gebhart/patrepeval huggingface dataset:
A mammalian origin of bidirectional DNA replication within the Chinese hamster RPS14 locus. (1994)

Two complementary experimental approaches have been used to identify a chromosomal origin of bidirectional DNA replication within or immediately downstream of the Chinese hamster ribosomal protein S14 gene (RPS14). The replication origin, designated oriS14, maps within a 1.6- to 2.0-kbp region of RPS14 that includes the gene's third and fourth introns, exons IV plus V, and approximately 500 bp of proximal downstream flanking DNA. The nucleic acid sequence encoding oriS14 closely resembles the other mammalian chromosomal replication origins whose primary structures are known. It contains DNA binding sites for a large number of transcription factors, replication proteins, and mammalian oncogenes as well as several dinucleotide repeat motifs, an AT-rich region, and a sequence that is likely to bend the DNA. In contrast to the other well-characterized mammalian replication origins, which are autosomal and therefore carried as two copies per somatic cell, oriS14 is encoded by single-copy DNA within a hemizygous segment of chromosome 2q in CHO-K1 cells. Also, other known mammalian replication origins are situated in nontranscribed, intergenic DNA, whereas the DNA sequence encoding oriS14 substantially overlaps the transcribed portion of a constitutively expressed housekeeping gene.
Complementation of the beige mutation in cultured cells by episomally replicating murine yeast artificial chromosomes. (1996)

Chédiak-Higashi syndrome in man and the beige mutation of mice are phenotypically similar disorders that have profound effects upon lysosome and melanosome morphology and function. We isolated two murine yeast artificial chromosomes (YACs) that, when introduced into beige mouse fibroblasts, complement the beige mutation. The complementing YACs exist as extrachromosomal elements that are amplified in high concentrations of G418. When YAC-complemented beige cells were fused to human Chédiak-Higashi syndrome or Aleutian mink fibroblasts, complementation of the mutant phenotype also occurred. These results localize the beige gene to a 500-kb interval and demonstrate that the same or homologous genes are defective in mice, minks, and humans.
Cytomegalovirus viremia and advanced HIV disease: is there an argument for anti-CMV treatment? (2023)

Evidence suggests that active CMV replication, manifest as CMV viremia (DNAemia), may play a key role in driving progression of HIV-associated opportunistic infections. We propose that control of CMV replication, independent of the known benefit of HAART therapy on reducing CMV end-organ disease, could reduce the risk of disease and mortality attributable to opportunistic infections such as cryptococcosis and tuberculosis. This could be achieved by the targeted use of CMV antivirals. The advent of newer (and safer) orally bioavailable CMV antivirals has renewed interest in, and opportunities for, randomized controlled trials to evaluate CMV viremia as a modifiable risk factor in high-risk persons with HIV disease.
Drug Release Analysis and Optimization for Drug‐Eluting Stents (2013)

The drug release analysis and optimization for drug-eluting stents in the arterial wall are studied, which involves mechanics, fluid dynamics, and mass transfer processes and design optimization. The Finite Element Method (FEM) is used to analyze the process of drug release in the vessels for drug-eluting stents (DES). Kriging surrogate model is used to build an approximate function relationship between the drug distribution and the coating parameters, replacing the expensive FEM reanalysis of drug release for DES in the optimization process. The diffusion coefficients and the coating thickness are selected as design variables. An adaptive optimization approach based on kriging surrogate model is proposed to optimize the lifetime of the drug in artery wall. The adaptive process is implemented by an infilling sampling criterion named Expected Improvement (EI), which is used to balance local and global search and tends to find the global optimal design. The effect of coating diffusivity and thickness on the drug release process for a typical DES is analyzed by means of FEM. An implementation of the optimization method for the drug release is then discussed. The results demonstrate that the optimized design can efficiently improve the efficacy of drug deposition and penetration into the arterial walls.
Raman spectroscopy: a potential tool for early objective diagnosis of neoplasia in the oesophagus (2011)

