gebhart/patrepeval huggingface dataset:
Cytotoxic Capacity of SIV-Specific CD8+ T Cells against Primary Autologous Targets Correlates with Immune Control in SIV-Infected Rhesus Macaques (2013)

Although the study of non-human primates has resulted in important advances for understanding HIV-specific immunity, a clear correlate of immune control over simian immunodeficiency virus (SIV) replication has not been found to date. In this study, CD8(+) T-cell cytotoxic capacity was examined to determine whether this function is a correlate of immune control in the rhesus macaque (RM) SIV infection model as has been suggested in chronic HIV infection. SIVmac251-infected human reverse transcriptase (hTERT)-transduced CD4(+) T-cell clone targets were co-incubated with autologous macaque effector cells to measure infected CD4(+) T-cell elimination (ICE). Twenty-three SIV-infected rhesus macaques with widely varying plasma viral RNA levels were evaluated in a blinded fashion. Nineteen of 23 subjects (83%) were correctly classified as long-term nonprogressor/elite controller (LTNP/EC), slow progressor, progressor or SIV-negative rhesus macaques based on measurements of ICE (weighted Kappa 0.75). LTNP/EC had higher median ICE than progressors (67.3% [22.0-91.7%] vs. 23.7% [0.0-58.0%], p = 0.002). In addition, significant correlations between ICE and viral load (r = -0.57, p = 0.01), and between granzyme B delivery and ICE (r = 0.89, p<0.001) were observed. Furthermore, the CD8(+) T cells of LTNP/EC exhibited higher per-cell cytotoxic capacity than those of progressors (p = 0.004). These findings support that greater lytic granule loading of virus-specific CD8(+) T cells and efficient delivery of active granzyme B to SIV-infected targets are associated with superior control of SIV infection in rhesus macaques, consistent with observations of HIV infection in humans. Therefore, such measurements appear to represent a correlate of control of viral replication in chronic SIV infection and their role as predictors of immunologic control in the vaccine setting should be evaluated.
Rewriting the Epigenetic Code for Tumor Resensitization: A Review (2014)

In cancer chemotherapy, one axiom, which has practically solidified into dogma, is that acquired resistance to antitumor agents or regimens, nearly inevitable in all patients with metastatic disease, remains unalterable and irreversible, rendering therapeutic rechallenge futile. However, the introduction of epigenetic therapies, including histone deacetylase inhibitors (HDACis) and DNA methyltransferase inhibitors (DNMTIs), provides oncologists, like computer programmers, with new techniques to "overwrite" the modifiable software pattern of gene expression in tumors and challenge the "one and done" treatment prescription. Taking the epigenetic code-as-software analogy a step further, if chemoresistance is the product of multiple nongenetic alterations, which develop and accumulate over time in response to treatment, then the possibility to hack or tweak the operating system and fall back on a "system restore" or "undo" feature, like the arrow icon in the Windows XP toolbar, reconfiguring the tumor to its baseline nonresistant state, holds tremendous promise for turning advanced, metastatic cancer from a fatal disease into a chronic, livable condition. This review aims 1) to explore the potential mechanisms by which a group of small molecule agents including HDACis (entinostat and vorinostat), DNMTIs (decitabine and 5-azacytidine), and redox modulators (RRx-001) may reprogram the tumor microenvironment from a refractory to a nonrefractory state, 2) highlight some recent findings, and 3) discuss whether the current "once burned forever spurned" paradigm in the treatment of metastatic disease should be revised to promote active resensitization attempts with formerly failed chemotherapies.
Breathing Rate Estimation From the Electrocardiogram and Photoplethysmogram: A Review (2017)

Breathing rate (BR) is a key physiological parameter used in a range of clinical settings. Despite its diagnostic and prognostic value, it is still widely measured by counting breaths manually. A plethora of algorithms have been proposed to estimate BR from the electrocardiogram (ECG) and pulse oximetry (photoplethysmogram, PPG) signals. These BR algorithms provide opportunity for automated, electronic, and unobtrusive measurement of BR in both healthcare and fitness monitoring. This paper presents a review of the literature on BR estimation from the ECG and PPG. First, the structure of BR algorithms and the mathematical techniques used at each stage are described. Second, the experimental methodologies that have been used to assess the performance of BR algorithms are reviewed, and a methodological framework for the assessment of BR algorithms is presented. Third, we outline the most pressing directions for future research, including the steps required to use BR algorithms in wearable sensors, remote video monitoring, and clinical practice.
Some remarks on contractive and existence sets (2021)

