gebhart/patrepeval huggingface dataset:
Multiplex messenger assay: simultaneous, quantitative measurement of expression of many genes in the context of T cell activation (1996)

The hybridization signature approach, using colony filters and labeled complex probes, can provide high throughput measurement of gene activity. We describe here the implementation of this method to follow the expression levels of 47 genes in resting and activated T cells, as well as in epithelial cells. Using 4-fold spotting of colonies, imaging plate detection and various correction and normalization procedures, the technique is sensitive enough to quantify expression levels for sequences present at 0.005% abundance in the probe. Comparison with Northern blotting shows good consistency between the two methods. Upon activation of a T cell clone by an anti-CD3 antibody variations ranging from 2- to 20-fold are measured, some of which had not been reported previously. This 'multiplex messenger assay' method, performed using available commercial apparatus, can be used in many cases where simultaneous assessment of mRNA levels for many genes is of interest.
Understanding the Osteosarcoma Pathobiology: A Comparative Oncology Approach (2016)

Osteosarcoma is an aggressive primary bone tumor in humans and is among the most common cancer afflicting dogs. Despite surgical advancements and intensification of chemo- and targeted therapies, the survival outcome for osteosarcoma patients is, as of yet, suboptimal. The presence of metastatic disease at diagnosis or its recurrence after initial therapy is a major factor for the poor outcomes. It is thought that most human and canine patients have at least microscopic metastatic lesions at diagnosis. Osteosarcoma in dogs occurs naturally with greater frequency and shares many biological and clinical similarities with osteosarcoma in humans. From a genetic perspective, osteosarcoma in both humans and dogs is characterized by complex karyotypes with highly variable structural and numerical chromosomal aberrations. Similar molecular abnormalities have been observed in human and canine osteosarcoma. For instance, loss of TP53 and RB regulated pathways are common. While there are several oncogenes that are commonly amplified in both humans and dogs, such as MYC and RAS, no commonly activated proto-oncogene has been identified that could form the basis for targeted therapies. It remains possible that recurrent aberrant gene expression changes due to gene amplification or epigenetic alterations could be uncovered and these could be used for developing new, targeted therapies. However, the remarkably high genomic complexity of osteosarcoma has precluded their definitive identification. Several advantageous murine models of osteosarcoma have been generated. These include spontaneous and genetically engineered mouse models, including a model based on forward genetics and transposon mutagenesis allowing new genes and genetic pathways to be implicated in osteosarcoma development. The proposition of this review is that careful comparative genomic studies between human, canine and mouse models of osteosarcoma may help identify commonly affected and targetable pathways for alternative therapies for osteosarcoma patients. Translational research may be found through a path that begins in mouse models, and then moves through canine patients, and then human patients.
Real-time Tracking of Complex Structures with On-line CameraCalibration (1999)

Abstract This paper presents a novel three-dimensional model-based tracking system which has been incorporated into a visual servoing system. The tracking system combines modern graphical rendering technology with constrained active contour tracking techniques to create wire-frame-snakes. It operates in real-time at video frame rate (25 Hz) and is based on an internal CAD model of the object to be tracked. This model is rendered using a binary space partition tree to perform hidden line removal and the visible features are identified on-line at each frame and are tracked in the video feed. The tracking system has been extended to incorporate real-time on-line calibration and tracking of internal camera parameters. Results from on-line calibration and visual servoing experiments are presented.
Rechargeable Li2O2 Electrode for Lithium Batteries (2006)

Rechargeable lithium batteries represent one of the most important developments in energy storage for 100 years, with the potential to address the key problem of global warming. However, their ability to store energy is limited by the quantity of lithium that may be removed from and reinserted into the positive intercalation electrode, Li(x)CoO(2), 0.5 < x < 1 (corresponding to 140 mA.h g(-1) of charge storage). Abandoning the intercalation electrode and allowing Li to react directly with O(2) from the air at a porous electrode increases the theoretical charge storage by a remarkable 5-10 times! Here we demonstrate two essential prerequisites for the successful operation of a rechargeable Li/O(2) battery; that the Li(2)O(2) formed on discharging such an O(2) electrode is decomposed to Li and O(2) on charging (shown here by in situ mass spectrometry), with or without a catalyst, and that charge/discharge cycling is sustainable for many cycles.
Uptake of Apoptotic Antigen-Coupled Cells by Lymphoid Dendritic Cells and Cross-Priming of CD8+ T Cells Produce Active Immune Unresponsiveness (2002)

