gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Dimeric Oligonucleotide Synthons Containing 2‐Deoxy‐3‐O‐phosphonomethyl‐α‐D‐erythro‐pentofuranosyl Nucleosides (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Three In-frame ATG, Clustered in the Translation Initiation Sequence of Human Factor IX Gene, Are Required for an Optimal Protein Production (1999)

Three in-frame potential methionine codons have been identified in human factor IX gene and are clustered at amino acids -46, -41 and -39. In view of initiating a gene therapy approach, human factor IX production has been evaluated after modifications of these first three in-frame translation start sites. To characterize the most efficient translation initiation context, five factor IX cDNA expression vectors directed by CMV promoter-enhancer were generated. These vectors contained different starting site combinations including one, two or three ATG. A quantitative analysis of factor IX production in stably transfected CHO cells and in a rabbit reticulocyte lysate cell free system revealed the ability of all single site to generate fully active factor IX. However, the factor IX production level increased with the ATG number and the wild type (WT) cDNA bearing the 3 ATG induced the highest protein production. A truncated intron I of factor IX, previously suggested of having an expression-augmenting activity, was also placed in the WT factor IX cDNA. In stably transfected CHO cells, a 8-fold increase in protein production was measured. These results show that at least in vitro, the presence of the three ATG seems to be crucial for a maximal factor IX production. The data also suggest that both the three ATG and the truncated intron I are required for an optimal factor IX production in a perspective of a human gene therapy of haemophilia.
28 GHz millimeter wave cellular communication measurements for reflection and penetration loss in and around buildings in New York city (2013)

In this paper, we present reflection coefficients and penetration losses for common building materials at 28 GHz for the design and deployment of future millimeter wave mobile communication networks. Reflections from walls and buildings and penetration losses were measured for indoor and outdoor materials, such as tinted glass, clear glass, brick, concrete, and drywall at 28 GHz in New York City. A 400 Mega-chip-per-second sliding correlator channel sounder and 24.5 dBi steerable horn antennas were used to emulate future mobile devices with adaptive antennas that will likely be used in future millimeter wave cellular systems [1]. Measurements in and around buildings show that outdoor building materials are excellent reflectors with the largest measured reflection coefficient of 0.896 for tinted glass as compared to indoor building materials that are less reflective. We also found that penetration loss is dependent not only on the number of obstructions and distance between transmitter and receiver, but also on the surrounding environment. The greatest penetration loss containing three interior walls of an office building was found to be 45.1 dB, with 11.39 m separation between the transmitter and receiver.
Selective Proteolysis of the J Chain Component in Human Polymeric Immunoglobulin (1977)

To clarify the losses that have been observed in the J chain portion of human IgM and IgA, were carried out studies on the enzymatic susceptibility of the J polypeptide. When Waldenström macroglobulins and myeloma IgA polymers were subjected to limited proteolysis with various endopeptidases, only subtilisin was found to attack the J chain component. The pattern of cleavage was a function of the polymer species. The J chain in IgM was highly susceptible to digestion, quantitative cleavage being achieved at very low enzyme to IgM ratios and without significant changes in the remaining pentamer structure. Analyses of the digestion products showed that the initial cleavage occurred at an exposed region midway in the J sequence and was followed by extensive degradation of the carboxy-terminal segment. These findings indicated that the observed loss of the IgM J component can be explained by the inadvertent introduction of subtilisin in vitro or by the attack of in vivo enzymes with a specificity similar to subtilisin. In contrast, the IgA J chain was found to be much more resistant to subtilisin proteolysis; its cleavage required higher enzyme concentrations and was accompanied by significant degradation of the alpha-chains. Thus, it appears unlikely that the IgA J polypeptide is degraded by either in vitro or in vivo enzymes unless its accessibility is first enhanced by changes in the IgA Fc structure.
Tissue-Specific Promoter Usage in the D 1A Dopamine Receptor Gene in Brain and Kidney (1997)