There is a profound clinical need for a diagnostic tool that will enable clinicians to identify early neoplastic change in the oesophagus. Raman Spectroscopy (RS) has demonstrated the potential to provide non-invasive, rapid, objective diagnosis of endoscopically invisible precancerous oesophageal dysplasia in vitro. RS analyses biological material to identify highly specific biochemical information that can be used to influence clinical care. Raman spectroscopic mapping could provide automated assessment of tissue biopsies to aid histopathological diagnosis in vitro. Furthermore, the recent development of fibre-optic Raman probes has enabled endoscopic assessment of oesophageal mucosa in vivo. Accurate identification of dysplasia will enable targeted endoscopic resection of early lesions preventing the development of oesophageal cancer. This review summarises the development of Raman systems for use as laboratory based analytical adjuncts and endoscopic diagnostic tools in the distal oesophagus.
Immunization with Attenuated Salmonella typhimurium Producing Catalase in Protection against Gastric Helicobacter pylori Infection in Mice (2003)

This study demonstrates that oral immunization of mice with catalase delivered by an attenuated S. typhimurium strain offers protection against H. pylori infection. This protective immunity was mediated through a predominantly Th1-type response and was associated with post-immunization gastritis.
Toward “Stable-on-the-Table” Enzymes: Improving Key Properties of Catalase by Covalent Conjugation with Poly(acrylic acid) (2014)

Several key properties of catalase such as thermal stability, resistance to protease degradation, and resistance to ascorbate inhibition were improved, while retaining its structure and activity, by conjugation to poly(acrylic acid) (PAA, Mw 8000) via carbodiimide chemistry where the amine groups on the protein are appended to the carboxyl groups of the polymer. Catalase conjugation was examined at three different pH values (pH 5.0, 6.0, and 7.0) and at three distinct mole ratios (1:100, 1:500, and 1:1000) of catalase to PAA at each reaction pH. The corresponding products are labeled as Cat-PAA(x)-y, where x is the protein to polymer mole ratio and y is the pH used for the synthesis. The coupling reaction consumed about 60-70% of the primary amines on the catalase; all samples were completely water-soluble and formed nanogels, as evidenced by gel electrophoresis and electron microscopy. The UV circular dichroism (CD) spectra indicated substantial retention of protein secondary structure for all samples, which increased to 100% with increasing pH of the synthesis and polymer mole fraction. Soret CD bands of all samples indicated loss of ∼50% of band intensities, independent of the reaction pH. Catalytic activities of the conjugates increased with increasing synthesis pH, where 55-80% and 90-100% activity was retained for all samples synthesized at pH 5.0 and pH 7.0, respectively, and the Km or Vmax values of Cat-PAA(100)-7 did not differ significantly from those of the free enzyme. All conjugates synthesized at pH 7.0 were thermally stable even when heated to ∼85-90 °C, while native catalase denatured between 55 and 65 °C. All conjugates retained 40-90% of their original activities even after storing for 10 weeks at 8 °C, while unmodified catalase lost all of its activity within 2 weeks, under similar storage conditions. Interestingly, PAA surrounding catalase limited access to the enzyme from large molecules like proteases and significantly increased resistance to trypsin digestion compared to unmodified catalase. Similarly, negatively charged PAA surrounding the catalase in these conjugates protected the enzyme against inhibition by negatively charged inhibitors such as ascorbate. While Cat-PAA(100)-7 did not show any inhibition by ascorbate in the presence of 270 μM ascorbate, unmodified catalase lost ∼70% of its activity under similar conditions. This simple, facile, and rational methodology produced thermostable, storable catalase that is also protected from protease digestion and ascorbate inhibition and most likely prevented the dissociation of the multimer. Using synthetic polymers to protect and improve enzyme properties could be an attractive approach for making "Stable-on-the-Table" enzymes, as a viable alternative to protein engineering.
OFDM sensing in low SNR with noise uncertainty (2009)