The induction of immunologic unresponsiveness by i.v. administration of Ag-coupled lymphoid cells has been studied extensively, but the mechanisms remain unclear. We have further explored this model by examining the role of Fas/Fas ligand (FasL)-mediated apoptosis. Using i.v. injection of trinitrophenyl-coupled splenocytes (TNP-spl) as tolerogen, we found that Fas signaling for apoptosis in the spleen cells delivered by FasL in the recipient is the critical event. The requirement for Fas and FasL was overcome by prior induction of apoptosis in TNP-spl, making the tolerogen 100 times more potent. Prevention of apoptosis by a caspase inhibitor blocks tolerance. Interestingly, while blocking CD40/CD40 ligand interaction does not prevent tolerance induction, an agonist anti-CD40 Ab turns tolerogenic TNP-spl into an immunizing Ag. Studies further showed that tolerance is induced through cross-presentation of Ag in a class I MHC-dependent manner by CD8(+)CD11c(+) lymphoid-derived dendritic cells to regulatory T cells. The results provide a mechanism for a well-established method of inducing immunologic unresponsiveness.
Tracing the Expression of CD7 and other Antigens during T- and Myeloid-cell Differentiation in the Human Fetal Liver and Thymus (1995)

During the last decade, the function/s of the cell membrane CD7 antigen have been investigated in human mature T and NK cells, showing the direct involvement of this molecule in multiple effector functions related with activation, proliferation, production of cytokines and modification of adhesion properties. The CD7 glycoprotein is not only expressed by mature lymphoid cells, but also by early hematopoietic progenitors and several types of leukemias, suggesting a role of CD7 during hematopoiesis. However, the function of CD7 in the early stages of hematopoietic development has not yet been elucidated. CD7 has been classically considered the earliest T-cell specific marker. This assumption was based on data indicating the presence of CD45+CD7+CD3-CD4-CD8- cells in the human embryonic/fetal liver at the gestational age at which the thymic rudiment is colonized by T-cell progenitors. In the present article, we review recent results obtained by several groups concerning the expression of CD7 and various other cell surface antigens by T-, B- and myeloid-cell progenitors generated in the adult bone marrow and fetal liver. In addition, we present an hypothetical model of hematopoiesis in the fetal liver and thymus.
IC31® and IC30, novel types of vaccine adjuvant based on peptide delivery systems (2007)

Toll-like receptor (TLR) agonists have a proven potential to become the adjuvants of the next generation when admixed and formulated with all kinds of vaccine compositions. The quality and magnitude of a vaccine-induced immune response is often strongly facilitated by TLR agonists, with the result that protection is increased and expanded toward type 1-driven immunity. DNA oligodeoxynucleotides bind to TLR9 and have been tested in a variety of vaccine settings with encouraging results. Combining oligodeoxynucleotides with poly-L-arginine (IC30) or certain artificial antimicrobial peptides dramatically improves and synergizes with the adjuvant action of TLR9 agonists, a notion that has prompted the development of IC31, an adjuvant with a promising profile in both preclinical and clinical trials.
Compressed sensing Block MAP-LMS adaptive filter for sparse channel estimation and a Bayesian Cramer-Rao bound (2009)

