gebhart/patrepeval huggingface dataset:
Dynamic Gene Expression After Systemic Delivery of Plasmid DNA as Determined by <i>In Vivo</i> Bioluminescence Imaging (2005)

Nonviral gene therapy approaches face the challenge of achieving stable gene expression in target organs and tissues. We used fluorescence microscopy and in vivo imaging after rapid, high-volume delivery of plasmid DNA (pDNA) encoding DsRed and luciferase as products of the same mRNA to detect localized gene expression in liver. Plasmids encoding the luciferase gene transcriptionally regulated by cellular and viral promoters were injected under similar conditions to test for potency and stability of gene expression in the liver of adult mice. Animals were imaged at 3, 6, 12, 24, and 48 hr and followed up at 1- to 2-week intervals over 2 months to identify maximum and persistent luciferase expression after injection of equimolar amounts of each plasmid. Emitted light representing luciferase expression was detected as early as 3 hr after pDNA infusion, reaching maximum levels at 12 hr for promoters containing viral sequences and at 24 hr for elements from human genes. Viral elements displayed 10- to 20-fold higher peak levels of expression but also yielded the most dramatic decline in expression over 8 weeks. In contrast, only a moderate decrease was observed for the cellular ubiquitin C promoter during that same period of time. Both promoter-deleted and phosphoglycerate kinase (PGK)-containing plasmids failed to maintain luciferase expression at levels above the limit of detection. These results demonstrate fine temporal analyses of reporter gene activity using promoters of various strength, suggesting an effective and reproducible method for studying gene therapy vectors in vivo.
DNA methylation and demethylating drugs in myelodysplastic syndromes and secondary leukemias. (2002)

Treatment with demethylating agents, 5-azacytidine and decitabine, at present results in significantly higher response rates, improved quality of life, reduced risk of leukemic transformation, and improved survival, when compared to supportive care. Azacytidine and decitabine provide a new treatment option, and should be the treatment choice for elderly patients with high risk MDS. It is whorty in fact that azacytidine and decitabine are especially active in patients with poor prognosis MDS. The combination with histone deacetylase inhibitors may increase the efficacy of hypomethylating agents in vivo.
Femoral canal reaming in the polytrauma patient with chest injury. A clinical perspective. (1995)

It has been well documented that early fracture stabilization reduces morbidity and mortality in the patient who is multiply injured. However, controversy has developed recently concerning the timing and type of stabilization for the patient with multiple injuries who has sustained a femoral fracture and an associated severe chest injury. Reports from Europe have indicated an increased mortality rate and adult respiratory distress syndrome rate in the patient treated with reamed femoral rodding. A retrospective review of patients with multiple injuries with Injury Severity Scores of 18 points or greater who also had severe chest trauma was done at the Erie County Medical Center, Buffalo, NY. Three groups of patients were developed and studied: The patients in Group 1 had femoral fractures that were treated with early stabilization with a reamed rod; the patients in Group 2 had femoral fractures stabilized with plate fixation; and in Group 3, there were no femoral fractures. The Injury Severity Score for each group was nearly the same; however, the intensive care unit time was more than doubled in Group 2 and Group 3. There was a 33% adult respiratory distress syndrome rate in Group 2, a 27% rate in Group 3, and a 0% rate in Group 1. The mortality rate was highest for the group of patients without femoral fractures (Group 3), 10.9%. These clinical data seem to associate the chest injury with the increased adult respiratory distress syndrome and mortality rate, not the method of treatment for the femoral fracture.
Significance and therapeutic potential of the natriuretic peptides/cGMP/cGMP-dependent protein kinase pathway in vascular regeneration (2003)

