gebhart/patrepeval huggingface dataset:
Investigation of the location effect of external markers in respiratory‐gated radiotherapy (2008)

The correlation of external marker to the internal target could be influenced by several factors such as patient population, marker locations, and breathing patterns, considerably. The quality of correlation and predictability to the internal target furnished by a single external marker is inferior to that of the composite signal generated from multiple external markers. The use of composite signal shows great potential in improving the predictability of internal target motion and presents an effective way to track tumor more accurately.
Eicosanoids and Platelet-activating Factor in Allergic Respiratory Diseases (1991)

The nature of the lipid mediators released at an inflammatory site in the airways is dependent not only on the individual cells and inflammatory stimuli present but also on a complex interaction between neighboring cells and their lipid products. These lipid mediators share overlapping activities, and current research is directed toward determining the critical molecules involved in the pathogenesis of particular inflammatory states. How may the release of these lipid mediators play a role in the pathogenesis of asthma? Allergic persons after inhalation of specific allergen have a dual bronchospastic response. The early asthmatic response occurring shortly after allergen challenge is most likely secondary to the action of bronchoconstrictor molecules (e.g., LTC4, PGD2, PAF) released by human lung mast cells as a consequence of IgE-mediated degranulation. An inflammatory process than occurs in the airways that is characterized by an influx of eosinophils and neutrophils into the airway epithelium and bronchial fluids. This inflammatory response corresponds to the late asthmatic phase occurring several hours after allergen challenge. Release of sulfidopeptide leukotrienes, PAF, and cyclooxygenase products by cells infiltrating the airways may be involved in the bronchial smooth muscle constriction, mucosal edema, and mucus hypersecretion observed during these late asthmatic responses. In the future, the therapeutic use of specific antagonists of the biosynthetic enzymes of the 5-lipoxygenase pathway and receptor antagonists of the eicosanoids and PAF holds great promise for the modulation of airway inflammation.
Injectable In Situ Forming Hybrid Iron Oxide-Hyaluronic Acid Hydrogel for Magnetic Resonance Imaging and Drug Delivery (2014)

The development of multimodal in situ cross-linkable hyaluronic acid nanogels hybridized with iron oxide nanoparticles is reported. Utilizing a chemoselective hydrazone coupling reaction, the nanogels are converted to a macroscopic hybrid hydrogel without any additional reagent. Hydrophobic cargos remain encapsulated in the hydrophobic domains of the hybrid hydrogel without leakage. However, hydrogel degradation with hyaluronidase liberates iron oxide nanoparticles. This allows the utilization of imaging agents as tracers of the hydrogel degradation. UV-vis spectrometry and MRI studies reveal that the degradability of the hydrogels correlates with their structure. The hydrogels presented here are very promising theranostic tools for hyaluronidase-mediated delivery of hydrophobic drugs, as well as imaging of hydrogel degradation and tracking of degradation products in vivo.
E3 ubiquitin ligase Mule ubiquitinates Miz1 and is required for TNFα-induced JNK activation (2010)

The zinc finger transcription factor Miz1 is a negative regulator of TNFalpha-induced JNK activation and cell death through inhibition of TRAF2 K63-polyubiquitination in a transcription-independent manner. Upon TNFalpha stimulation, Miz1 undergoes K48-linked polyubiquitination and proteasomal degradation, thereby relieving its inhibition. However, the underling regulatory mechanism is not known. Here, we report that HECT-domain-containing Mule is the E3 ligase that catalyzes TNFalpha-induced Miz1 polyubiquitination. Mule is a Miz1-associated protein and catalyzes its K48-linked polyubiquitination. TNFalpha-induced polyubiquitination and degradation of Miz1 were inhibited by silencing of Mule and were promoted by ectopic expression of Mule. The interaction between Mule and Miz1 was promoted by TNFalpha independently of the pox virus and zinc finger domain of Miz1. Silencing of Mule stabilized Miz1, thereby suppressing TNFalpha-induced JNK activation and cell death. Thus, our study reveals a molecular mechanism by which Mule regulates TNFalpha-induced JNK activation and apoptosis by catalyzing the polyubiquitination of Miz1.
Steroids for Pneumocystis carinii Pneumonia and Respiratory Failure in the Acquired Immunodeficiency Syndrome (1990)

