gebhart/patrepeval huggingface dataset:
Codon-Optimized RPGR Improves Stability and Efficacy of AAV8 Gene Therapy in Two Mouse Models of X-Linked Retinitis Pigmentosa (2017)

X-linked retinitis pigmentosa (XLRP) is generally a severe form of retinitis pigmentosa, a neurodegenerative, blinding disorder of the retina. 70% of XLRP cases are due to mutations in the retina-specific isoform of the gene encoding retinitis pigmentosa GTPase regulator (RPGR<sup>ORF15</sup>). Despite successful RPGR<sup>ORF15</sup> gene replacement with adeno-associated viral (AAV) vectors being established in a number of animal models of XLRP, progression to human trials has not yet been possible. The inherent sequence instability in the purine-rich region of RPGR<sup>ORF15</sup> (which contains highly repetitive nucleotide sequences) leads to unpredictable recombination errors during viral vector cloning. While deleted RPGR may show some efficacy in animal models, which have milder disease, the therapeutic effect of a mutated RPGR variant in patients with XLRP cannot be predicted. Here, we describe an optimized gene replacement therapy for human XLRP disease using an AAV8 vector that reliably and consistently produces the full-length correct RPGR protein. The glutamylation pattern in the RPGR protein derived from the codon-optimized sequence is indistinguishable from the wild-type variant, implying that codon optimization does not significantly alter post-translational modification. The codon-optimized sequence has superior stability and expression levels in vitro. Significantly, when delivered by AAV8 vector and driven by the rhodopsin kinase promoter, the codon-optimized RPGR rescues the disease phenotype in two relevant animal models (Rpgr<sup>-/y</sup> and C57BL/6J<sup>Rd9/Boc</sup>) and shows good safety in C57BL6/J wild-type mice. This work provides the basis for clinical trial development to treat patients with XLRP caused by RPGR mutations.
Synthesis and Characterization of Poly(2,5-bis(N-methyl-N-hexylamino)phenylene vinylene), a Conjugated Polymer for Light-Emitting Diodes (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTSynthesis and Characterization of Poly(2,5-bis(N-methyl-N-hexylamino)phenylene vinylene), a Conjugated Polymer for Light-Emitting DiodesJ. D. Stenger-Smith, P. Zarras, L. H. Merwin, S. E. Shaheen, B. Kippelen, and N. PeyghambarianView Author Information Chemistry and Materials Branch, Naval Air Warfare Center, Weapons Division, China Lake, California 93555 Optical Sciences Center, University of Arizona, Tucson, Arizona 85721 Cite this: Macromolecules 1998, 31, 21, 7566–7569Publication Date (Web):October 2, 1998Publication History Received2 June 1998Revised26 August 1998Published online2 October 1998Published inissue 1 October 1998https://pubs.acs.org/doi/10.1021/ma980865lhttps://doi.org/10.1021/ma980865lrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views407Altmetric-Citations26LEARN 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 SUBJECTS:Alcohols,Anions,Aromatic compounds,Diodes,Mixtures Get e-Alerts
Continuous trichloroethylene biodegradation by Pseudomonas putida F1 in a biofilm reactor and determination of an optimal feeding path via a response surface model (2021)

Abstract Reactor design and feeding strategies are the key to successful trichloroethylene (TCE) treatment via cometabolism. An easy to maintain and operate laboratory scale packed‐bed biofilm reactor, featuring recycled gas and liquid effluent streams, was developed for continuous aerobic aqueous‐phase TCE biodegradation using Pseudomonas putida F1 as the biocatalyst and toluene as the primary substrate. The impacts of the influent toluene and TCE concentrations, flow rates, and recycle rates on TCE biodegradation were studied. Multivariate factors, including influent toluene and TCE concentrations, their interactions, and flow rates were further analyzed via a response surface model (RSM). Results showed that such bioreactor design eliminated oxygen limitation and removed or substantially reduced toluene competitive inhibition on TCE degradation. A TCE removal efficiency of &gt;90% was achieved at an influent TCE concentration of ≤0.3 mg/L under an ˜8‐min mean hydraulic retention time. Toluene and TCE concentrations, in both linear and quadratic forms, were the most significant factors for TCE degradation, indicating both cell regenerating and inhibiting effects from toluene and a toxic effect from TCE. This RSM analysis has successfully identified an optimal influent toluene concentration path for each influent TCE concentration and provided insight for an extended TCE degradation at higher TCE concentrations.
Heat-Shock and Fresh Cut Lettuce (1998)

