gebhart/patrepeval huggingface dataset:
Comparison of Methods for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae Using Commercially Available Nucleic Acid Amplification Tests and a Liquid Pap Smear Medium (2003)

Annual screening for Chlamydia trachomatis infection is currently recommended for sexually active women 15 to 25 years old and for women older than 25 if they have a new or multiple sex partners and have not used condoms during the previous 3 months. Annual screening for cervical abnormalities using the Pap smear has achieved a substantial reduction in morbidity and mortality from cervical cancer. Screening for Neisseria gonorrhoeae infection has likely contributed significantly to the reduction in the rates of gonococcal infection. The introduction of liquid Pap smear methods using exfoliated cervical cells presents an opportunity to screen for these three conditions using one specimen. We evaluated the preservation of C. trachomatis and Neisseria gonorrhoeae DNAs from ThinPrep liquid media (PreservCyt; Cytyc Corp., Boxborough, Mass.); tested the feasibility of using a clinical specimen of this medium for the detection of cytologic abnormalities, C. trachomatis, and N. gonorrhoeae; evaluated the agreement between ligase chain reaction (LCR) performed on PreservCyt and LCR performed on a cervical specimen; and compared the performance of LCR performed on PreservCyt to those of LCR performed on a cervical specimen, culture, PCR performed on a cervical specimen, on urine, and on a vaginal specimen (a multiple-site infection status standard), and transcription-mediated amplification (for C. trachomatis only) from 255 sexually active adolescent women. The agreement between LCR performed on PreservCyt and LCR from a cervical swab in LCx transport medium was high (for C. trachomatis, agreement = 0.97 and kappa = 0.92; for N. gonorrhoeae, agreement = 0.99 and kappa = 0.96). Test performances were similar for LCR-urine, LCR-cervix, and LCR-ThinPrep, with sensitivities from 93 to 99% for C. trachomatis and 81 to 83% for N. gonorrhoeae and specificities from 95.5 to 99% for C. trachomatis and 99.1 to 99.6% for N. gonorrhoeae using a PCR-based multiple-site infection status standard. This is the first study to examine the agreement between liquid cytologic media and multiple nucleic acid amplification tests for the detection of C. trachomatis and N. gonorrhoeae from patient samples. Cytologic fluid shows promise for simultaneous screening for cytologic abnormalities and sexually transmitted infections.
Precise localization of human beta-globin gene complex on chromosome 11. (1979)

Cloned DNA probes were used in combination with a panel of five hybrid cell clones containing a series of different terminal deletions in human chromosome 11 to map precisely the human hemoglobin beta and delta chain structural genes contained on this chromosome. The region of deletion in each clone of the panel has been defined by biochemical, immunologic, and cytogenetic markers. DNA from clones containing successively larger terminal deletions was tested with appropriate DNA probes to determine the point on the chromosome at which DNA for these two closely linked hemoglobin genes is deleted. These genes, and by inference the closely linked G gamma and A gamma globin genes as well, have been assigned to the intraband region 11p1205 leads to 11p1208 on the short arm of chromosome 11, an interval containing approximately 4500 kilobases of DNA. The approach appears to have potential for even greater resolution and reasonably wide applicability for gene mapping.
Immunohistochemical Expression of Endothelial Markers CD31, CD34, von Willebrand Factor, and Fli-1 in Normal Human Tissues (2005)

Few systematic studies have been published comparing the expression and distribution of endothelial cell (EC) markers in different vascular beds in normal human tissues. We investigated by immunohistochemistry the expression of CD31, CD34, von Willebrand factor (vWF), and Fli-1 in EC of the major organs and large vessels. Tissue samples obtained from autopsies and biopsy specimens were routinely processed and stained immunohistochemically for CD31, CD34, and vWF. Biopsy material was also stained immunohistochemically for Fli-1, D2-40, and Lyve-1. The expression pattern of the markers was heterogeneous in some of the organs studied. In the kidney, fenestrated endothelium of the glomeruli strongly expressed CD31 and CD34 but was only focally positive or completely negative for vWF. Alveolar wall capillaries of the lung strongly stained for CD31 and CD34 but were usually negative for vWF. The staining intensity for vWF increased gradually with the vessel caliber in the lung. Sinusoids of the spleen and liver were diffusely positive for CD31. They were negative for CD34 in the spleen and only expressed CD34 in the periportal area in the liver. Fli-1 was expressed in all types of EC but also in lymphocytes. D2-40 stained lymphatic endothelium only. Lyve-1 immunostaining was too variable to be applied to routinely processed tissues. The expression of EC markers CD31, CD34, and vWF in the vascular tree is heterogeneous with a specific pattern for individual vessel types and different anatomic compartments of the same organ. D2-40 labels lymphatic EC only.
Mitochondrial Reactive Oxygen Species Trigger Hypoxia-Inducible Factor-Dependent Extension of the Replicative Life Span during Hypoxia (2007)