The D1A dopamine receptor gene consists of a short, noncoding exon 1 separated from a longer coding exon 2 by a small intron. Recently, we found that in addition to its original TATA-less promoter located upstream of exon 1, the human D1A dopamine receptor gene is transcribed in neural cells from a second strong promoter located in its intron. In the present study, we addressed the possibility that these two promoters are used for the tissue-specific regulation of the D1A gene in neuronal and renal cells. Reverse transcription polymerase chain reaction revealed that D1A transcripts in the kidneys of humans and rats lack exon 1. Transient transfection analysis of these two promoters in D1A-expressing cells indicated that the upstream promoter has no detectable activity in the opossum kidney (OK) cell line, in contrast to its strong activity in two neuronal cell lines, SK-N-MC and NS20Y. On the other hand, the D1A intron promoter showed transcriptional activity both in OK cells and in neuronal cells. The activator sequence AR1, which enhances transcription from the upstream promoter in SK-N-MC and NS20Y cells, could not activate this promoter in OK cells. In addition, no protein binding to AR1 could be detected by gel mobility shift assay using nuclear extracts from either OK cells or from rat kidney tissue. These findings indicate that the differential expression of short and long D1A transcripts is due, at least in part, to the tissue-specific expression of the activator protein binding to AR1 driving transcription from the upstream promoter. Absence of this activator protein accounts for the nonfunctional D1A upstream promoter in the kidney.
Foxp3+CD25+CD4+ natural regulatory T cells in dominant self‐tolerance and autoimmune disease (2006)

Naturally arising CD25+ CD4+ regulatory T (Treg) cells, most of which are produced by the normal thymus as a functionally mature T-cell subpopulation, play key roles in the maintenance of immunologic self-tolerance and negative control of a variety of physiological and pathological immune responses. Natural Tregs specifically express Foxp3, a transcription factor that plays a critical role in their development and function. Complete depletion of Foxp3-expressing natural Tregs, whether they are CD25+ or CD25-, activates even weak or rare self-reactive T-cell clones, inducing severe and widespread autoimmune/inflammatory diseases. Natural Tregs are highly dependent on exogenously provided interleukin (IL)-2 for their survival in the periphery. In addition to Foxp3 and IL-2/IL-2 receptor, deficiency or functional alteration of other molecules, expressed by T cells or non-T cells, may affect the development/function of Tregs or self-reactive T cells, or both, and consequently tip the peripheral balance between the two populations toward autoimmunity. Elucidation of the molecular and cellular basis of this Treg-mediated active maintenance of self-tolerance will facilitate both our understanding of the pathogenetic mechanism of autoimmune disease and the development of novel methods of autoimmune disease prevention and treatment via enhancing and re-establishing Treg-mediated dominant control over self-reactive T cells.
Cost-effectiveness of PCSK9 Inhibitor Therapy (2016)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
mCiRNA—Synaptic Crystal Ball? (2012)

Comment on: Sheinerman KS, Tsivinsky VG, Crawford F, Mullan MJ, Abdullah L, Umansky SR. Plasma microRNA biomarkers for detection of mild cognitive impairment. Aging (Albany NY). 2012; 4:590-605.
Predicting outcome in hematological stem cell transplantation. (2002)

This review summarizes recent results investigating the role of certain cytokine gene polymorphisms, including those of TNF-alpha, IFN-gamma, IL-6, IL-10 and IL-1 receptor antagonist (IL-1Ra), in allogeneic stem cell transplantation. It discusses their role in predicting outcome and the development of a genetic risk index for graft versus host disease (GvHD) in HLA-matched sibling transplants. By the comparative use of an in vitro human skin explant model, initial results suggest that certain cytokine gene polymorphisms may be associated with more severe disease.
Optically active chlorohydrins as chiral C3 and C4 building units: Microbial resolution and synthetic applications (1998)