Introduct ion Browning of fresh fruits and vegetables reduces quality and is often the factor limiting shelflife and marketability (Bolin and Huxoll, 1991; Couture et al., 1993). This is especially true when these horticultural commodities are wounded by cutting, peeling, or abrading the surface. Enzymatic and non-enzymatic reactions with phenolic compounds produce brown pigments in plant tissue. Some tissues (e.g., artichokes) contain high levels of preformed phenolic compounds and rapidly brown in the air after wounding. Preventing browning in these tissues requires deactivation of the enzymes responsible for browning (e.g., polyphenoloxidase), exclusion of oxygen (e.g., oxygen levels below 1%), or application of chemical antioxidants (e.g., ascorbic acid). In other tissue, (e.g., lettuce) the quantity of phenolic compounds in uninjured tissue is low and browning follows the enhanced synthesis and accumulation of phenolic compounds (TomasBarberan et al., 1997). Wounding (e.g., cutting, cracking or breaking of lettuce) produces a signal that migrates through the tissue and induces the synthesis of enzymes in the metabolic pathway responsible for increased production of phenolic compounds (Ke and Saltveit, 1989; Peiser et al., 1998). The first enzyme in the phenylpropanoid pathway is phenylalanine ammonia-lyase (PAL). Induced synthesis of this enzyme after wounding is rapidly followed by the accumulation of phenolic compounds like chlorogenic, isochlorogenic and dicaffeoyl tartaric acid, compounds that are associated with browning in lettuce (Tomas-Barberan et al., 1997.).
Hospitalization Trends for Acute Kidney Injury in Kidney Transplant Recipients in the United States, 2004–2014 (2019)

The incidence of hospitalizations for AKI and AKI-D among KTRs is rapidly rising. This has been accompanied by significant improvements in in-hospital mortality, LOS, and cost.
Adenovirus-mediated gene delivery: Potential applications for gene and cell-based therapies in the new era of personalized medicine (2017)

With rapid advances in understanding molecular pathogenesis of human diseases in the era of genome sciences and systems biology, it is anticipated that increasing numbers of therapeutic genes or targets will become available for targeted therapies. Despite numerous setbacks, efficacious gene and/or cell-based therapies still hold the great promise to revolutionize the clinical management of human diseases. It is wildly recognized that poor gene delivery is the limiting factor for most <i>in vivo</i> gene therapies. There has been a long-lasting interest in using viral vectors, especially adenoviral vectors, to deliver therapeutic genes for the past two decades. Among all currently available viral vectors, adenovirus is the most efficient gene delivery system in a broad range of cell and tissue types. The applications of adenoviral vectors in gene delivery have greatly increased in number and efficiency since their initial development. In fact, among over 2,000 gene therapy clinical trials approved worldwide since 1989, a significant portion of the trials have utilized adenoviral vectors. This review aims to provide a comprehensive overview on the characteristics of adenoviral vectors, including adenoviral biology, approaches to engineering adenoviral vectors, and their applications in clinical and pre-clinical studies with an emphasis in the areas of cancer treatment, vaccination and regenerative medicine. Current challenges and future directions regarding the use of adenoviral vectors are also discussed. It is expected that the continued improvements in adenoviral vectors should provide great opportunities for cell and gene therapies to live up to its enormous potential in personalized medicine.
Tumor Necrosis Factor Alpha System and Plasma Adiponectin Concentration in Women with Gestational Diabetes (2005)