Natriuretic peptides (NPs), which consist of atrial, brain, and C-type natriuretic peptides (ANP, BNP, and CNP, respectively), are characterized as cardiac or vascular hormones that elicit their biological effects by activation of the cGMPcGMP-dependent protein kinase (cGK) pathway. We recently reported that adenoviral gene transfer of CNP into rabbit blood vessels not only suppressed neointimal formation but also accelerated reendothelialization, a required step for endothelium-dependent vasorelaxation and antithrombogenicity. Accordingly, we investigated the therapeutic potential of the NPscGMPcGK pathway for vascular regeneration. In transgenic (Tg) mice that overexpress BNP in response to hindlimb ischemia, neovascularization with appropriate mural cell coating was accelerated without edema or bleeding, and impaired angiogenesis by the suppression of nitric oxide production was effectively rescued. Furthermore, in BNP-Tg mice, inflammatory cell infiltration in ischemic tissue and vascular superoxide production were suppressed compared with control mice. Ischemia-induced angiogenesis was also significantly potentiated in cGK type I Tg mice, but attenuated in cGK type I knockout mice. NPs significantly stimulated capillary network formation of cultured endothelial cells by cGK stimulation and subsequent Erk12 activation. Furthermore, gene transfer of CNP into ischemic muscles effectively accelerated angiogenesis. These findings reveal an action of the NPscGMPcGK pathway to exert multiple vasculoprotective and regenerative actions in the absence of apparent adverse effects, and therefore suggest that NPs as the endogenous cardiovascular hormone can be used as a strategy of therapeutic angiogenesis in patients with tissue ischemia.
Automated formal specification generation and refinement from requirement documents (2008)

Abstract The automatic generation of formal specifications from requirements suppresses the complexity of formal models manual creation and reveals the immediate benefits of its usage, such as the possibility to carry out refinements, and property verification, which contributes to project cost reduction and quality improvement. This paper proposes a Controlled Natural Language (CNL), a subset of English, used to write use case specifications according to a template. From these use cases a complete strategy and tools enable the generation of process algebraic formal models in the CSP notation. We define templates that represent requirements at different levels of abstraction, capturing different views of the system behavior. Moreover, a refinement notion is defined to connect the generated CSP models through an event mapping relation between abstract and concrete models. This notion is further applied to detail use case specifications and to automate its execution.
L-citrulline production from L-arginine by macrophage nitric oxide synthase. The ureido oxygen derives from dioxygen. (1990)

Previously proposed mechanisms for the production of L-citrulline from L-arginine by macrophage nitric oxide (NO.) synthase involve either hydrolysis of arginine or hydration of an intermediate and thus predict incorporation of water oxygen into L-citrulline. Macrophage NO. synthase was incubated with L-arginine, NADPH, tetrahydrobiopterin, FAD, and dithiothreitol in H2(18)/16O2. L-Citrulline produced in this reaction was analyzed with gas chromatography/mass spectrometry. Its mass spectrum matched that of L-citrulline generated in H2(16)O/16O2. The base fragment ion of m/z 99 was shown to contain the ureido carbonyl group by using L-[guanidino-13C]arginine as substrate. When the enzyme reaction was performed in H2(16)O/18O2, the base fragment ion shifted to m/z 101 with L-[guanidino-12C]arginine as the substrate and to m/z 102 with L-[guanidino-13C]arginine. These results indicate that the ureido oxygen of the L-citrulline product of macrophage NO.synthase derives from dioxygen and not from water.
Incorporating the human hearing properties in the signal subspace approach for speech enhancement (2003)

The major drawback of most noise reduction methods in speech applications is the annoying residual noise known as musical noise. A potential solution to this artifact is the incorporation of a human hearing model in the suppression filter design. However, since the available models are usually developed in the frequency domain, it is not clear how they can be applied in the signal subspace approach for speech enhancement. In this paper, we present a Frequency to Eigendomain Transformation (FET) which permits to calculate a perceptually based eigenfilter. This filter yields an improved result where better shaping of the residual noise, from a perceptual perspective, is achieved. The proposed method can also be used with the general case of colored noise. Spectrogram illustrations and listening test results are given to show the superiority of the proposed method over the conventional signal subspace approach.
Inactivation of radiolabeled RTEM .beta.-lactamase from Escherichia coli by clavulanic acid and 9-deoxyclavulanic acid (1981)