The autocorrelation-based detection of OFDM signals with cyclic prefix is an appealing method for cognitive radio because it has low complexity and it allows to separate between different OFDM-based legacy systems. Unfortunately, it is also sensitive to noise estimation errors provided that a single estimate of the autocorrelation function is calculated. In this paper we design an autocorrelation-based detector for OFDM signals with cyclic prefix that is also robust in the low SNR under noise uncertainty. The proposed decision statistic allows us to calculate the error probabilities in a closed-form.
Antitumor agent poly (amino acid) conjugates as a drug carrier in cancer chemotherapy. (1984)

Antitumor agent melphalan was conjugated through a carbodiimide-catalyzed reaction to poly (L-lysine) (71.3K and 2K) and poly (L-glutamic acid) (60K and 14K) at a ratio of approximately one molecule per 7-lysyl and 23-glutamate residues, respectively. These conjugates had 40-70% of alkylating activities by themselves in vitro as compared with free melphalan. Poly (glutamic acid) conjugates showed the antitumor activity in vivo against Yoshida sarcoma in rats. In addition, poly (glutamic acid) conjugates containing 3H-phenylalanine which was used as a model compound instead of melphalan had a sustained release property of radioactivity and the release rates could be regulated by exopeptidases. After subcutaneous injection as the first choice of routes of administration, moreover, the conjugates were found to be absorbed through the lymphatic transport system, probably due to the macromolecularity. These results suggest that the melphalan-poly (amino acid) conjugates are one of good candidates to attain the sustained release and targeting of drugs in cancer chemotherapy.
TNAZ Based Melt-Cast Explosives: Technology Review and AMRL Research Directions (1998)

Abstract : 1,3,3-Trinitroazetidine (TNAZ) is a new melt-castable explosive with the potential to replace TNT in melt-cast munition fillings. TNAZ possesses an extremely high energy density and, if used in melt-cast systems could substantially increase the performance of currently used munitions. The purpose of this review is to examine work performed to date and identify technology gaps AMRL can address to further this technology. The chemical synthesis of TNAZ is well advanced with pilot plant production underway in the United States. chemical and physical characterization has been extensively performed; however, certain sensitiveness results vary and will require further examination. Thermal decomposition studies have been performed and show similar trends with decomposition occurring via consecutive NO2 losses. Calculated and experimentally measured explosive properties show TNAZ to have performance similar to HMX, the most powerful commonly used energetic material, and offer a 30-40% improvement over TNT. High quality pressed TNAZ charges have been produced, but melt-casting of TNAZ has not yet been perfected. It is suggested that future AMRL research directions should include an examination of some of the technological problems existing with TNAZ; in particular, overcoming melt-cast difficulties, examining TNAZ as a TNT replacement in TNT/nitramine melt- cast fillings, and assessing the performance and sensitiveness/ sensitivity of TNAZ/ nitramine compositions.
Purely interpretative optimizations (2011)

Interpreters are easy to implement and can be made portable with only little extra effort.Therefore, many popular programming languages choose an interpreter instead of a compiler as an execution platform.While the characteristics of interpreters are regarded as an upside, usually, their major downside is considered to be sub-optimal performance.Fortunately, in 1984 L. Peter Deutsch and Allan Schiffman introduced the modern concept of dynamic compilation sub-systems to the programming language implementation community, which subsequently became a success story, resulting in today's high performance just-in-time compilers for Java and .NET.Unfortunately, on the other hand, deciding to implement a dynamic compilation sub-system involves trading off the valuable innate characteristics of interpreters.This dissertation a) explains why for some interpreters known techniques do not yield reported speedups, b) provides orientation for focusing on other optimization targets, and c) presents several purely-interpretative optimization techniques that result in substantial speedups-we report speedups of up to 2.4176-while simultaneously preserving the ease of implementation and portability characteristics.
Dielectric Properties of (BaxSr1-x)TiO3 Thin Films Prepared by RF Sputtering for Dynamic Random Access Memory Application (1994)