Let X be a real or complex Banach space and let F in X be a non-empty set. F is called an existence set of best coapproximation (existence set for brevity), if for any x in X, $R_F(x)$ is not the empty set, where $$ R_F (x) = \{ d \in F : \|d-c\| \leq \|x-c\| \hbox{ for any } c \in F \}.$$ It is clear that any existence set is a contractive subset of X. The aim of this paper is to present some conditions on F and X under which the notions of exsistence set and contractive set are equivalent.
Microstructural Investigation of the Aging Behavior of (3Y‐TZP)–Al <sub>2</sub> O <sub>3</sub> Composites (2005)

The low‐temperature autoclave aging behavior of zirconia‐toughened alumina composites processed by a classical powder mixing processing route was analyzed using atomic force microscopy (AFM), scanning electron microscopy, and X‐ray diffraction (XRD). The transformation was evaluated in terms of nucleation and growth, assessed by XRD. The time–temperature equivalency of the transformation was used to measure an apparent activation energy of the nucleation stage of the transformation of 78 kJ/mol. The microstructural features influencing the transformation were identified, and the influence of the alumina matrix on the transformation was investigated. Transformation progression grain by grain was observed by AFM. Transformation does not only occur in zirconia agglomerates but also in isolated zirconia grains. The matrix could partially inhibit the transformation. This behavior could be rationalized considering the constraining effect of the alumina matrix, shape strain accommodation arguments, and microstructural homogeneity effects.
Amino Acid Signaling in <i>Saccharomyces cerevisiae</i> : a Permease-Like Sensor of External Amino Acids and F-Box Protein Grr1p Are Required for Transcriptional Induction of the <i>AGP1</i> Gene, Which Encodes a Broad-Specificity Amino Acid Permease (1999)

The SSY1 gene of Saccharomyces cerevisiae encodes a member of a large family of amino acid permeases. Compared to the 17 other proteins of this family, however, Ssy1p displays unusual structural features reminiscent of those distinguishing the Snf3p and Rgt2p glucose sensors from the other proteins of the sugar transporter family. We show here that SSY1 is required for transcriptional induction, in response to multiple amino acids, of the AGP1 gene encoding a low-affinity, broad-specificity amino acid permease. Total noninduction of the AGP1 gene in the ssy1Delta mutant is not due to impaired incorporation of inducing amino acids. Conversely, AGP1 is strongly induced by tryptophan in a mutant strain largely deficient in tryptophan uptake, but it remains unexpressed in a mutant that accumulates high levels of tryptophan endogenously. Induction of AGP1 requires Uga35p(Dal81p/DurLp), a transcription factor of the Cys6-Zn2 family previously shown to participate in several nitrogen induction pathways. Induction of AGP1 by amino acids also requires Grr1p, the F-box protein of the SCFGrr1 ubiquitin-protein ligase complex also required for transduction of the glucose signal generated by the Snf3p and Rgt2p glucose sensors. Systematic analysis of amino acid permease genes showed that Ssy1p is involved in transcriptional induction of at least five genes in addition to AGP1. Our results show that the amino acid permease homologue Ssy1p is a sensor of external amino acids, coupling availability of amino acids to transcriptional events. The essential role of Grr1p in this amino acid signaling pathway lends further support to the hypothesis that this protein participates in integrating nutrient availability with the cell cycle.
Genetic Basin Analysis and Paleoenvironmental Reconstructions of the Mesozoic and Cenozoic Strata of the Libya Region (2007)