Plasma concentrations of adiponectin, tumor necrosis factor-alpha (TNF-alpha) and its soluble receptors sTNFR-1 and sTNFR-2 were measured in 80 patients with gestational diabetes (GDM) (mean age 29.0 +/- 4.9 years) and 30 pregnant women with normal glucose tolerance (NGT) (mean age 28.2 +/- 6.0 years). We found that GDM patients had significantly lower concentrations of adiponectin (11.28 +/- 5.91 vs. 16.31 +/- 6.04 microg/ml, p = 0.00009) and elevated levels of TNF-alpha (1.71 +/- 0.92 vs. 1.27 +/- 0.42 pg/ml, p = 0.0175) in comparison to NGT women. The differences remained statistically significant after adjusting for BMI. Plasma levels of sTNFR-1 and sTNFR-2 also tended to be higher in GDM patients. In the GDM group TNF-alpha concentrations correlated significantly with sTNFR-1 (r = 0.444, p = 0.00008), sTNFR-2 (r = 0.364, p = 0.0016) and with C-peptide concentrations (r = 0.318, p = 0.016), whereas in women with NGT TNF-alpha correlated only with TG levels (r = 0.50, p = 0.024). Multivariate linear regression analysis revealed that prepregnant BMI was the most predictive indicator of TNF-alpha concentrations in GDM women. TG concentrations as well as BMI before pregnancy and at the time of sampling in pregnant NGT women were significant predictors, explaining 62% of the variance in TNF-alpha concentration. There were also negative correlations between adiponectin concentrations and a pregestational BMI (r = - 0.298, p = 0.009), BMI at the time of sampling (r = - 0.239, p = 0.034) and TG concentrations (r = - 0.379, p = 0.039) in GDM patients, whereas women with NGT showed only a negative correlation between adiponectin and TG concentrations (r = - 0.488, p = 0.025). In a multivariate regression analysis, prepregnancy BMI and TG levels remained significant predictors, explaining 39% of the variation in plasma adiponectin concentration in GDM women. In conclusion, our results suggest that decreased adiponectin concentration in GDM may not simply reflect maternal adiposity and insulin resistant state, but may contribute to the impaired glucose metabolism during pregnancy, with potential implications for screening and prevention of the disease.
Environmental Friendly Ways to Generate Renewable Energy from Municipal Solid Waste (2016)

Economic growth and rapid urbanization are resulting into increase in generation of municipal solid waste (MSW). In India, approximately 68 MT of MSW generated annually in urban areas and more than 80% is disposed in unhygienic manner leading to problems of health and environment to inhabitants. To manage MSW, there is a need to plan infrastructure development. There are many technologies available for handling MSW which treat plastic to convert fuel oil by gasification, pyrolysis, biomethanation and catalytic conversions. The useful products like liquid fuels, chemicals and power are being generated through these processes. The final products need to comply with environmental regulations and demand a lot of technological improvement. Based on MSW/feed quality, there is a need to identify the suitable technology for converting MSW into useful products, which can meet the statuary regulations. Hence, treating MSW, converting into useful products and selection of suitable technology is a big challenge. The present paper focuses to compare: All suitable treatment technologies and products generated from MSW. Types of thermal treatments like combustion/incineration, gasification and pyrolysis. It also highlights development of a systematic approach to comply with all environmental regulations to create value for all types of MSW and reduce landfill.
Cartoon+Texture Image Decomposition (2011)

In this article we give a thorough description of the algorithm proposed in [A. Buades, T. Le, J.M. Morel and L. Vese, Fast cartoon + texture image filters, IEEE Transactions on Image Processing, 2010] for cartoon+texture decomposition using of a nonlinear low pass-high pass filter pair.
Wide area disk-shaped vacuum ultraviolet lamp (1990)