The interaction of the TEM-2 beta-lactamase with 9-deoxyclavulanic acid (3) and with both extensively labeled (2) and specifically labeled (1) clavulanic acid has been studied. The close similarity between 9-doexyclavulanate and clavulanate in kinetics, spectroscopic, and protein chemical terms show that the allyl alcohol group of clavulanate is irrelevant to its action as a beta-lactamase inactivator. Use of the radiolabeled samples of clavulanate shows that, of three irreversibly inactivated forms of the enzymes, two contain the whole clavulanate skeleton and the third only retains the carbon atoms of the original beta-lactam ring. These findings allow the complex interaction between clavulanic acid and the beta-lactamase to be defined more narrowly in chemical terms.
CORNEAL EPITHELIAL DEFECTS FOLLOWING VITRECTOMY SURGERY USING HAND-HELD, SEW-ON, AND NONCONTACT VIEWING LENSES (1999)

Purpose: To compare the incidence of corneal epithelial defects following vitrectomy surgery with Charles hand-held infusion lenses, Landers sew-on lenses, and the Oculus BIOM noncontact lens system. Methods: We performed a retrospective chart review of 234 patients who underwent initial vitrectomy surgery by one surgeon. We determined the presence and duration of postoperative epithelial defects and identified predisposing factors. Results: There were more corneal epithelial defects noted postoperatively in eyes with hand-held infusion lenses (23.8%) compared with eyes with sew-on lenses (8.6%; P = 0.010) and eyes with noncontact lenses (0%; P < 0.001). There were also more defects in sew-on versus noncontact lenses (P = 0.014). Diabetic patients had more postoperative epithelial defects with hand-held infusion lenses (32.1%) than with sew-on lenses (8.8%; P = 0.011) or with noncontact lenses (0%; P < 0.001). The average operative time for patients with epithelial defects (169 minutes) was longer than for patients without defects (117 minutes) (P < 0.001). The risk of these defects remained significant after controlling for both length of surgery and diabetes status. Conclusions: Corneal epithelial defects were more common after vitrectomy surgery using hand-held infusion lenses than after surgery using sew-on lenses and did not occur with the noncontact lens system. In addition, reducing the operative time may independently reduce the risk of epithelial defects, regardless of lens type.
Enhanced polarization of electron spins in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">He</mml:mi></mml:mrow><mml:mprescripts/><mml:mrow/><mml:mrow><mml:mn>4</mml:mn></mml:mrow><mml:mrow/><mml:mrow/></mml:mmultiscripts></mml:mrow></mml:math>by simultaneous optical pumping with circularly and linearly polarized resonance radiation (1990)

The polarization of helium (2 $^{3}$${\mathit{S}}_{1}$) metastable atoms saturates at 50% when the ensemble is optically pumped with the ${\mathit{D}}_{0}$ (2 $^{3}$${\mathit{S}}_{1--}$2 $^{3}$${\mathit{P}}_{0}$) transition. We have obtained polarizations approaching 100% with a simple, straightforward modification to the conventional experimental arrangement. The addition of a small amount of \ensuremath{\pi}-polarized ${\mathit{D}}_{0}$ light incident on the cell perpendicular to the defining field direction doubles the polarization produced by circularly polarized ${\mathrm{\ensuremath{\sigma}}}^{+}$ light along the field direction. A simple rate-equation model illustrates the enhancement.
Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories (2008)