Our analysis of the Libya region was built on foundation of previous proprietary and published studies and employed recent proprietary research on concepts and tools and newly available data and a new age model that included significant thicknesses of Mesozoic strata offshore. These allowed calibration of the seismic character of source and reservoir facies and their stratal packaging in proven onshore areas, and extrapolation to similar seismic facies &amp; stratal packaging seen in offshore data. We concluded that the Libya region was in a favorable setting for accumulating source, reservoir, and seal-prone strata throughout the Mesozoic and Cenozoic, due to the: 1) common occurrence of shelfal water depths and paleogeographic restriction, 2) low-latitude setting, 3) warm, dry to sub humid paleoclimate, commonly with low seasonality, 4) some coastal upwelling, along with water mass mixing under ITCZ &amp; tropical cyclones, 5) dominantly quartz-sand-prone provenance lithotypes, and 6) late development of shelf-bypass clastic dispersal systems. The incorporation of paleo-environmental reconstructions is a powerful tool in exploration, enabling evaluation of numerous frontier areas in less than 10 weeks of work by using our fundamental understanding of the dynamics of basin formation integrated with the regional paleo-environmental context.
X-ray lathe: An X-ray lithographic exposure tool for nonplanar objects (1996)

An X-ray lithography lathe has been developed that can pattern cylindrical, ellipsoidal, and other nonplanar objects. This lathe is capable of patterning on a micron scale a wide variety of shapes including shapes impossible to achieve with a conventional lathe. A cylindrical core covered with a suitable resist is rotated while being exposed with a collimated X-ray source through a mask. The mask absorbs X rays up to a particular radius from the center of the core and the resist beyond that radius is removed in a developer. Several cylindrical cores were coated with poly(methylmethacrylate) (PMMA) 5 to 125 /spl mu/m thick and patterned with X-rays down to a 250-/spl mu/m horizontal scale (along the lathe axis). The exposure time for a cylindrical PMMA layer is /spl sim/three-four times longer than a planar layer with the same thickness. The capabilities of this technology, lathe apparatus, dose calculations, and initial exposure results are described.
Models in Pancreatic Neuroendocrine Neoplasms: Current Perspectives and Future Directions (2023)

Pancreatic neuroendocrine neoplasms (pNENs) are a heterogeneous group of tumors derived from multiple neuroendocrine origin cell subtypes. Incidence rates for pNENs have steadily risen over the last decade, and outcomes continue to vary widely due to inability to properly screen. These tumors encompass a wide range of functional and non-functional subtypes, with their rarity and slow growth making therapeutic development difficult as most clinically used therapeutics are derived from retrospective analyses. Improved molecular understanding of these cancers has increased our knowledge of the tumor biology for pNENs. Despite these advances in our understanding of pNENs, there remains a dearth of models for further investigation. In this review, we will cover the current field of pNEN models, which include established cell lines, animal models such as mice and zebrafish, and three-dimensional (3D) cell models, and compare their uses in modeling various disease aspects. While no study model is a complete representation of pNEN biology, each has advantages which allow for new scientific understanding of these rare tumors. Future efforts and advancements in technology will continue to create new options in modeling these cancers.
Filter Capacity Predictions for the Capture of Magnetic Microparticles by High-Gradient Magnetic Separation (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We present experimental and theoretical methods to predict maximum and working filter capacities for the capture of superparamagnetic microparticles through high-gradient magnetic separation (HGMS). For this, we employed various combinations of nine different HGMS filter matrices and two types of superparamagnetic microparticles. By calculating the separated particle mass per filter mesh area, we clearly demonstrated the influences of wire diameter and wire mesh spacing on the particle build-up density. Here, we introduce a simple experimental method for estimating average build-up densities in HGMS. Together with known physical parameters of the filter matrix and the background field, such average build-up densities allow good predictions of the operational working filter capacities. </para>
HVAC CAD Layout Tools: A Case Study of University/Industry Collaboration (1996)

Abstract An effective partnership between industry and the university resulted in the system of design tools for the layout of HVAC systems presented in this paper and illustrated with the design of a heat pump. The system provides tools to assist in the placement of components and routing of tubes between the components. Traditional tubes, tubes that have minimized length and number of bends, and those that are impossible to route in the traditional manner, are generated. The paper provides insight on both the collaborative research interaction and the resulting set of tools.
Introduction of CORC<sup>®</sup>wires: highly flexible, round high-temperature superconducting wires for magnet and power transmission applications (2016)