This paper suggests to use a block MAP-LMS (BMAP-LMS) adaptive filter instead of an adaptive filter called MAP-LMS for estimating the sparse channels. Moreover to faster convergence than MAP-LMS, this block-based adaptive filter enables us to use a compressed sensing version of it which exploits the sparsity of the channel outputs to reduce the sampling rate of the received signal and to alleviate the complexity of the BMAP-LMS. Our simulations show that our proposed algorithm has faster convergence and less final MSE than MAP-LMS, while it is more complex than MAP-LMS. Moreover, some lower bounds for sparse channel estimation is discussed. Specially, a Cramer-Rao bound and a Bayesian Cramer-Rao bound is also calculated.
Synthesis of Diethyl (1-Aminoalkyl)phosphonates Under Solid-Liquid Phase-Transfer Catalysis Conditions (1990)

Alkylations of the stable diethyl N-(diphenylmethylene) aminomethylphosphonate (1) under solid-liquid phase-transfer catalysis (PTC) with or without solvent to give N-(diphenylmethylene) aminomethylphosphonic esters 2 are described. Acidic hydrolysis of 2 afforded diethyl (1-aminoalkyl)phosphonates 3 in good yields.
Subcellular Localization Patterns and Their Relationship to Photodynamic Activity of Pyropheophorbide-a Derivatives (1999)

To determine if subcellular localization is important to photodynamic therapy (PDT) efficacy, an in vitro fluorescence microscopy study was conducted with a congeneric series of pyropheophorbide-a derivatives in human pharyngeal squamous cell carcinoma (FaDu) cells and murine radiation-induced fibrosarcoma (RIF) mutant cells. In the FaDu cells the octyl, decyl and dodecyl ether derivatives localized to the lysosomes at extracellular concentrations less than needed to produce a 50% cell kill (LD50). At extracellular concentrations equal or greater than the LD50 the compounds localized mainly to mitochondria. The propyl, pentyl, hexyl and heptyl ether derivatives localized mainly to the mitochondria at all concentrations studied. This suggested that mitochondria are a sensitive PDT target for these derivatives. Similar experiments were performed with two Photofrin®-PDT resistant RIF cell lines, one of which was found to be resistant to hexyl ether derivative (C6) mediated-PDT and the other sensitive to C6-PDT relative to the parent line. At extracellular concentrations of C6 below the LD50 of each cell line, the mutants exhibited lysosomal localization. At concentrations above these values the patterns shifted to a mainly mitochondrial pattern. In these cell lines mitochondrial localization also correlated with PDT sensitivity. Localization to mitochondria or lysosomes appeared to be affected by the aggregation state of the congeners, all of which are highly aggregated in aqueous medium. Monomers apparently were the active fraction of these compounds because equalizing the extracellular monomer concentrations produced equivalent intracellular concentrations, photoxicity and localization patterns. Compounds that were mainly aggregates localized to the lysosomes where they were rendered less active. Mitochondria appear to be a sensitive target for pyro-pheophorbide-a-mediated photodamage, and the degree of aggregation seems to be a determinant of the localization site.
3-D System in Package: How to Cope with Increasing Challenges (2012)

Abstract It seems that scaling of chip technology according to Moore’s Law will continue for digital functionalities (logic and memory); however, increasing system integration on chip and package levels, called “More than Moore,” has been observed in the past several years. This strong trend in the worldwide semiconductor industry enables more functionality, diversification, and higher value by creating smart microsystems. This article discusses the many challenges faced in FA of 3-D chips, where well-staffed and equipped FA labs are essential. Furthermore, FA is becoming an important strategic enabling factor for new products, not just another “cost factor.”
RNAi in arthritis: prospects of a future antisense therapy in inflammation. (2007)

Rheumatoid arthritis is a chronic autoimmune disease of unknown etiology that is characterized by chronic systemic inflammation, mainly affecting the joints, leading to subsequent destruction of the cartilage and bone. RNA interference (RNAi) has been used as a remarkable new research tool to control gene expression and is ultimately envisioned to be useful in clinical treatments. The potential application of RNAi-based therapy in rheumatoid disorders is evaluated. The first successful attempts at TNFalpha silencing by local and systemic delivery of small interfering RNA in experimental arthritic models are discussed. In addition, RNAi and current biotherapies used in the clinic are compared and contrasted.
High-efficiency multilayer dielectric diffraction gratings (1995)