Physiological hypoxia extends the replicative life span of human cells in culture. Here, we report that hypoxic extension of replicative life span is associated with an increase in mitochondrial reactive oxygen species (ROS) in primary human lung fibroblasts. The generation of mitochondrial ROS is necessary for hypoxic activation of the transcription factor hypoxia-inducible factor (HIF). The hypoxic extension of replicative life span is ablated by a dominant negative HIF. HIF is sufficient to induce telomerase reverse transcriptase mRNA and telomerase activity and to extend replicative life span. Furthermore, the down-regulation of the von Hippel-Lindau tumor suppressor protein by RNA interference increases HIF activity and extends replicative life span under normoxia. These findings provide genetic evidence that hypoxia utilizes mitochondrial ROS as signaling molecules to activate HIF-dependent extension of replicative life span.
Transient expression of lysyl oxidase by liver myofibroblasts in murine schistosomiasis. (1993)

This study demonstrates that the lysyl oxidase was transiently up-regulated at the transcriptional level parallely to alpha(1)I procollagen within developing granulomas. Myofibroblasts are involved in the expression of the lysyl oxidase which may be secreted as a proenzyme and an activated enzyme.
In Vivo Replication-Deficient Adenovirus Vector-Mediated Transduction of the Cytosine Deaminase Gene Sensitizes Glioma Cells to 5-Fluorocytosine (1996)

Viral vector-mediated transfer of chemosensitization genes represents a promising new approach to the treatment of cancer. Previous reports have demonstrated that transfection of the bacterial cytosine deaminase (cd) gene into mammalian cells can sensitize them to the otherwise nontoxic nucleoside, 5-fluorocytosine (5-FC). We now report that a replication-deficient adenovirus vector that transduces the cd gene (Ad.CMV-cd) highly sensitizes 9L gliosarcoma cells to 5-FC, and that gene transduction is associated with a potent bystander effect that is not dependent on direct cell-to-cell contact. Stereotactic injection of Ad.CMV-cd into established rat gliomas, followed by systemic administration of 5-FC in vivo, results in prolongation of survival.
Infrared absorption of substituents in heterocyclic systems. Part X. Amine–imine tautomerism by infrared spectroscopy: further examples (1966)

An infrared study involving deuteration has shown that compounds previously designated as 5,6-dihydro-2-imino-1H, 4H-imidazo[4,5,1-ij]quinoline and 1,2-dihydro-2-imino-4H-3,1-benzoxazin-4-one exist predominantly as their amino-tautomers.
Preliminary steps towards implementing intimate 3D-IC stacking with layer transfer and atomic bonding methods (2015)

Preliminary studies of radiation damage and recovery of E <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> PROM sensor devices following exposure to a high-dose, 1 MeV proton beam give encouragement to the use of H-cut and layer transfer methods for vertical integration of 3D-IC's with fully-formed CMOS devices and metal interconnect.
The binding of Gla‐containing proteins to phospholipids (1984)

It is demonstrated here that osteocalcin, the Gla-containing protein from bone, is unable to interfere with the binding of the blood coagulation factors to phospholipid vesicles. Therefore, it seems that besides the Gla residues other structural features of the coagulation factors are required for their effective binding to phospholipid surfaces.
Two-dimensional active pixel InGaAs focal plane arrays (2001)

