gebhart/patrepeval huggingface dataset:
Regeneration of lesioned entorhino‐hippocampal axons in vitro by combined degradation of inhibitory proteoglycans and blockade of Nogo‐66/NgR signaling (2006)

Damaged axons do not regenerate after axotomy in the adult mammalian central nervous system (CNS). This may be due to local inhibitory factors at the site of injury, such as overexpression of chondroitin sulfate (CS) proteoglycans (CSPG), and the presence of myelin-associated inhibitors (MAI). To overcome CSPG- or myelin-induced inhibition, strategies based on extrinsic and intrinsic treatments have been developed. For example, NEP1-40 is a synthetic peptide that promotes axonal regeneration by blocking Nogo-66/NgR interaction and chondroitinase ABC (ChABC), which degrades CS, thereby also promoting axon regrowth. Here, we examined whether the combination of these complementary strategies facilitates regeneration of the lesioned entorhino-hippocampal pathway (EHP) in slice cultures. In this model, overexpressed CSPG and MAI impaired axon regrowth, which mimics regeneration failure in vivo. Both CS cleavage with ChABC and NEP1-40 strongly facilitated the regrowth of entorhinal axons after axotomy, permitting the re-establishment of synaptic contacts with target cells. However, the combined treatment did not improve the regeneration induced by ChABC alone, and the delayed treatment of ChABC, but not NEP1-40, had a less pronounced effect on axonal regrowth compared with acute treatment. These results provide insight into the development of new assays and strategies to enhance axon regeneration in injured cortical connections.
Depth Of Investigation In Direct Current Methods (1971)

Abstract The depth of investigation in any direct current resistivity method of surface geophysical prospecting is defined, following Evjen (1938), as that depth at which a thin horizontal (parallel to ground surface) layer of ground contributes the maximum amount to the total measured signal at the ground surface. Using the equivalence between static and stationary fields, we have found the following values for the absolute depths of investigation in homogeneous ground.
Plasmonics Meets Far-Field Optical Nanoscopy (2012)

Plasmonics and near-field optical nanoscopy both deal with expanding optics into the subwavelength regime. However, these two fields have so far followed parallel paths of development and only recently have researchers started to explore combinations of their concepts with potential synergy. In this Perspective, we provide an up-to-date summary of the successful combinations reported and give insight into some new possibilities.
Automated Filter Paper Assay for Determination of Cellulase Activity (2003)

Recent developments in molecular breeding and directed evolution have promised great developments in industrial enzymes as demonstrated by exponential improvements in β-lactamase and green fluorescent protein (GFP). Detection of and screening for improved enzymes are relatively easy if the target enzyme is expressible in a suitable high-throughput screening host and a clearly defined and usable screen or selection is available, as with GFP and β-lactamase. Fungal cellulases, however, are difficult to measure and have limited expressibility in heterologous hosts. Furthermore, traditional cellulase assays are tedious and time-consuming. Multiple enzyme components, an insoluble substrate, and generally slow reaction rates have plagued cellulase researchers interested in creating cellulase mixtures with increased activities and/or enhanced biochemical properties. Although the International Union of Pure and Applied Chemists standard measure of cellulase activity, the filter paper assay (FPA), can be reproduced in most laboratories with some effort, this method has long been recognized for its complexity and susceptibility to operator error. Our current automated FPA method is based on a Cyberlabs C400 robotics deck equipped with customized incubation, reagent storage, and plate-reading capabilities that allow rapid evaluation of cellulases acting on cellulose and has a maximum throughput of 84 enzyme samples per day when performing the automated FPA.
Luciferase expression and bioluminescence does not affect tumor cell growth in vitro or in vivo (2010)

Live animal imaging is becoming an increasingly common technique for accurate and quantitative assessment of tumor burden over time. Bioluminescence imaging systems rely on a bioluminescent signal from tumor cells, typically generated from expression of the firefly luciferase gene. However, previous reports have suggested that either a high level of luciferase or the resultant light reaction produced upon addition of D-luciferin substrate can have a negative influence on tumor cell growth. To address this issue, we designed an expression vector that allows simultaneous fluorescence and luminescence imaging. Using fluorescence activated cell sorting (FACS), we generated clonal cell populations from a human breast cancer (MCF-7) and a mouse melanoma (B16-F10) cell line that stably expressed different levels of luciferase. We then compared the growth capabilities of these clones in vitro by MTT proliferation assay and in vivo by bioluminescence imaging of tumor growth in live mice. Surprisingly, we found that neither the amount of luciferase nor biophotonic activity was sufficient to inhibit tumor cell growth, in vitro or in vivo. These results suggest that luciferase toxicity is not a necessary consideration when designing bioluminescence experiments, and therefore our approach can be used to rapidly generate high levels of luciferase expression for sensitive imaging experiments.
Limiting CDR-H3 Diversity Abrogates the Antibody Response to the Bacterial Polysaccharide α 1→3 Dextran (2011)