A wide area vacuum ultraviolet (VUV) lamp employs a ring-shaped cold cathode to produce an electron beam excited plasma of disk geometry. When excited by the soft vacuum electron beam, molecular hydrogen, nitrogen, and atomic helium emit strong atomic resonance radiation at 121.6, 120, and 58 nm, respectively. The VUV optical power emitted on the atomic resonance line is typically 6–10% of the total applied discharge power. The spatial uniformity of the VUV emission intensity at a discharge input power level of 30 W approaches 6% across the entire disk diameter, up to a maximum of 20 cm.
ChemInform Abstract: SYNTHETIC APPROACHES TO PEDERIN. A SYNTHESIS OF (.+‐.)‐BENZOYLPEDAMIDE (1984)

Abstract Die im Titel genannte Verbindung (IX) wird auf dem im Formelschema skizzierten Weg synthetisiert.
Strategy for Cross-Bores in High Pressure Containers (1969)

It is frequently necessary to drill a cross-bore through the wall of a cylindrical pressure vessel, and it tends to be taken for granted that the cross-bore—itself of circular section— should lie along a diameter of the main cross-section. The weakening effect of such a hole is well known, and reduces the safe working pressure down to 2/5 of the value for the undisturbed cylinder in the case of a Tresca material, or nearly down to 1/3 in the case of a von Mises material. The paper shows how it is possible to reclaim a large proportion of the ‘lost’ pressure capacity by use of a cross-bore which is either elliptical in section, or, more conveniently, round but offset from a diametral centre-line. Such procedure could thus also greatly improve the fatigue life of the pressure vessel.
Haloferax volcanii UbaA, catalytic engine for sampylation and sulfur transfer (2016)

The Small Archaeal Modifier Proteins (SAMPs) from Haloferax volcanii belong to the group of ubiquitin like proteins (Ubls) that act both as protein modifiers and sulfur carriers. The E1-like enzyme UbaA is essential for SAMP activation and therefore required for both sampylation and sulfur transfer. Here, we provide a commentary on the thorough characterization of UbaA by J. Maupin-Furlow and colleagues.
Human lactobacilli as supplementation of clindamycin to patients with bacterial vaginosis reduce the recurrence rate; a 6-month, double-blind, randomized, placebo-controlled study (2008)

ISRCTN62879834.
Photonic Crystal and Quantum Dot Technologies for Ultra-small and Ultra-fast All-optical Flip-flop (2009)

Nano-photonic technologies of GaAs-based two-dimensional photonic crystal (2DPC) slab waveguides and InAs quantum dots (QDs) are reviewed for symmetric Mach-Zehnder type, ultra-small and ultra-fast all-optical switch (PC-SMZ) and optical flip-flop device (PC-FF). In the 1st phase of this work, ultra-fast (~ps) and ultra-low energy (~100 fJ) switching has been demonstrated using the PC-SMZ chip with 600 μm × 300 μm in size. In the 2nd phase, the concept of the PC-FF based on the dual PC-SMZs for providing a latch function has been proposed for a future ultra-fast optical digital processor. One of the priority subjects is to establish a new design method, i.e., topology optimization method of the 2DPC waveguide with wide/flat bandwidth, high transmittance and low reflectivity. Another one is to develop a selective-area-MBE growth technique with a metal-mask method for high-density and highly uniform InAs QDs with different absorption wavelengths in different areas.
Enantioselective total synthesis of (+)-negamycin and (-)-epinegamycin by an asymmetric 1,3-dipolar cycloaddition (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantioselective total synthesis of (+)-negamycin and (-)-epinegamycin by an asymmetric 1,3-dipolar cycloadditionHideo. Iida, Katsura. Kasahara, and Chihiro. KibayashiCite this: J. Am. Chem. Soc. 1986, 108, 15, 4647–4648Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/ja00275a064https://doi.org/10.1021/ja00275a064research-articleACS PublicationsRequest reuse permissionsArticle Views524Altmetric-Citations77LEARN 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
ACR Guidance Document for Safe MR Practices: 2007 (2007)