Switching and amplifying characteristics of a newly developed 2D InGaAs Active Pixel Imager Array are presented. The sensor array is fabricated from InGaAs material epitaxially deposited on an InP substrate. It consists of an InGaAs photodiode connected to InP depletion-mode junction field effect transistors for low leakage, low power and fast control of circuit signal amplifying, buffering, selection and reset. This monolithically integrated active pixel sensor configuration eliminates the need for hybridization with a silicon multiplexer, and in addition, allows the sensor to be front illuminated, making it sensitive to visible as well as near IR signal radiation. Adapting the existing 1.55 micrometers fiber optical communication technology, this integration will be an ideal system of optoelectronic integration for dual band applications near room temperature, for use in atmospheric gas sensing in space and target identification on earth. In this paper, 4 by 4 test arrays will be described. The effectiveness of switching and amplifying circuits will be discussed in terms of circuit in preparation for 2D InGaAs active pixel sensor arrays for applications in multifunctional, transportable shipboard surveillance, night vision and emission spectroscopy.
Estimation of formation temperature and thermal property from dissipation of heat generated by drilling (1982)

Abstract Dissipation of heat generated in the process of drilling depends upon the physical properties and condition of the rock and drilling mud, drilling rate and duration, mud circulation rate, casing, and depth of penetration. By treating the initial condition as an instantaneous temperature drop near the bottom of a drill hole, an analytical solution is obtained to show drilling-induced heat dissipation. Two graphical methods are presented and illustrated with examples to determine, from transient temperature measurements, the equilibrium formation temperature as well as in-situ thermal conductivity ratio and diffusivity of rock and drilling mud. One method requires the measurement of initial mud temperature T m , while the other method requires knowing the thermal diffusivity of drilling mud kappa 1 . Either T m or kappa 1 can also be estimated with the trial-and-error procedure. A finite-element analysis is further developed to handle thermal disturbance for the case where the temperature drop is not necessarily instantaneous; hence the solution is applicable at any depth in a drill hole.
Rapid controlled movement through a virtual 3D workspace (1990)

Computer graphics hardware supporting real-time interactive 3D animation has the potential to support effective user interfaces by enabling virtual 3D workspaces. However, this potential requires development of viewpoint movement techniques that support rapid and controlled movement through workspaces. Rapid movement through large distances avoids wasted work time; controlled movement near target objects allows the user to examine and interact with objects in the workspace. Current techniques for viewpoint movement typically use high velocities to cover distances rapidly, but high velocities are hard to control near objects. This paper describes a new technique for targeted viewpoint movement that solves this problem. The key idea is to have the user indicate a point of interest (target) on a 3D object and use the distance to this target to move the viewpoint logarithmically, by moving the same relative percentage of distance to the target on every animation cycle. the result is rapid motion over distances that slows as the viewpoint approaches the target object. The technique can be used with 2D and multidimensional input devices. We also extend the technique to move objects in the workspace.
An α1A-Adrenergic–Extracellular Signal-Regulated Kinase Survival Signaling Pathway in Cardiac Myocytes (2007)

Our results demonstrate a direct protective effect of the alpha1A subtype in cardiac myocytes and define an alpha1A-ERK signaling pathway that is required for myocyte survival. Absence of the alpha1A-ERK pathway can explain the failure to activate ERK after aortic constriction in alpha1ABKO mice and can contribute to the development of apoptosis, dilated cardiomyopathy, and death.
Two–toxin strategies for management of insecticidal transgenic crops: can pyramiding succeed where pesticide mixtures have not? (1998)

Transgenic insect–resistant crops that express toxins from Bacillus thuringiensis (Bt) offer significant advantages to pest management, but are at risk of losing these advantages to the evolution of resistance in the targeted insect pests. All commercially available cultivars of these crops carry only a single Bt gene, and are particularly at risk where the targeted insect pests are not highly sensitive to the Bt toxin used. Under such circumstances, the most prudent method of avoiding resistance is to ensure that a large proportion of the pest population develops on non–transgenic ‘refuge’ hosts, generally of the crop itself. This has generated recommendations that 20% or more of the cotton and maize in any given area should be non–transgenic. This may be costly in terms of yields and may encourage further reliance on and resistance to pesticides. The use of two or more toxins in the same variety (pyramiding) can reduce the amount of refuge required to delay resistance for an extended period. Cross–resistance among the toxins appears to have been overestimated as a potential risk to the use of pyramids (and pesticide mixtures) because cross–resistance is at least as important when toxicants are used independently. Far more critical is that there should be nearly 100% mortality of susceptible insects on the transgenic crops. The past failures of pesticide mixtures to manage resistance provide important lessons for the most efficacious deployment of multiple toxins in transgenic crops.
Potential Clinical Applications for Human Pluripotent Stem Cell-Derived Blood Components (2011)