Anti-polysaccharide Ab responses in mice are often oligoclonal, and the mechanisms involved in Ag-specific clone production and selection remain poorly understood. We evaluated the relative contribution of D(H) germline content versus N nucleotide addition in a classic oligoclonal, T-independent Ab response (α 1→3 dextran [DEX]) by challenging adult TdT-sufficient (TdT(+/+)) and TdT-deficient (TdT(-/-)) gene-targeted mice, limited to the use of a single D(H) gene segment (D-limited mice), with Enterobacter cloacae. D-limited mice achieved anti-DEX-specific levels of Abs that were broadly comparable to those of wild-type (WT) BALB/c mice. Sequence analysis of the third CDR of the H chain intervals obtained by PCR amplification of V(H) domain DNA from DEX-specific plasmablasts revealed the near universal presence of an aspartic acid residue (D99) at the V-D junction, irrespective of the composition of the D(H) locus. Although WT mice were able to use germline D(H) (DQ52, DSP, or DST) gene segment sequence, TdT activity, or both to produce D99, all three D-limited mouse strains relied exclusively on N addition. Additionally, in the absence of TdT, D-limited mice failed to produce a DEX response. Coupled with previous studies demonstrating a reduced response to DEX in TdT(-/-) mice with a WT D(H) locus, we concluded that in the case of the anti-DEX repertoire, which uses a short third CDR of the H chain, the anti-DEX response relies more intensely on sequences created by postnatal N nucleotide addition than on the germline sequence of the D(H).
Case studies in swelling polymeric gastric retentive tablets (2006)

Swelling tablets administered in the fed state have been shown to provide therapeutic advantages in two marketed products, with the duration of delivery characterised with respect to food and tablet size. Metformin extended-release tablets are a diffusion-based swelling tablet demonstrating once-daily efficacy with good gastrointestinal solubility. Ciprofloxacin extended-release tablets are based on an erosional matrix that delivers the drug to the upper gastrointestinal tract over 6 h to provide once-daily efficacy with reduced incidences of nausea and diarrhoea. Furosemide extended-release tablets are another example of an erosional matrix designed to deliver furosemide to the duodenum and upper jejunum over 6 h to provide a more gradual diuresis and naturesis compared with the immediate-release product.
Natural Atypical Listeria innocua Strains with Listeria monocytogenes Pathogenicity Island 1 Genes (2004)

Identification of bona fide Listeria isolates into the six species of the genus normally requires only a few tests. Aberrant isolates do occur, but even then only one or two extra confirmatory tests are generally needed for identification to species level. We have discovered a hemolytic-positive, rhamnose and xylose fermentation-negative Listeria strain with surprising recalcitrance to identification to the species level due to contradictory results in standard confirmatory tests. The issue had to be resolved by using total DNA-DNA hybridization testing and then confirmed by further specific PCR-based tests including a Listeria microarray assay. The results show that this isolate is indeed a novel one. Its discovery provides the first fully documented instance of a hemolytic Listeria innocua strain. This species, by definition, is typically nonhemolytic. The L. innocua isolate contains all the members of the PrfA-regulated virulence gene cluster (Listeria pathogenicity island 1) of L. monocytogenes. It is avirulent in the mouse pathogenicity test. Avirulence is likely at least partly due to the absence of the L. monocytogenes-specific allele of iap, as well as the absence of inlA, inlB, inlC, and daaA. At least two of the virulence cluster genes, hly and plcA, which encode the L. monocytogenes hemolysin (listeriolysin O) and inositol-specific phospholipase C, respectively, are phenotypically expressed in this L. innocua strain. The detection by PCR assays of specific L. innocua genes (lin0198, lin0372, lin0419, lin0558, lin1068, lin1073, lin1074, lin2454, and lin2693) and noncoding intergenic regions (lin0454-lin0455 and nadA-lin2134) in the strain is consistent with its L. innocua DNA-DNA hybridization identity. Additional distinctly different hemolytic L. innocua strains were also studied.
Oral Hypoglycemic Drugs: Pathophysiological Basis of Their Mechanism of ActionOral Hypoglycemic Drugs: Pathophysiological Basis of Their Mechanism of Action (2010)