Patients with acquired immunodeficiency syndrome who have Pneumocystis carinii pneumonia (PCP) and respiratory failure have a high mortality. Previous reports have suggested that corticosteroids administered in conjunction with antibiotics improve the outcome in these patients. We reviewed our experience with adjunctive corticosteroids in 20 patients with acquired immunodeficiency syndrome and respiratory failure due to PCP to determine if this was the case. Fourteen patients responded to therapy with initial reversal of their respiratory failure. However, nine of these relapsed with recurrence of respiratory failure after steroid therapy was withdrawn. Eight (40%) of the patients remained alive and well 3 months or more following treatment. When the analysis was restricted to patients requiring intubation, only 25% were alive 3 months later. Despite good initial response to steroids in PCP and respiratory failure, survival remains limited. Controlled trials are needed to define better the role of steroid treatment in these patients.
Pharmacophore-Based Repositioning of Approved Drugs as Novel <i>Staphylococcus aureus</i> NorA Efflux Pump Inhibitors (2017)

An intriguing opportunity to address antimicrobial resistance is represented by the inhibition of efflux pumps. Focusing on NorA, the most important efflux pump of Staphylococcus aureus, an efflux pump inhibitors (EPIs) library was used for ligand-based pharmacophore modeling studies. By exploitation of the obtained models, an in silico drug repositioning approach allowed for the identification of novel and potent NorA EPIs.
Estimation of discontinuous solutions of ill-posed problems via adaptive grid regularization (2006)

In this paper we treat a new regularization method which is well-suited for ill-posed problems with discontinuous solutions: adaptive grid regularization. After describing the method we present several numerical examples showing that this method is a powerful tool to identify discontinuities in ill-posed problems.
FIELD EFFECT TRANSISTORS ON EPITAXIAL GaAs AS TRANSDUCERS FOR ACOUSTIC SURFACE WAVES (1971)

Two field effect transistor structures on epitaxial GaAs have been used as input and output transducers on an acoustic delay line. The transducer mechanism is described in terms of a piezoelectric coupling between the current modulation produced in the field effect transistor and the acoustic waves. The conversion loss at 90 MHz was 44 dB which is close to what can be estimated using a simple model.
Curcumin Represses NLRP3 Inflammasome Activation via TLR4/MyD88/NF-κB and P2X7R Signaling in PMA-Induced Macrophages (2016)

<b>Aims:</b> In the NOD-like receptor (NLR) family, the pyrin domain containing 3 (NLRP3) inflammasome is closely related to the progression of atherosclerosis. This study aimed to assess the effects of curcumin on NLRP3 inflammasome in phorbol 12-myristate 13-acetate (PMA)-induced macrophages and explore its underlying mechanism. <b>Methods:</b> Human monocytic THP-1 cells were pretreated with curcumin for 1 h and subsequently induced with PMA for 48 h. Total protein was collected for Western blot analysis. Cytokine interleukin (IL)-1β release and nuclear factor kappa B (NF-κB) p65 translocation were detected by ELISA assay and cellular NF-κB translocation kit, respectively. <b>Results:</b> Curcumin significantly reduced the expression of NLRP3 and cleavage of caspase-1 and IL-1β secretion in PMA-induced macrophages. Moreover, Bay (a NF-κB inhibitor) treatment considerably suppressed the expression of NLRP3 inflammasome in PMA-induced THP-1 cells. Curcumin also markedly inhibited the upregulation of toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (MyD88), phosphorylation level of IκB-α, and activation of NF-κB in PMA-induced macrophages. In addition, purinergic 2X7 receptor (P2X7R) siRNA was administered, and it significantly decreased NLRP3 inflammasome expression in PMA-induced macrophages. Furthermore, curcumin reversed PMA-stimulated P2X7R activation, which further reduced the expression of NLRP3 and cleavage of caspase-1 and IL-1β secretion. Silencing of P2X7R using siRNA also suppressed the activation of NF-κB pathway in PMA-induced macrophages, but P2X7R-silenced cells did not significantly decrease the expression of TLR4 and MyD88. <b>Conclusion:</b> Curcumin inhibited NLRP3 inflammasome through suppressing TLR4/MyD88/NF-κB and P2X7R pathways in PMA-induced macrophages.
Changes in Collagen With Aging Maintain Molecular Stability After Overload: Evidence From an In Vitro Tendon Model (2010)