The design and performance of a new type of high-efficiency diffraction grating for use in either transmission or reflection are described. The gratings are produced in a multilayer dielectric coating deposited upon optically flat substrates. By proper design of the multilayer stack and grating structure, a diffraction efficiency in excess of 96% for polarized light in the m = -1 order in reflection has been achieved.
The Hypothermia of Hypoglycemia (1972)

Abstract An inhibitor of glucose utilization, 2-deoxy-D-glucose (2-DG) was employed to study the hypothermia of hypoglycemia. After 2-DG infusions, rectal temperatures in normal human subjects fell to nadir levels averaging 1.1°C below base-line values in two to 2.5 hours coincident with maximal increases of plasma growth hormone. Temperatures remained below basal values for six hours in the face of increases in plasma glucose and insulin, and urinary catecholamines. The findings indicate that the hypothermia is conditioned by intracellular glucopenia rather than the availability of circulating glucose or glucoregulatory hormones. To assess the role of central thermoregulatory mechanisms, 2-DG was injected into tail veins or cerebral ventricles of conscious mice. Although rectal temperatures fell with either route, hypothermic potencies were approximately fivefold greater with intracerebral administration. Thus, exclusion of glucose from central rather than peripheral sites plays the major part in the hyp...
Initial results from a prototype whole-body photon-counting computed tomography system (2015)

X-ray computed tomography (CT) with energy-discriminating capabilities presents exciting opportunities for increased dose efficiency and improved material decomposition analyses. However, due to constraints imposed by the inability of photon-counting detectors (PCD) to respond accurately at high photon flux, to date there has been no clinical application of PCD-CT. Recently, our lab installed a research prototype system consisting of two x-ray sources and two corresponding detectors, one using an energy-integrating detector (EID) and the other using a PCD. In this work, we report the first third-party evaluation of this prototype CT system using both phantoms and a cadaver head. The phantom studies demonstrated several promising characteristics of the PCD sub-system, including improved longitudinal spatial resolution and reduced beam hardening artifacts, relative to the EID sub-system. More importantly, we found that the PCD sub-system offers excellent pulse pileup control in cases of x-ray flux up to 550 mA at 140 kV, which corresponds to approximately 2.5×10<sup>11</sup> photons per cm<sup>2</sup> per second. In an anthropomorphic phantom and a cadaver head, the PCD sub-system provided image quality comparable to the EID sub-system for the same dose level. Our results demonstrate the potential of the prototype system to produce clinically-acceptable images <i>in vivo</i>.
ErbB-1 and ErbB-2 Acquire Distinct Signaling Properties Dependent upon Their Dimerization Partner (1998)

The different epidermal growth factor (EGF)-related peptides elicit a diverse array of biological responses as the result of their ability to activate distinct subsets of ErbB receptor dimers, leading to the recruitment of different intracellular signaling networks. To specifically examine dimerization-dependent modulation of receptor signaling, we constructed NIH 3T3 cell lines expressing ErbB-1 and ErbB-2 singly and in pairwise combinations with each other ErbB family member. This model system allowed the comparison of EGF-activated ErbB-1 with ErbB-1 activated by Neu differentiation factor (NDF)-induced heterodimerization with ErbB-4. In both cases, ErbB-1 coupled to the adaptor protein Shc, but only when activated by EGF was it able to interact with Grb2. Compared to the rapid internalization of EGF-activated ErbB-1, NDF-activated ErbB-1 showed delayed internalization characteristics. Furthermore, the p85 subunit of phosphatidylinositol kinase (PI3-K) associated with EGF-activated ErbB-1 in a biphasic manner, whereas association with ErbB-1 transactivated by ErbB-4 was monophasic. The signaling properties of ErbB-2 following heterodimerization with the other ErbB receptors or homodimerization induced by point mutation or monoclonal antibody treatment were also analyzed. ErbB-2 binding to peptides containing the Src homology 2 domain of Grb2 or p85 and the phosphotyrosine binding domain of Shc varied according to the mode of receptor activation. Finally, tryptic phosphopeptide mapping of both ErbB-1 and ErbB-2 revealed that receptor phosphorylation is dependent on the dimerization partner. Differential receptor phosphorylation may, therefore, be the basis for the differences in the signaling properties observed.
Key Contract Management Issues and Recommendations on IT Outsourcing in Taiwanese Hospitals (2011)