ACR Guidance Document for Safe MR Practices: 2007Emanuel Kanal1, A. James Barkovich2, Charlotte Bell3, James P. Borgstede4, William G. Bradley, Jr.5, Jerry W. Froelich6, Tobias Gilk7, J. Rod Gimbel8, John Gosbee9, Ellisa Kuhni-Kaminski1, James W. Lester, Jr.10, John Nyenhuis11, Yoav Parag1, Daniel J. Schaefer12, Elizabeth A. Sebek-Scoumis1, Jeffrey Weinreb13, Loren A. Zaremba14, Pamela Wilcox15, Leonard Lucey15, Nancy Sass15 and the ACR Blue Ribbon Panel on MR SafetyAudio Available | Share
Synthesis and Stereochemical Analysis of Dynamic Planar Chiral Nine-Membered Diallylic Amide: Significant Substituent Effect on Stereochemical Stability (2019)

C4-Methyl substituted nine-membered diallylic cyclic amide 1ac was synthesized.HPLC analysis using a chiral stationary phase revealed the presence of isolable enantiomers, whose absolute stereochemistry were determined by X-ray analysis.Studies on the stereochemical stability of 1ac showed that its chirality is more labile than that of the non-substituted congener 1aa and C3-methyl substituted congener 1ab.Recently, we found that a series of nine-membered diallylic heterocycles 1 displayed appreciable planar chirality arising from the topological constraints in the ring system. 1 The stereochemical stability of 1 was strongly dependent on the heteroatom X (NY, O, SO n ) embedded in the ring and the substituent R on the alkene moiety. 1 X (R)-1 X
A NEW BIOMECHANICAL ASSESSMENT OF MILD TRAUMATIC BRAIN INJURY. PART I: METHODOLOGY (1999)

American professional football provides a unique opportunity to study mild traumatic brain injury (MTBI). That opportunity comes not from the particularly high frequency of occurrence, but from the following facts: (1)The game is played on a precisely laid out grid; (2) The movement of players is recorded by video cameras from a multitude of directions and angles; (3) The subjects are all of comparable stature, age and physical condition, and they are all equipped with virtually the same protective headgear; and (4) physicians at the sidelines are available immediately to diagnose and treat an injury. This unique laboratory is analyzed through a programme involving four complimentary approaches: (i) Video recordings of MTBI events are analyzed to determine the relative speed, direction and impact sites on player's heads; (ii) In addition to clinical observations made by team physicians, concussed and uninjured players are subjected to neuropsychological assessment; (iii) Re-enactments of certain collisions are conducted with instrumented anthropometric test devices (ATD's); and (iv) responses from the ATD heads are used to derive a mathematical model (finite element model (FEM)) of the human brain that predicts intracranial distortion patterns. The overall objective of this programme is to develop new biomechanical criteria for MTBI. This paper outlines the methodology, and considers one example of incident reconstruction. For the covering abstract of the conference see ITRD E203643.
Serum cytochrome c indicates in vivo apoptosis and can serve as a prognostic marker during cancer therapy (2005)

Despite significant progress in cancer therapy, the outcome of the treatment is often unfavorable. Better treatment monitoring would not only allow an individual more effective, patient-adjusted therapy, but also it would eliminate some of the side effects. Using a cytochrome c ELISA that was modified to increase sensitivity, we demonstrate that serum cytochrome c is a sensitive apoptotic marker in vivo reflecting therapy-induced cell death burden. Furthermore, increased serum cytochrome c level is a negative prognostic marker. Cancer patients whose serum cytochrome c level was normal 3 years ago have a twice as high probability to be still alive, as judged from sera samples collected for 3 years, analyzed recently and matched with survival data. Moreover, we show that serum cytochrome c and serum LDH-activity reflect different stages and different forms of cell death. Cellular cytochrome c release is specific for apoptosis, whereas increased LDH activity is an indicator of (secondary) necrosis. Whereas serum LDH activity reflects the "global" degree of cell death over a period of time, the sensitive cytochrome c-based method allows confirmation of the individual cancer therapy-induced and spontaneous cell death events. The combination of cytochrome c with tissue-specific markers may provide the foundation for precise monitoring of apoptosis in vivo, by "lab-on-the-chip" technology.