Type 2 diabetes is a syndrome characterized by relative insulin deficiency, insulin resistance and increased hepatic glucose output. Medications used to treat the disease are designed to correct one or more of these metabolic abnormalities. Current recommendations of the American Diabetes Association (ADA) and European Association for the Study of Diabetes (EASD) include diet and exercise as first-line therapy plus hypoglycemic drugs. Actually there are seven distinct classes of anti-hyperglicemic agents, each of them displaying unique pharmacologic properties. The aim of this review is to describe the pathophysiological basis of their mechanism of action, a necessary step to individualize treatment of diabetic people, taking into proper consideration potential benefits and secondary effects of drugs.
Heparin-binding Growth-associated Molecule Contains Two Heparin-binding β-Sheet Domains That Are Homologous to the Thrombospondin Type I Repeat (2000)

Heparin-binding growth-associated molecule (HB-GAM) is an extracellular matrix-associated protein implicated in the development and plasticity of neuronal connections of brain. Binding to cell surface heparan sulfate is indispensable for the biological activity of HB-GAM. In the present paper we have studied the structure of recombinant HB-GAM using heteronuclear NMR. These studies show that HB-GAM contains two beta-sheet domains connected by a flexible linker. Both of these domains contain three antiparallel beta-strands. In addition to this domain structure, HB-GAM contains the N- and C-terminal lysine-rich sequences that lack a detectable structure and appear to form random coils. Studies using CD and NMR spectroscopy suggest that HB-GAM undergoes a conformational change upon binding to heparin, and that the binding occurs primarily to the beta-sheet domains of the protein. Search of sequence data bases shows that the beta-sheet domains of HB-GAM are homologous to the thrombospondin type I repeat (TSR). Sequence comparisions show that the beta-sheet structures found previously in midkine, a protein homologous with HB-GAM, also correspond to the TSR motif. We suggest that the TSR sequence motif found in various extracellular proteins defines a beta-sheet structure similar to that found in HB-GAM and midkine. In addition to the apparent structural similarity, a similarity in biological functions is suggested by the occurrence of the TSR sequence motif in a wide variety of proteins that mediate cell-to-extracellular matrix and cell-to-cell interactions, in which the TSR domain mediates specific cell surface binding.
Generation of Reflected Second Harmonic at Semiconductor Quantum Dots (2023)

Generation of the reflected second harmonic has been observed for the first time in a composite material: a glass matrix containing microscopic CdSe crystals, ranging in size from 500 to 50 Å. The violation of polarization selection rules in the second-harmonic generation indicates that the nonlinear sources are of a fluctuational nature. A size effect has also been observed: The intensity of the second harmonic increases by a factor of 102 as the size of the microscopic crystals is reduced. A possible mechanism for this size effect is analyzed.
The InfoSleuth Project: Intelligent Search Management via Semantic Agents (1994)

InfoSleuth is a research project at MCC that is developing and deploying new technologies for finding information available both in corporate networks and in external networks, such as networks based on the emerging National Information Infrastructure (NII). The InfoSleuth research is based on the Carnot technology that has been developed at MCC over the last 4 years. Carnot has been successfully used to integrate heterogeneous corporate information resources. Carnot executes queries in a distributed environment by dispatching autonomous computing agents to remote sites where they access databases and cooperate among themselves to properly merge resulting data into understandable information.The InfoSleuth project will investigate the use of Carnot technology in a more dynamically changing environment, such as the Internet, where new information sources are constantly being added and for which there is no formal control of the registration of new information sources. In this type of en...
Development and Validation of an ECG Algorithm for Identifying Accessory Pathway Ablation Site in Wolff‐Parkinson‐White Syndrome (1998)

A simple ECG algorithm identifies accessory pathway ablation site in Wolff-Parkinson-White syndrome. A truly negative delta wave in lead II predicts ablation within the coronary venous system.
Array Formatting of the Heat-Transfer Method (HTM) for the Detection of Small Organic Molecules by Molecularly Imprinted Polymers (2014)

In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications.
Amoeba co-culture of soil specimens recovered 33 different bacteria, including four new species and Streptococcus pneumoniae (2009)