Dielectric properties of (Ba 0.5 Sr 0.5 )TiO 3 and (Ba 0.75 Sr 0.25 )TiO 3 thin films have been investigated, focusing on the effects of film structure and Ba/Sr compositions on the dielectric properties. Dielectric constant of the films increased with increasing grain size and with improvement in film crystallinity. For the 50-nm-thick films deposited at 660° C, the dielectric constant of 400 for the (Ba 0.5 Sr 0.5 )TiO 3 film is larger than that of 320 for the (Ba 0.75 Sr 0.25 )TiO 3 film. This indicated that dielectric constant is affected by the ratio of Ba/Sr composition. Leakage current density of less than 1×10 -7 A/cm 2 at 1 V and SiO 2 equivalent thickness of 0.38 nm are measured at 120° C for 660° C-deposited (Ba 0.5 Sr 0.5 )TiO 3 film of 30 nm in thickness. The (Ba 0.5 Sr 0.5 )TiO 3 film has the possibility for application to generations beyond 256 Mbit dynamic random access memories.
604. TALE-VP64 Targeting the Frataxin Promoter Increase the Expression of That Gene in Friedreich Fibroblasts (2015)

Friedreich's ataxia (FRDA) is due to a reduced frataxin expression due to a trinucleotide repeat. It is 30% in patients with 200 GAA repeats and only 5% in patients with 900 GAA repeats 33. However, carriers of this disease produce about only 50% of the normal level of frataxin but do not develop symptoms. We have engineered 12 genes coding for TALE proteins targeting different nucleotide sequences present in the frataxin promoter. Each expression plasmid contains a TALEFrat gene fused with a transcription activator, VP64 under the EF1α promoter, a 2A peptide and an EGFP. When one of these plasmids was transfected alone in human cells, only green fluorescence was detected by FACS indirectly confirming the expression of the TALEFrat/VP64 protein. To identify which of our 12 different TALEFrat/VP64 proteins were able to better induce the expression of the frataxin gene, we have constructed a reporter plasmid containing the proximal region of the frataxin promoter, followed by a minimal CMV promoter and a mCherry reporter gene (pCR3.1 proximal-promoter-frataxin-miniCMV-mCherry). This reporter plasmid was initially transfected in human cells alone. Very few cells expressed the red fluorescence because the promoter was not effective without transactivation by binding factors. When the reporter plasmid was co-transfected in human cells with one of the pCR3.1-TALEFrat/VP64-2A-EGFP plasmids, a much higher number of cells expressed the red fluorescence because the TALEFrat/VP64 attached to the proximal frataxin promoter and induced the transcription of mCherry. The 3 TALEFrat/VP64, which induced the strongest expression of mCherry, were targeting promoter sequences close to each other. A plasmid coding for TALEFrat#8/VP64 was nucleofected in normal fibroblasts. Using quantitative RT-PCR, we have confirmed in 3 independent experiments that the expression of the frataxin mRNA (relative to GAPDH mRNA) in human cells was doubled or triple by TALEFrat#8/VP64 when results were normalized with cells transfected with EGFP or non-transfected cells. We have also shown that this TALE also increased by 2 folds the frataxin protein in fibroblasts from a FRDA patient. In a recent preliminary result, we have shown that the transfection of TALEFrat#8/VP64 plasmid in YG8R fibroblasts also increases frataxin mRNA (by about 1.4 to 1.9 fold) and protein (by about 1.4 fold). Such increases would be in the therapeutic range (i. e., 50% of normal frataxin level) for many patients. However, for patients that have less than 25% of the normal level of frataxin expression, a further increase of frataxin would be required and this project may permit to obtain higher frataxin increases and thus this would lead to an increased number of FRDA patients who would benefit from our therapy.
Application of base drift field measurement to processing optimization of advanced bipolar transistors (2003)