Production of highly optically active C3 and C4 chlorohydrins was developed by using the bacteria stereoselectively dehalogenating and assimilating the racemic substrate: Pseudomonas sp. and Alcaligenes sp. These bacteria stereoselectively assimilate (RS)-2,3-dichloro-1-propanol (DCP) and (RS)-3-chloro-1,2-propanediol (CPD) followed by microbial preparation of (R)- and (S)-DCP, and (R)- and (S)-CPD with >99% ee. A novel dehalogenating enzyme, halohydrin dehydro-dehalogenase from one of the above strains, Alcaligenes sp. DS-S-7G, was applicable for preparation of optically active 1,2-diols with 60–99% ee. Moreover, microbial resolution of C4 chlorohydrins with whole cells of Pseudomonas sp. was carried out. This resolution reaction using the resting cells gave (R)- and (S)-4-chloro-3-hydroxybutyrate (CHB) and (S)-4-chloro-3-hydroxybutyronitrile (BN) with >98% ee. In the case of the resting cells of Enterobacter sp., both (R)-CHB (>99% ee) and (S)-3-hydroxy-γ-butyrolactone (95% ee) with excellent yield were obtained. Also, some typical synthetic applications using the above chiral C3 and C4 synthons were introduced: ferroelectric liquid crystals, optically active β-blockers, and other chiral pharmaceuticals. Chirality 10:682–692, 1998. © 1998 Wiley-Liss, Inc.
Application of adhesives in MEMS and MOEMS assembly: a review (2003)

This paper presents a review of the recent literature on the use of adhesives in MEMS packaging applications. The aim of this review has been to establish the current applications of adhesives in MEMS and MOEMS assembly and to investigate the limitations and future requirements of these materials. The review has shown that while there is a wealth of information available on the packaging of MEMS devices, there is very limited detail available within the public domain regarding the specific uses of adhesives and in particular exactly which products are in use. The paper begins with an overview of the uses of adhesives in MEMS packaging, subdivided into sections on structural adhesives, adhesives for optical applications and other applications. The paper then describes methods for adhesive dispensing and issues with adhesive use which affect the reliability of the package. The reliability of MEMS devices assembled using adhesives is a challenging issue, being more than a simple combination of electrical, mechanical and material reliability. Many failure modes in MEMS devices can be attributed to the adhesives used in the assembly; for example, thermal expansion mismatches can cause stress in the die attach, while outgassing from epoxies can cause failure of sealed devices and contamination of optical surfaces.
Adenoviral Gene Transfer of Phospholamban in Isolated Rat Cardiomyocytes (1997)

Phospholamban forms an integral part of the cardiac sarcoplasmic reticulum (SR) and regulates the activity of SR Ca(2+)-ATPase (SERCA2a). A number of studies have suggested a decrease in SERCA2a relative to phospholamban in heart failure. To test the hypothesis that changes in the relative abundance of phospholamban to SERCA2a could account for the pathophysiological abnormalities in Ca2+ handling observed in failing myocardium, we created a recombinant adenovirus designed to overexpress phospholamban (Ad.RSV.PL). In neonatal rat cardiomyocytes, Ad.RSV.PL increased the expression of phospholamban in a concentration-dependent fashion, reaching 280 +/- 43% at a multiplicity of infection (MOI) of 10.0 plaque forming units (pfu)/cell at 48 hours. The relationship between Ca(2+)-ATPase activity and [Ca2+] was shifted rightward in membrane preparations from cardiomyocytes infected with Ad.RSV.PL. Intracellular Ca2+ transients measured in the neonatal cells infected with Ad.RSV.PL (MOI, 10 pfu/cell) were characterized by (1) a significant prolongation of the relaxation phase (344 +/- 26 versus 710 +/- 56 milliseconds, P < .01), (2) a decrease in peak [Ca2+]i (967 +/- 43 versus 630 +/- 33 nmol/L, P < .01), and (3) an elevation in resting [Ca2+]i (143 +/- 14 versus 213 +/- 17 nmol/L, P < .05). Similarly, the time course of shortening was prolonged in myocytes infected with Ad.RSV.PL. These effects were partially restored by simultaneous transduction with an adenovirus carrying SERCA2a. Cardiomyocytes infected with Ad.RSV.PL had an abnormal frequency response: a decrease in peak [Ca2+]i and an increase in resting [Ca2+]i with increasing frequency. These findings indicate that adenovirus-mediated gene transfer of phospholamban modifies intracellular Ca2+ handling and the frequency response in cardiomyocytes. Our results suggest that alterations in the ratio of phospholamban to SERCA2a could account for the abnormalities in Ca2+ handling observed in heart failure and that overexpression of SERCA2a can largely correct these abnormalities.
Fast in situ generated ɛ-polylysine-poly (ethylene glycol) hydrogels as tissue adhesives and hemostatic materials using an enzyme-catalyzed method (2014)