Conductor on Round Core (CORC ) technology has achieved a long sought-after benchmark by enabling the production of round, multifilament, (RE)Ba 2 Ca 3 O 7-x coated conductors with practical current densities for use in magnets and power applications. Recent progress, including the demonstration of engineering current density beyond 300 Amm -2 at 4.2 K and 20 T, indicates that CORC cables are a viable conductor for next generation high field magnets. Tapes with 30 m substrate thickness and tape widths down to 2 mm have improved the capabilities of CORC technology by allowing the production of CORC wires as thin as 3 mm in diameter with the potential to enhance the engineering current density further. An important benefit of the thin CORC wires is their improved flexibility compared to thicker (7-8 mm diameter) CORC cables. Critical current measurements were carried out on tapes extracted from CORC wires made using 2 and 3 mm wide tape after bending the wires to various diameters from 10 to 3.5 cm. These thin wires are highly flexible and retain close to 90% of their original critical current even after bending to a diameter of 3.5 cm. A small 5-turn solenoid was constructed and measured as a function of applied magnetic field, exhibiting an engineering current density of 233 Amm -2 at 4.2 K and 10 T. CORC wires thus form an attractive solution for applications between 4.2 and 77 K, including high-field magnets that require high current densities with small bending diameters, benefiting from a ready-to-use form (similar to NbTi and contrary to Nb 3 Sn wires) that does not require additional processing following coil construction.
Early development of cancer chemoprevention clinical trials: studies of dietary calcium as a chemopreventive agent for human subjects. (2002)

Early cancer chemoprevention clinical trials in human subjects had to be carried out with large numbers of subjects studied for long durations, measuring cancer as an end point. However new findings on abnormal epithelial cell growth and development during the multistage evolution of colonic tumors made it possible to carry out chemoprevention clinical trials in several stages, with fewer subjects studied for shorter durations, thus enabling investigators to analyze increasing numbers of chemopreventive agents and nutritional regimens in clinical trials. Supplemental dietary calcium was the first candidate chemopreventive agent studied in this multistage approach in human subjects, as a putative agent for colon cancer prevention. Early- and late-stage intermediate biomarker studies in humans have strongly suggested utility for supplemental dietary calcium to inhibit the development of benign and subsequent malignant colonic neoplasms. Preclinical experimental studies have further demonstrated the ability of increased dietary calcium to inhibit the evolution of colonic tumors when they were induced by targeted mutations, dietary factors, and particularly when given over a long duration of lifespan.
Investigation of Tone Reservation-based PAPR Techniques for Improving Power Amplifier Efficiency (2019)

OFDM suffers from high peak-to-average power ratio (PAPR), and these large peaks require a linear (i.e. with a large input back-off) and consequently inefficient power amplifier (PA) at the analogue radio frequency (RF) front-end. This paper will investigate the potential improvement in PA efficiency and RF energy savings achieved through tone reservation-based PAPR reduction methods.
Implementation of the Actuator Cylinder flow model in the HAWC2 code for aeroelastic simulations on Vertical Axis Wind Turbines (2013)

The paper presents the implementation of the Actuator Cylinder (AC) flow model in the HAWC2 aeroelastic code originally developed for simulation of Horizontal Axis Wind Turbine (HAWT) aeroelasticity. This is done within the DeepWind project where the main objective is to explore the competitiveness of VAWTs for floating MW concepts. The AC model is a 2D flow model and has thus some advantages compared with the stream tube models often used in VAWT aerodynamic and aeroelastic simulation models. A major finding presented in the present paper is a simple way to correct the results from the linear version of the AC model so that they correlate closely with the results of the full AC model. The linear model has very low computational requirements and is thus well suited for implementation in an aeroelastic model where the induction in a number of points on the rotor swept surface is updated at each time step. The AC model is described and the implementation of the model in HAWC2 is briefly presented. Results illustrating the accuracy of the different versions of the AC model are presented. Finally, initial simulations on the 5MW baseline rotor with the new HAWC2 version with the AC model implemented are presented.
Laminotomy for Lumbar Dorsal Root Ganglion Access and Injection in Swine (2017)