Amoeba-resistant bacteria (ARB), such as Legionella spp., are currently regarded as potential human pathogens that live in the natural environment, and thus their habitat is regarded as a reservoir of human pathogens. To detect ARB in human and environmental samples, co-culture with amoebae has been demonstrated to be an efficient tool. However, to date, only water samples from cooling towers and hospital water supplies have been investigated as possible reservoirs of ARB using this procedure. In the present study, we studied the ARB population of 11 diverse soil and sand sources in proximity to human environments; these sources included the university, the station, hospitals, the square, parks and public beaches in the city of Marseilles, France. As a result, a total of 33 different species of ARB were identified. The ability to grow within and/or lyse amoebae was demonstrated, for what is believed to be the first time, for several species; moreover, 20 of the isolates (61%), including Streptococcus pneumoniae, have been described as human pathogens. However, Legionella spp. were not isolated. Four isolates are likely to be the members of new or uncharacterized genera or species, and their capability to be human pathogens needs to be determined. This preliminary work demonstrates that soils and sands in the vicinity of humans are reservoirs of human pathogenic ARB.
Probing the Microenvironment of Polymer-Impregnated Composite Glass Using Solvatochromic Dye (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProbing the Microenvironment of Polymer-Impregnated Composite Glass Using Solvatochromic DyeR. Gvishi, U. Narang, F. V. Bright, and P. N. PrasadCite this: Chem. Mater. 1995, 7, 9, 1703–1708Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/cm00057a020https://doi.org/10.1021/cm00057a020research-articleACS PublicationsRequest reuse permissionsArticle Views147Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase epsilon (1993)

The cDNA encoding the catalytic polypeptide of human DNA polymerase epsilon was cloned. The deduced amino acid sequence reveals that the catalytic polypeptide is 2257 amino acids in length and its calculated molecular mass is 258 kDa. A single RNA message of 7.5 kilobases was recognized by isolated cDNA clones. The identity of the cDNA was verified by direct amino acid sequencing of tryptic fragments derived from the catalytic polypeptide of the HeLa DNA polymerase epsilon. The primary structure comparison with multiple DNA polymerases indicates that human DNA polymerase epsilon catalytic polypeptide is a homolog of the yeast Saccharomyces cerevisiae DNA polymerase II catalytic polypeptide. The proteins are 39% identical. In the region containing known DNA polymerase consensus motifs, the identity is 63%. The expression of the mRNA encoding DNA polymerase epsilon is strongly dependent on cell proliferation.
Reconfiguration techniques for a single scan chain (1995)

A major drawback in using scan techniques is the long test application times incurred in shifting test data in and out of a device. This problem assumes even greater significance with the rapid growth in both the number of test patterns and scan registers occurring in complex VLSI designs. This paper presents a novel methodology based on reconfiguring a single scan chain to minimize the shifting time in applying test patterns to a device. The main idea is to employ multiplexers to bypass registers that are not frequently accessed in the test process and hence reduce the overall test application time, For partitioned scan designs, we describe two different modes of test application which can be used to efficiently tradeoff the logic and routing overheads of the reconfiguration strategy with the test application time. In each case we provide detailed analysis and optimization techniques to minimize the number of added multiplexers and the corresponding test time. Implementation results on two data path circuits demonstrate test time reductions as large as 75% over traditional schemes at the expense of 1-3 multiplexers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Rhodopsin Mutant Linked to Autosomal Dominant Retinitis Pigmentosa Is Prone to Aggregate and Interacts with the Ubiquitin Proteasome System (2002)

The inherited retinal degenerations are typified by retinitis pigmentosa (RP), a heterogeneous group of inherited disorders that causes the destruction of photoreceptor cells, the retinal pigmented epithelium, and choroid. This group of blinding conditions affects over 1.5 million persons worldwide. Approximately 30-40% of human autosomal dominant (AD) RP is caused by dominantly inherited missense mutations in the rhodopsin gene. Here we show that P23H, the most frequent RP mutation in American patients, renders rhodopsin extremely prone to form high molecular weight oligomeric species in the cytoplasm of transfected cells. Aggregated P23H accumulates in aggresomes, which are pericentriolar inclusion bodies that require an intact microtubule cytoskeleton to form. Using fluorescence resonance energy transfer (FRET), we observe that P23H aggregates in the cytoplasm even at extremely low expression levels. Our data show that the P23H mutation destabilizes the protein and targets it for degradation by the ubiquitin proteasome system. P23H is stabilized by proteasome inhibitors and by co-expression of a dominant negative form of ubiquitin. We show that expression of P23H, but not wild-type rhodopsin, results in a generalized impairment of the ubiquitin proteasome system, suggesting a mechanism for photoreceptor degeneration that links RP to a broad class of neurodegenerative diseases.
Evolving strategies for preventing biofilm on implantable materials (2013)

Implantable devices have improved the lives of many patients, but implant-associated infection remains a serious complication with significant morbidity and mortality. In recent years, the role of biofilm in the development of these infections has become increasingly recognized, and strategies to combat biofilm are beginning to proliferate in the literature. This review will explore how implant-associated infections have historically been treated, where the research currently stands, and the future trends of infection control.