In this study, novel bio-inspired in situ hydrogels as tissue adhesives and hemostatic materials were designed and prepared based on ɛ-polylysine-grafted poly(ethylene glycol) and tyramine via enzymatic cross-linking. The enzymatic cross-linked method enabled fast gelation within seconds, which facilitated its therapeutic applications. By changing the cross-linking conditions, the storage modulus of the hydrogels could be tunable and the mechanical strength influenced the tissue adhesiveness of the hydrogels. Besides, the hydrogels showed fine network structures with appropriate pore sizes, which were thought to be a contributing factor to the strong adhesiveness. Benefiting from the strong mechanical properties and fine network structures, the ɛ-polylysine-grafted poly(ethylene glycol) and tyramine hydrogels exhibited superior wound-healing and hemostatic ability compared to conventional and commercially available medical materials. Moreover, indirect cytotoxicity assessment indicated that the ɛ-polylysine-grafted poly(ethylene glycol) and tyramine hydrogels were nontoxic to the L929 cell. These results demonstrated that the enzymatic cross-linked in situ ɛ-polylysine hydrogels hold high potential for tissue sealants and hemostatic materials.
Expanded dynamic range of fluorescent indicators for Ca 2+ by circularly permuted yellow fluorescent proteins (2004)

Fluorescence resonance energy transfer (FRET) technology has been used to develop genetically encoded fluorescent indicators for various cellular functions. Although most indicators have cyan- and yellow-emitting fluorescent proteins (CFP and YFP) as FRET donor and acceptor, their poor dynamic range often prevents detection of subtle but significant signals. Here, we optimized the relative orientation of the two chromophores in the Ca(2+) indicator, yellow cameleon (YC), by fusing YFP at different angles. We generated circularly permuted YFPs (cpYFPs) that showed efficient maturation and acid stability. One of the cpYFPs incorporated in YC absorbs a great amount of excited energy from CFP in its Ca(2+)-saturated form, thereby increasing the Ca(2+)-dependent change in the ratio of YFP/CFP by nearly 600%. Both in cultured cells and in the nervous system of transgenic mice, the new YC enables visualization of subcellular Ca(2+) dynamics with better spatial and temporal resolution than before. Our study provides an important guide for the development and improvement of indicators using GFP-based FRET.
Immunosuppressive effects of photodynamic therapy by topical aminolevulinic acid (2007)

Photodynamic therapy (PDT) has been used for inflammatory skin disorders as well as superficial skin cancers such as solar keratosis and Bowen's disease. Whether PDT with topical application of aminolevulinic acid (ALA) and exposure to visible light has a similar immunosuppressive action to ultraviolet phototherapy was investigated using a murine contact hypersensitivity (CHS) model. The number of epidermal Langerhans cells (LC) was decreased with their morphological changes 1 day after PDT with the minimal level at 5 days and gradual recovery thereafter. Conversely, the number of CD11c(+) I-A(+) cells was significantly increased in the draining lymph nodes after PDT. This suggests that LC moved from PDT-treated skin, resulting in the decrement of epidermal LC and migration to lymph nodes. CHS response to DNFB applied on the PDT-treated skin with 20% ALA and 40 J/cm(2) visible light was significantly suppressed (local immunosuppression). When mice were treated with 80 J/cm(2) of PDT, CHS response to the antigen applied on untreated distant skin was also significantly suppressed (systemic immunosuppression). The locally or systemically immunosuppressed mice by PDT were attempted to sensitize again with DNFB on non-treated skin, but elicitation responses were significantly suppressed. However, these mice were able to be sensitized with another hapten, oxasolone. Thus, a hapten-specific immunological unresponsiveness (tolerance) was induced in mice by topical ALA-PDT. These findings suggest that PDT has a potential immunological contribution to clinical efficacy for inflammatory diseases identical to ultraviolet phototherapies.
Influence of probe pressure on the diffuse correlation spectroscopy blood flow signal: extra-cerebral contributions (2013)