A technique for directly measuring the base drift field in bipolar transistors has been developed and used to study the effects of various base-formation and emitter drive-in conditions on the effective base drift field, a major factor determining the unity-current-gain cutoff frequency f/sub T/, has been studied. Measurements of base drift fields created with these drive-in conditions revealed that insufficient thermal treatment leaves a large portion of the base region with a retarding field, producing low base drift fields and low f/sub T/'s. An appropriate thermal treatment creates a monotonically varying base profile with large drift fields and therefore high f/sub T/'s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modeling routing overhead generated by wireless proactive routing protocols (2011)

In this paper, we present a detailed framework consisting of modeling of routing overhead generated by three widely used proactive routing protocols; Destination-Sequenced Distance Vector (DSDV), Fish-eye State Routing (FSR) and Optimized Link State Routing (OLSR). The questions like, how these protocols differ from each other on the basis of implementing different routing strategies, how neighbor estimation errors affect broadcast of route requests, how reduction of broadcast overhead achieves bandwidth, how to cope with the problem of mobility and density, etc, are attempted to respond. In all of the above mentioned situations, routing overhead and delay generated by the chosen protocols can exactly be calculated from our modeled equations. Finally, we analyze the performance of selected routing protocols using our proposed framework in NS-2 by considering different performance parameters; Route REQuest (RREQ) packet generation, End-to-End Delay (E2ED) and Normalized Routing Load (NRL) with respect to varying rates of mobility and density of nodes in the underlying wireless network.
Weight loss maintenance after a digital commercial behavior change program (Noom Weight): Observational cross‐sectional survey study (2023)

This study provides real-world data on the long-term weight maintenance achieved using a fully digital behavioral program. The results suggest that Noom Weight is associated with successful weight maintenance in a substantial proportion of users. Future research will use a randomized controlled trial to track weight maintenance after random assignment and at a 2 year follow-up.
Stereospecific formation of five-membered metallacycles. Zirconaindans from thermally generated (.eta.2-dehydrobenzene)dicyclopentadienylzirconium(II) and cis- and trans-stilbene (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecific formation of five-membered metallacycles. Zirconaindans from thermally generated (.eta.2-dehydrobenzene)dicyclopentadienylzirconium(II) and cis- and trans-stilbeneKurt Kropp and Gerhard ErkerCite this: Organometallics 1982, 1, 9, 1246–1247Publication Date (Print):September 1, 1982Publication History Published online1 May 2002Published inissue 1 September 1982https://pubs.acs.org/doi/10.1021/om00069a029https://doi.org/10.1021/om00069a029research-articleACS PublicationsRequest reuse permissionsArticle Views219Altmetric-Citations54LEARN 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
Peptides in apoptosis research (2002)

Apoptosis is a complex process that plays a central role in physiological and pathological cell death. This fast evolving research area has experienced incredible development in the past few years. Progress in the knowledge of the structure of many of the main molecular actors of the apoptotic signal transduction pathways has driven the design of synthetic peptides that in some cases can function as simplified versions of their parent proteins. These molecules are contributing to a better understanding of the activity and regulation of apoptotic proteins and also are setting the basis for the discovery of effective drugs to combat important diseases related to apoptosis. Most applications of peptides in apoptosis research are so far related to caspases, caspase regulatory proteins, such as LAPs and Smac, and proteins of the Bcl-2 family. Additionally, important perspectives are open to other systems, such as the macromolecular assemblies that are responsible for the activation of initiator caspases.
Neuroparasitic Infections: Nematodes (2005)

Globalization has produced an increase in the number of people at risk for contracting parasitic infection. Central nervous system infection by nematodal parasites can be devastating. Early recognition and treatment of infection can significantly decrease morbidity of the parasitic infection, as well as the risk of secondary superinfection. The clinical presentation, diagnosis, and treatment for five of the more common nematodal infections of the nervous system--Angiostrongylus spp., Baylisacaris procyonis, Gnathostoma spinigerum, Strongyloides stercoralis, and Toxocara spp.--is reviewed.