The ability of human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) to divide indefinitely without losing pluripotency and to theoretically differentiate into any cell type in the body makes them highly attractive cell sources for large scale regenerative medicine purposes. The current use of adult stem cell-derived products in hematologic intervention sets an important precedent and provides a guide for developing hESC/iPSC based therapies for the blood system. In this review, we highlight biological functions of mature cells of the blood, clinical conditions requiring the transfusion or stimulation of these cells, and the potential for hESC/iPSC-derivatives to serve as functional replacements. Many researchers have already been able to differentiate hESCs and/or iPSCs into specific mature blood cell types. For example, hESC-derived red blood cells and platelets are functional in tasks such as oxygen delivery and blood clotting, respectively and may be able to serve as substitutes for their donor-derived counterparts in emergencies. hESC-derived dendritic cells are functional in antigen-presentation and may be used as off-the-shelf vaccine therapies to stimulate antigen-specific immune responses against cancer cells. However, in vitro differentiation systems used to generate these cells will need further optimization before hESC/iPSC-derived blood components can be used clinically.
Primer Extension Mutagenesis Powered by Selective Rolling Circle Amplification (2012)

Primer extension mutagenesis is a popular tool to create libraries for in vitro evolution experiments. Here we describe a further improvement of the method described by T.A. Kunkel using uracil-containing single-stranded DNA as the template for the primer extension by additional uracil-DNA glycosylase treatment and rolling circle amplification (RCA) steps. It is shown that removal of uracil bases from the template leads to selective amplification of the nascently synthesized circular DNA strand carrying the desired mutations by phi29 DNA polymerase. Selective RCA (sRCA) of the DNA heteroduplex formed in Kunkel's mutagenesis increases the mutagenesis efficiency from 50% close to 100% and the number of transformants 300-fold without notable diversity bias. We also observed that both the mutated and the wild-type DNA were present in at least one third of the cells transformed directly with Kunkel's heteroduplex. In contrast, the cells transformed with sRCA product contained only mutated DNA. In sRCA, the complex cell-based selection for the mutant strand is replaced with the more controllable enzyme-based selection and less DNA is needed for library creation. Construction of a gene library of ten billion members is demonstrated with the described method with 240 nanograms of DNA as starting material.
Demand Side Management: Demand Response, Intelligent Energy Systems, and Smart Loads (2011)

Energy management means to optimize one of the most complex and important technical creations that we know: the energy system. While there is plenty of experience in optimizing energy generation and distribution, it is the demand side that receives increasing attention by research and industry. Demand Side Management (DSM) is a portfolio of measures to improve the energy system at the side of consumption. It ranges from improving energy efficiency by using better materials, over smart energy tariffs with incentives for certain consumption patterns, up to sophisticated real-time control of distributed energy resources. This paper gives an overview and a taxonomy for DSM, analyzes the various types of DSM, and gives an outlook on the latest demonstration projects in this domain.
Female mice chimeric for expression of the simian virus 40 TAg under control of the MISIIR promoter develop epithelial ovarian cancer. (2003)

In women, >80% of malignant ovarian tumors are of epithelial origin. Early detection of these tumors is very challenging,and extensive i.p. dissemination is common by the time of diagnosis. The lack of adequate geneticmouse models of ovarian carcinomas significantly delays advances in early detection and treatment. We report that female transgenic mice expressing the transforming region of SV40 under control of the Mullerian inhibitory substance type II receptor gene promoter develop bilateral ovarian tumors in approximately 50% of cases. Histologically, these tumors are poorly differentiated carcinomas with occasional cysts and papillary structures present at the surface of the ovary. These tumors disseminate i.p., invade omentum, and form ascites as do human ovarian carcinomas. The epithelial origin of these tumors is supported by detection of cytokeratins 8 and 19, and the absence of alpha-inhibin, a protein characteristically expressed in normal granulosa cells and most granulosa cell tumors. Cell lines derived from the ascites exhibit the properties of epithelial ovarian cancer, such as anchorage-independent growth, tumorigenicity in immunocompromised mice, expression of epithelial cell markers, and organotropic implantation. The availability of a transgenic mouse model of disseminated ovarian carcinoma and respective cell lines should advance our understanding of this neoplasm, and serve as a useful tool for the evaluation of emerging detection and treatment strategies.
633. Studies in the azole series. Part XXIV. The interaction of carbonyl compounds and 2-thio-5-thiazolidone (1949)

