interactions have been identified in several systems. Major determinants are conserved in evolution; however, the mechanisms by which they are expressed are species dependent. Recent studies show that alternate identity sets can be recognized by a single synthetase, and emphasize the importance of tRNA architecture and anti-determinants preventing false recognition. Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities.
Improving the Distribution of Industrial Gases with an On-Line Computerized Routing and Scheduling Optimizer (1983)

For Air Products and Chemicals, Inc., inventory management of industrial gases at customer locations is integrated with vehicle scheduling and dispatching. Their advanced decision support system includes on-line data entry functions, customer usage forecasting, a time/distance network with a shortest path algorithm to compute intercustomer travel times and distances, a mathematical optimization module to produce daily delivery schedules, and an interactive schedule change interface. The optimization module uses a sophisticated Lagrangian relaxation algorithm to solve mixed integer programs with up to 800,000 variables and 200,000 constraints to near optimality. The system, first implemented in October, 1981, has been saving between 6% to 10% of operating costs.
Posterior cervical interspinous compression wiring and fusion for mid to low cervical spinal injuries (1989)

A technique of posterior cervical interspinous compression wiring and fusion, which offers significant immediate stability, is presented. Its efficacy in 50 consecutive cases illustrates its utility. The technique involves the passage of an interspinous cerclage wire. Rather than placement of onlay laminar and facet grafts, a split-thickness tricortical iliac-crest graft is compressed against the involved medial laminae and spinous processes bilaterally. These grafts are held in place by a compression wire, which encircles the grafts and thus sandwiches the spinous processes between them. This virtually ensures subsequent bone fusion and offers substantial acute stability. The compression wire offers an added advantage of encircling the cerclage wire, thus pulling it dorsally. This significantly diminishes translational mobility at the unstable segment. It also minimizes hyperextension at the unstable segment via medial compression of the grafts into the interspinous space. The fusion of a minimal number of spinal segments is emphasized. This substantially diminishes the chance of flexible kyphosis and degenerative changes, both above and below the fusion site. A three- or four-level fusion was performed in only 11 patients. The remaining 39 patients underwent two-level fusion. A solid bone fusion was achieved in all cases, with a follow-up period of at least 6 months. In one patient, the spinous process fractured, necessitating an anterior fusion procedure. The technique presented here appears to acutely offer a very stable construct and, in addition, is a simple and straightforward procedure for the treatment of the unstable cervical spine.
Preparation and Characterization of Membranes Formed by Nonsolvent Induced Phase Separation: A Review (2011)

The methods and mechanisms of nonsolvent induced phase separation have been studied for more than fifty years. Today, phase inversion membranes are widely used in numerous chemical industries, biotechnology, and environmental separation processes. The body of knowledge has grown exponentially in the past fifty years, which suggests the need for a critical review of the literature. Here we present a review of nonsolvent induced phase separation membrane preparation and characterization for many commonly used membrane polymers. The key factors in membrane preparation discussed include the solvent type, polymer type and concentration, nonsolvent system type and composition, additives to the polymer solution, and film casting conditions. A brief introduction to membrane characterization is also given, which includes membrane porosity and pore size distribution characterization, membrane physical and chemical properties characterization, and thermodynamic and kinetic evaluation of the phase inversion process. One aim of this review is to lay out the basics for selecting polymer−solvent−nonsolvent systems with appropriate film casting conditions to produce membranes with the desired performance, morphology, and stability, and to choose the proper way to characterize these properties of nonsolvent induced phase inversion membranes.