A pilot study explores relative contributions of extra-cerebral (scalp/skull) versus brain (cerebral) tissues to the blood flow index determined by diffuse correlation spectroscopy (DCS). Microvascular DCS flow measurements were made on the head during baseline and breath-holding/hyperventilation tasks, both with and without pressure. Baseline (resting) data enabled estimation of extra-cerebral flow signals and their pressure dependencies. A simple two-component model was used to derive baseline and activated cerebral blood flow (CBF) signals, and the DCS flow indices were also cross-correlated with concurrent Transcranial Doppler Ultrasound (TCD) blood velocity measurements. The study suggests new pressure-dependent experimental paradigms for elucidation of blood flow contributions from extra-cerebral and cerebral tissues.
The cytomorphological features of low‐grade urothelial neoplasms vary by specimen type (2016)

Approximately 50% of UT specimens with LGUN on follow-up demonstrated atypical features. Based on comparison with benign UW controls, TFs, cytoplasmic tails, nuclear eccentricity, and enlarged nuclei were more pronounced in neoplastic UW than VU specimens, suggesting that the method of urine specimen procurement affects the presence of certain low-grade features. Cancer Cytopathol 2016;124:552-64. © 2016 American Cancer Society.
Preventing nondesired RNA‐primed RNA extension catalyzed by T7 RNA polymerase (2003)

The transcription patterns of 64 linear double stranded DNA templates obtained with T7 RNA polymerase were investigated. These templates consisted of 17 nucleotide-long sequences under the control of the minimal bacteriophage T7 promoter and represented all possible combinations of nucleotides at positions +8, +10 and +11. Two clearly distinct types of template were identified, which produced the range of transcription patterns observed: (a) those that yielded 17-nucleotide-long RNA as the only detectable run-off product (only 15% of the total), and (b) templates that in addition to the expected full-length RNA, produced other products longer than 17 nucleotides. Self-complementarity analysis of the expected run-off transcripts showed that those obtained from the first type of template were able to form stable intermolecular duplexes with non-base-paired 3'-ends. However, the second type of template yielded RNAs able to generate energetically favorable intermolecular duplexes with 3'-end complementarity, therefore yielding an RNA-primed RNA-template. The gel-purified 17-nucleotide-long RNAs transcribed from the latter yielded longer products when incubated under in vitro transcription conditions in the absence of a DNA template. No extension was observed when assaying the 17-nucleotide RNA products resulting from the first type of template. We observed that just a single nucleotide change within the DNA template could convert the RNA product from an RNA-primed template into a nonextendible dimer thus leading to a drastic switch of the 17-nucleotide product yield from less than 10% to 100%. Further, two type B DNA templates were extended by two nucleotides at the 3'-end, to produce RNA transcripts theoretically unable to form 3'-end base-paired duplexes. The full-length products of these modified DNA templates were found to be nonextendible by T7 RNA polymerase under the standard in vitro transcription conditions.
Fitting formal methods into the design cycle (1994)

This tutorial introduces several methods of formal hardware verification that could potentially have a practical impact on the design process. The measure of success in integrating these methods into a design methodology is arguably not the ability to provide formal guarantees of correctness, but rather to detect design errors in a timely manner, as the design evolves. Based on this criterion, and some limited practical experience, we consider where the various methods might fit into the life cycle of a design, what their capabilities and shortcomings are, and how the design process might change in order to accommodate formal methods.