A. H. Cook and J. R. A. Pollock, J. Chem. Soc., 1949, 3007 DOI: 10.1039/JR9490003007
Fate of intravenously injected human tumor cells in the lung of nude mice following whole-body X-irradiation. (1985)

X-irradiation administered to nude mice and the ensuing pulmonary metastasis of injected human tumor cells were investigated. When human tumor cells (5 X 10(5)) were injected into the tail vein of male adult nude mice 5 days after 3 Gy whole-body X-irradiation, the incidence of pulmonary metastasis was more frequent in the irradiated mice than in the nonirradiated controls. Platelet aggregation and fibrin deposition around the tumor cells were present in the capillaries of the lung in the irradiated mice while prominent neutrophilic infiltration was noted around the tumor cells in the nonirradiated controls. Fibrinolytic activity of the lung was decreased in the irradiated mice, while serum fibrinogen level was increased after irradiation. Natural killer cell activity was decreased after irradiation. We conclude from this study that increase in serum fibrinogen levels and decrease in fibrinolytic activity of the lung, as a target organ, together with decreased infiltration of neutrophils, may be related to the trapping and lodgement of tumor cells when nude mice are subjected to irradiation.
Stabilized111In-Labeled sCCK8 Analogues for Targeting CCK2-Receptor Positive Tumors: Synthesis and Evaluation (2010)

Radiolabeled cholecystokinin-8 (CCK8) peptide analogues can be used for peptide receptor radionuclide imaging and therapy for tumors expressing CCK2/gastrin receptors. Earlier findings indicated that sulfated CCK8 (sCCK8, Asp-Tyr(OSO(3)H)-Met-Gly-Trp-Met-Asp-Phe-NH(2)) may have better characteristics for peptide receptor radionuclide therapy (PRRT) than gastrin analogues. However, sCCK8 contains an easily hydrolyzable sulfated tyrosine residue and two methionine residues which are prone to oxidation. Here, we describe the synthesis of stabilized sCCK8 analogues, resistant to hydrolysis and oxidation. Hydrolytic stability was achieved by replacement of the Tyr(OSO(3)H) moiety by a robust isosteric sulfonate, Phe(p-CH(2)SO(3)H). Replacement of methionine by norleucine (Nle) or homopropargylglycine (HPG) avoided undesired oxidation side-reactions. The phenylalanine analogue Phe(p-CH(2)SO(3)H) of l-tyrosine, synthesized by a modification of known synthetic routes, was incorporated in three peptides: sCCK8[Phe(2)(p-CH(2)SO(3)H),Met(3,6)], sCCK8[Phe(2)(p-CH(2)SO(3)H),Nle(3,6)], and sCCK8[Phe(2)(p-CH(2)SO(3)H),HPG(3,6)]. All peptides were N-terminally conjugated with the macrocyclic chelator DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) and radiolabeled with In-111. In vitro binding assays on CCK2R-expressing HEK293 cells revealed that all three peptides showed specific binding and receptor-mediated internalization, with binding affinity values (IC(50)) in the nanomolar range. In vitro oxidation studies demonstrated that peptides with Nle or HPG indeed were resistant to oxidation. In vivo targeting studies in mice with AR42J tumors showed that tumor uptake was highest for (111)In-DOTA-sCCK8 and (111)In-DOTA-sCCK8[Phe(2)(p-CH(2)SO(3)H),Nle(3,6)] (4.78 +/- 0.64 and 4.54 +/- 1.15%ID/g, respectively, 2 h p.i.). The peptide with the methionine residues replaced by norleucine ((111)In-DOTA-sCCK8[Phe(2)(p-CH(2)SO(3)H), Nle(3,6)]) showed promising in vivo characteristics and will be further investigated for radionuclide imaging and therapy of CCK2R-expressing tumors.