Soft tissue injuries are poorly understood at the molecular level. Previous work using differential scanning calorimetry (DSC) has shown that tendon collagen becomes less thermally stable with rupture. However, most soft tissue injuries do not result in complete tissue rupture but in damaging fiber overextension. Covalent crosslinking, which increases with animal maturity and age, plays an important role in collagenous fiber mechanics. It is also a determinant of tissue strength and is hypothesized to inhibit the loss of thermal stability of collagen due to mechanical damage. Controlled overextension without rupture was investigated to determine if overextension was sufficient to reduce the thermal stability of collagen in the bovine tail tendon (BTT) model and to examine the effects of aging on the phenomenon. Baseline data from DSC and hydrothermal isometric tension (HIT) techniques were compared between two groups: steers aged 24-30 months (young group), and skeletally mature bulls and oxen aged greater than five years (old group). Covalent crosslinks were quantified by ion exchange chromatography. Overextension resulted in reduced collagen thermal stability in the BTT model. The Young specimens, showing detectably lower tissue thermomechanical competence, lost more thermal stability with overextension than did the old specimens. The effect on old specimens, while smaller, was detectable. Multiple overextension cycles increased the loss of stability in the young group. Compositional differences in covalent crosslinking corresponded with tissue thermomechanical competence and therefore inversely with the loss of thermal stability. HIT testing gave thermal denaturation temperatures similar to those measured with DSC. The thermal stability of collagen was reduced by overextension of the tendon--without tissue rupture--and this effect was amplified by increased cycles of overextension. Increased tissue thermomechanical competence with aging seemed to mitigate the loss of collagen stability due to mechanical overextension. Surprisingly, the higher tissue thermomechanical competence did not directly correlate with the concentration of endogenous enzymatically derived covalent crosslinking on a mole per mole of collagen basis. It did, however, correlate with the percentage of mature and thermally stable crosslinks. Compositional changes in fibrous collagens that occur with aging affect fibrous collagen mechanics and partially determine the nature of mechanical damage at the intermolecular level. As techniques develop and improve, this new information may lead to important future studies concerning improved detection, prediction, and modeling of mechanical damage at much finer levels of tissue hierarchy than currently possible.
Getting Physical with the Digital Investigation Process (2003)

In this paper, a process model for digital investigations is defined using the theories and techniques from the physical investigation world. While digital investigations have recently become more common, physical investigations have existed for thousands of years and the experience from them can be applied to the digital world. This paper introduces the notion of a digital crime scene with its own witnesses, evidence, and events that can be investigated using the same model as a physical crime scene. The proposed model integrates the physical crime scene investigation with the digital crime scene investigation to identify a person who is responsible for the digital activity. The proposed model applies to both law enforcement and corporate investigations.
Unsteady MHD Flow in a Rotating Parallel Plate Channel under the Influence of Pressure Gradient with Hall Current Effects (2016)

In this paper we discussed the unsteady flow of an incompressible electrically conducting viscous fluid in a rotating porous media, with a variable pressure gradient and in the presence of hall current. We have considered three different cases, like impulsive change, cosine and sine oscillations of pressure gradient. It is found that, the rotational and Lorentz forces are having significant effect on velocity profile in the presence of pressure gradient and hall current. The physical significance of various dimensionless parameter’s are discussed analytically and numerically on velocity distribution and frictional force.
Information Olfactation: Harnessing Scent to Convey Data (2018)

Olfactory feedback for analytical tasks is a virtually unexplored area in spite of the advantages it offers for information recall, feature identification, and location detection. Here we introduce the concept of information olfactation as the fragrant sibling of information visualization, and discuss how scent can be used to convey data. Building on a review of the human olfactory system and mirroring common visualization practice, we propose olfactory marks, the substrate in which they exist, and their olfactory channels that are available to designers. To exemplify this idea, we present VISCENT: A six-scent stereo olfactory display capable of conveying olfactory glyphs of varying temperature and direction, as well as a corresponding software system that integrates the display with a traditional visualization display. Finally, we present three applications that make use of the viScent system: A 2D graph visualization, a 2D line and point chart, and an immersive analytics graph visualization in 3D virtual reality. We close the paper with a review of possible extensions of viScent and applications of information olfactation for general visualization beyond the examples in this paper.
Supravital Blood Studies, Using Acridine Orange Fluorescence (1961)