All organizations including hospitals have goals and objectives, regardless of size. To achieve these goals and objectives, hospitals have to outsource some of their information technology (IT) functions. There is no guarantee that IT outsourcing will be perceived as successful due to the very different expectations held by the various stakeholders. However, the contract management process of IT outsourcing in hospitals is particularly under-studied. Hence, the major objective of this paper is to identify and examine key IT outsourcing contract management issues in Taiwanese hospitals. Based on our data, recommendations are provided to deal with the identified key issues that are crucial in managing IT outsourcing contracts in Taiwanese hospitals.
Synthesis of Rhazinicine by a Metal‐Catalyzed CH Bond Functionalization Strategy (2008)

Iterative and regioselective metal-catalyzed CH bond functionalization has been utilized to develop a strategy for the first total synthesis of the pyrrole alkaloid rhazinicine (see scheme). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z705005_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Urogynecologic conditions: interstitial cystitis/painful bladder syndrome. (2015)

Interstitial cystitis, also known as painful bladder syndrome, is a debilitating condition. The diagnosis is difficult and often is one of exclusion. Cystoscopy is the best way to confirm the diagnosis, but treatment can be initiated based on symptoms alone. Most patients benefit from an array of different drugs, including pentosan polysulfate, amitriptyline, hydroxyzine, and cimetidine. These treatments must be tailored for each patient. If oral drugs are ineffective, intravesical therapy can be attempted with dimethyl sulfoxide, heparin, or an anesthetic therapeutic combination containing lidocaine. Fulguration typically is performed if Hunner ulcers are found on cystoscopy. Hydrodistention, sacral neuromodulation, and intradetrusor onabotulinumtoxinA are sometimes useful.
Combined discrete-continuous simulation models in ProModel for Windows (1995)

Although ProModel for Windows is primarily intended as a discrete event simulator aimed at part manufacturing systems, it supports construction of models that combine continuously varying processes that interact with discrete events. This paper proposes a general approach to modeling of combined discrete-continuous systems, describes the details of a particular example problem, and discusses some modeling issues.
Stable association of activated pp60src with two tyrosine-phosphorylated cellular proteins. (1989)

We have identified two phosphotyrosine-containing cellular proteins with relative molecular masses of 130,000 (pp130) and 110,000 (pp110) daltons in chicken embryo cells that coimmunoprecipitated with pp60v-src and activated forms of chicken pp60c-src (pp60(527)F). Most if not all of the tyrosine-phosphorylated forms of pp130 and pp110 could be immunoprecipitated from lysates with any of several src protein-specific monoclonal antibodies directed against at least three spatially distinct epitopes. Consequently, of the more than 15 prominent phosphoproteins detected on immunoblots with phosphotyrosine-specific antibodies, pp130 and pp110 were selectively removed by src protein-specific immunoprecipitation, and their presence in the immunoprecipitates appears to have been due to a direct interaction with activated src proteins. src protein variants that induce different morphological phenotypes were altered in their ability to form detergent-stable complexes with pp130 and pp110 or with pp110 alone. Mutant src proteins, defective for myristylation, showed increased tyrosine phosphorylation of and association with pp110. Expression of src variants with mutations in the A box (pp60dl92/527F) or B box (pp60dl155/527F) of the src homology region induced differences in phosphorylation of pp130 and pp110, as well as changes in their association with variant src proteins. Sequences within the B-box region appeared to be necessary for stable complex formation with pp130 and pp110 and may be involved in the interaction of activated src proteins with cellular substrates.