Efficient screening of unknown DNA variations is one of the substantive matters of molecular biology even today. Historically, SSCP and heteroduplex analysis (HA) are the most commonly used methods for detecting DNA variations everywhere in the world because of their simplicity. However, the sensitivity of these methods is not satisfactory for screening purpose. Recently, several new PCR-based mutation screening methods have been developed, but most of them require special instruments and adjustment of conditions for each DNA sequence to attain the maximum sensitivity, eventually becoming as inconvenient as old methods. Enzyme mismatch cleavage (EMC) is potentially an ideal screening method. With high-performance nucleases and once experimental conditions are optimized, it requires only conventional staff and conditions remain the same for each PCR product. In this study we tested four commercially available endonucleases for EMC and optimized the electrophoresis and developing conditions. We prepared 25 known DNA variations consisting of 18 single base substitutions (8 transitions and 10 transversions, including all possible sets of mismatches) and 7 small deletions or insertions. The combination of CEL nuclease, 12% PAGE and rapid silver staining can detect all types of mutations and achieved 100% sensitivity.
Chemical ionization mass spectrometry of complex molecules. Biogenic amines (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical ionization mass spectrometry of complex molecules. Biogenic aminesG. W. A. Milne, H. M. Fales, and R. W. ColburnCite this: Anal. Chem. 1973, 45, 11, 1952–1954Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/ac60333a034https://doi.org/10.1021/ac60333a034research-articleACS PublicationsRequest reuse permissionsArticle Views84Altmetric-Citations24LEARN 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
A dominant negative c-jun specifically blocks okadaic acid-induced skin tumor promotion. (2002)

Okadaic acid (OA) is a prototypical non-phorbol ester skin tumor-promoting agent that works by inhibiting protein phosphatases, leading to an increase in protein phosphorylation. Increased protein phosphorylation can lead to stimulated signaling through various signal transduction pathways. One or more of the pathways affected by OA leads to increased signaling via the activator protein 1 (AP-1) transcription factor. Because AP-1 signaling has been shown to be required for skin tumor promotion by phorbol ester, studies were undertaken to determine whether AP-1 signaling is also required for 7,12-dimethylbenz(a)anthracene (DMBA)-initiated/OA-promoted skin tumorigenesis. Transgenic mice expressing a dominant negative c-jun (TAM-67) controlled by the keratin 14 promoter in ICR mice were used to determine the effects of OA on AP-1 signaling. By crossing the TAM-67 mice with mice expressing an AP-1-responsive luciferase, it was shown that TAM-67 decreases AP-1 activation in response to OA treatment by 95%. After 7,12-dimethylbenz(a)anthracene initiation, the TAM-67 mice and nontransgenic littermates were promoted with twice weekly applications of OA. These experiments showed that TAM-67 expression decreased tumor multiplicity by 90%. Additional experiments with TAM-67 mice showed that the hyperplastic response to OA is not impaired in these mice, nor were there differences in OA-induced transcription of various genes known to be AP-1 responsive under other conditions. This result suggests that only a subset of AP-1-regulated genes is targeted by TAM-67 when it prevents tumor promotion by OA. A determination of the mechanism by which TAM-67 can block tumor promotion without affecting hyperplasia will be important.
Designing Collective Behavior in a Termite-Inspired Robot Construction Team (2014)

Complex systems are characterized by many independent components whose low-level actions produce collective high-level results. Predicting high-level results given low-level rules is a key open challenge; the inverse problem, finding low-level rules that give specific outcomes, is in general still less understood. We present a multi-agent construction system inspired by mound-building termites, solving such an inverse problem. A user specifies a desired structure, and the system automatically generates low-level rules for independent climbing robots that guarantee production of that structure. Robots use only local sensing and coordinate their activity via the shared environment. We demonstrate the approach via a physical realization with three autonomous climbing robots limited to onboard sensing. This work advances the aim of engineering complex systems that achieve specific human-designed goals.
Convenient synthesis of 2-substituted indoles from 2-ethynylanilines with tetrabutylammonium fluoride (1999)

The cyclization reaction of various 2-ethynylanilines, which were easily synthesized from 2-haloanilines by the palladium-catalyzed reaction with terminal alkynes, with tetrabutylammonium fluoride (TBAF) to yield 2-substituted indoles proceeded at refluxing or room temperature in THF in excellent yields without affecting the bromo, chloro, cyano, ethoxycarbonyl, and ethynyl groups.
Expression of the putative tumor suppressor gene<i>PTPN13/PTPL1</i>is an independent prognostic marker for overall survival in breast cancer (2008)