Dorsal root ganglia (DRG) are anatomically well defined structures that contain all primary sensory neurons below the head. This fact makes DRG attractive targets for injection of novel therapeutics aimed at treating chronic pain. In small animal models, laminectomy has been used to facilitate DRG injection because it involves surgical removal of the vertebral bone surrounding each DRG. We demonstrate a technique for intraganglionic injection of lumbar DRG in a large animal species, namely, swine. Laminotomy is performed to allow direct access to DRG using standard neurosurgical techniques, instruments, and materials. Compared with more extensive bone removal via laminectomy, we implement laminotomy to conserve spinal anatomy while achieving sufficient DRG access. Intraoperative progress of DRG injection is monitored using a non-toxic dye. Following euthanasia on post-operative day 21, the success of injection is determined by histology for intraganglionic distribution of 4',6-diamidino-2-phenylindole (DAPI). We inject a biologically inactive solution to demonstrate the protocol. This method could be applied in future preclinical studies to target therapeutic solutions to DRG. Our methodology should facilitate testing the translatability of intraganglionic small animal paradigms in a large animal species. Additionally, this protocol may serve as a key resource for those planning preclinical studies of DRG injection in swine.
Cardiac Glycosides Inhibit p53 Synthesis by a Mechanism Relieved by Src or MAPK Inhibition (2009)

p53 is regulated at multiple levels. We report here that p53, in multiple lines of human cancer cells, is down-regulated by cardiac glycoside drugs digoxin and ouabain, potent inhibitors of Na(+)/K(+)-ATPase. These drugs reduced the basal levels of p53 protein at nanomolar concentrations in a dose-, time-, and cancer cell line-dependent manner, but independent of p53 status of wild-type or mutant. The drugs also reduced the levels of p53 induced by its activators as well as p53 transfected into human cancer cells, regardless of its status. Interestingly, the drugs had no effect on endogenous p53 in two immortalized human cell lines. Mechanistically, p53 reduction occurred not at the mRNA levels but at the protein levels, as a result of reduced protein synthesis rather than enhanced degradation. The cellular sensitivity to drug-induced p53 reduction was not associated with the levels of alphasubunits of Na(+)/K(+)-ATPase in different cell lines. Although lowering extracellular K(+) did not reduce p53 as did ouabain and digoxin, it did potentiate both digoxin- and ouabain-induced p53 reduction in sensitive lines. Finally, p53 reduction seems to be triggered by activation of Src/mitogen-activated protein kinase (MAPK) signaling pathways upon drug binding to the Na(+)/K(+)-ATPase and can be completely blocked by the inhibitors of Src or MAP/ERK kinase. This is the first report that cardiac glycoside drugs, by initiating the Src/MAPK signaling pathways, reduce the p53 levels via inhibition of p53 protein synthesis. The drugs may be useful in the treatment of human cancers with a gain-of-function p53 mutation.
Regulation of growth in a neoplastic B cell line by transfected subunits of 3',5'-cyclic adenosine monophosphate-dependent protein kinase. (1994)

cAMP inhibits the proliferation of both normal peripheral blood B and T lymphocytes as well as the proliferation of a human neoplastic B precursor cell line (Reh). To positively show that this is mediated via the the catalytic subunit, C alpha, of cAMP-dependent protein kinase, stably transfected Reh cell lines overexpressing C alpha were established. This was achieved by transfection with a construct confering hygromycin resistance together with a zinc-inducible expression of C alpha from the human metallothionine promoter. C alpha transfected clones were shown to confer a 2- to 2.5-fold zinc-dependent increase in C alpha messenger RNA, immunoreactive C, and phosphotransferase activity. The growth rate of clones transfected with C alpha was retarded, and a zinc-dependent inhibition of cell proliferation was demonstrated in the presence of a small trigger dose of forskolin. In contrast, overexpression of the regulatory subunit I alpha had no effect on cAMP-dependent inhibition of cell proliferation. Furthermore, expression of mutant regulatory subunit I alpha AB, which renders cAMP-dependent protein kinase unresponsive to cAMP, clearly protected against that inhibitory effect of cAMP. These data provides evidence that activation of the C subunit (C alpha) of cAMP-dependent protein kinase mediates the inhibitory action of cAMP on cell proliferation in Reh cells.