Although it is well established that some protein tyrosine kinases have a prognostic value in breast cancer, the involvement of protein tyrosine phosphatases (PTPs) is poorly substantiated for breast tumors. Three of these enzymes (PTP-gamma, LAR, and PTPL1) are already known to be regulated by estrogens or their antagonists in human breast cancer cells. We used a real-time reverse transcriptase polymerase chain reaction method to test the expression levels of PTP-gamma, LAR and its neuronal isoform, and PTPL1 in a training set of RNA from 59 breast tumors. We sought correlations between levels of these molecular markers, current tumor markers, and survival. We then quantified the expression level of the selected phosphatase in 232 additional samples, resulting in a testing set of 291 breast tumor RNAs from patients with a median follow-up of 6.4 years. The Spearman nonparametric test revealed correlations between PTPL1 expression and differentiation markers. Cox univariate analysis of the overall survival studies demonstrated that PTPL1 is a prognostic factor [risk ratio (RR)=0.45], together with the progesterone receptor (PR) (RR=0.52) and node involvement (RR=1.58). In multivariate analyses, PTPL1 and PR retained their prognostic value (RRs of 0.48 and 0.55, respectively). This study demonstrates for the first time that PTPL1 expression level is an independent prognostic indicator of favorable outcome for patients with breast cancer. In conjunction with our mechanistic studies, this finding identifies PTPL1 as an important regulatory element of human breast tumor aggressiveness and sensitivity to treatments such as antiestrogens and antiaromatase.
Reversible MOF-Based Sensors for the Electrical Detection of Iodine Gas (2019)

Iodine detection is crucial for nuclear waste clean-up and first responder activities. For ease of use and durability of response, robust active materials that enable the direct electrical detection of I<sub>2</sub> are needed. Herein, a large reversible electrical response is demonstrated as I<sub>2</sub> is controllably and repeatedly adsorbed and desorbed from a series of metal-organic frameworks (MOFs) MFM-300(X), each possessing a different metal center (X = Al, Fe, In, or Sc) bridged by biphenyl-3,3',5,5'-tetracarboxylate linkers. Impedance spectroscopy is used to evaluate how the different metal centers influence the electrical response upon cycling of I<sub>2</sub> gas, ranging from 10× to 10<sup>6</sup>× decrease in resistance upon I<sub>2</sub> adsorption in air. This large variation in electrical response is attributed not only to the differing structural characteristics of the MOFs but also to the differing MOF morphologies and how this influences the degree of reversibility of I<sub>2</sub> adsorption. Interestingly, MFM-300(Al) and MFM-300(In) displayed the largest changes in resistance (up to 10<sup>6</sup>×) yet lost much of their adsorption capacity after five I<sub>2</sub> adsorption cycles in air. On the other hand, MFM-300(Fe) and MFM-300(Sc) revealed more moderate changes in resistance (10-100×), maintaining most of their original adsorption capacity after five cycles. This work demonstrates how changes in MOFs can profoundly affect the magnitude and reversibility of the electrical response of sensor materials. Tuning both the intrinsic (resistivity and adsorption capacity) and extrinsic (surface area and particle morphology) properties is necessary to develop highly reversible, large signal-generating MOF materials for direct electrical readout for I<sub>2</sub> sensing.
A 400-Gb/s and Low-Power Physical-Layer Architecture for Next-Generation Ethernet (2011)

A new 400-Gb/s (100-Gb/s×4) physical-layer architecture for the next-generation Ethernet-using 100-Gb/s serial (optical single wavelength) transmission-is proposed. For the next-generation 400-Gb/s Ethernet, there are additional requirements from the market, such as power reduction and further compactization in addition to attaining even higher transmission speed. To meet these requirements, a 100-Gb/s×4 physical-layer architecture is proposed. This architecture uses a 100-Gb/s serial (optical single wavelength) transmission Ethernet and low-power control technologies, which include transmission-capacity-degeneracy control for multi-lane transmission Ethernet. These technologies were implemented on a 100-Gb/s serial (optical single wavelength) transmission Ethernet using a field-programmable gate array (FPGA). Experimental evaluation of this implementation demonstrates the feasibility of low-power and fault-tolerant 400-Gb/s Ethernet.