Abstract A simple method for supravital fluorochroming of blood with acridine orange has been described. The supravital method is of value in distinguishing nucleated cellular elements, reticulocytes and erythrocytic inclusions. Preliminary studies of peripheral blood in leukemia indicate that it may be helpful in differentiating certain abnormal cellular elements. The chemistry of acridine orange with respect to metachromatic color differentiation of DNA and RNA has been discussed. Based on supravital observations of the L. E. cell phenomenon, speculation has been offered as to the site of interaction of the L.E. factor with DNA.
Thematic Review Series: Skin Lipids. Antimicrobial lipids at the skin surface (2007)

The skin surface represents our interface with the external environment, and as such, is our first line of defense against microbial colonization and infection. Lipids at the skin surface are thought to underlie at least part of an antimicrobial barrier. Some of these lipids are synthesized in the epidermis and are carried to the surface as cells differentiate, whereas others are secreted onto the surface from the sebaceous glands. One such group, free sphingoid bases, are known to have broad antimicrobial activity, and our previous studies demonstrate their presence at the skin surface. Free sphingoid bases may be generated by enzymatic hydrolysis of epidermal ceramides. In addition, our preliminary results demonstrate potent antibacterial activity associated with two specific fatty acids derived from sebaceous triglycerides. Most remarkably, one of these fatty acids (sapienic acid, C16:1Delta6), in combination with a low concentration of ethanol, is very effective against methicillin-resistant Staphylococcus aureus (MRSA). In fact, this combination was far more effective than mupirocin with or without ethanol. Mupirocin is a "gold standard" for activity against MRSA.
Combination of Column Temperature Gradient and Mobile Phase Flow Gradient in Microcolumn and Capillary Column High-Performance Liquid Chromatography (1997)

The combination of several gradient modes (solvent, temperature, and flow programming) is rarely used in HPLC analysis. In this work, the separations obtained utilizing simultaneous flow and temperature gradient in capillary column and microcolumn HPLC were compared with the separations performed under isocratic, isothermal, and isorheic (constant flow) conditions. When the mobile phase flow rate and the column temperature were changed simultaneously during the separation run, the analysis time was shortened up to 50%, while the separation efficiency was preserved. The separations obtained with combined temperature and flow gradients show high reproducibility (relative standard deviation <2.0%), comparable to the reproducibility normally seen with a mobile phase gradient. For capillary HPLC, simultaneous temperature and flow programming is the method of choice because of the great technical difficulties involved in performing solvent gradient elution.
Expression and <i>in‐situ</i> localization of genes coding for extracellular matrix proteins and extracellular matrix degrading proteases in pancreatic cancer (1995)

Pancreatic cancer shows a strong desmoplastic reaction characterized by a remarkable proliferation of interstitial connective tissue (collagens type I and III, fibronectin). In this study we have analyzed the balance of expression of mRNAs encoding extracellular matrix components (collagens I, III and IV, laminin, fibronectin), extracellular matrix-degrading metalloproteinases (MMP-1, -2, -3 and -9) and tissue inhibitors of metalloproteinases (TIMP-1 and -2) in pancreatic cancer and control pancreatic tissue by Northern-blot analysis and mRNA in situ hybridization. Transcripts for MMP-1 (interstitial collagenase) and MMP-3 (stromelysin-1) were not detectable in pancreatic cancer and control tissues. Steady-state levels of transcripts encoding extracellular matrix proteins, MMP-2 (72-kDa collagenase IV), MMP-9 (92-kDa collagenase type IV), TIMP-1 and TIMP-2 were elevated in the majority of pancreatic-cancer tissue samples as compared to control pancreatic tissue. A good correlation was seen between overexpression of these MMPs and TIMPs and the steady-state levels of transcripts coding for extracellular matrix proteins, the amount of collagen protein and the severity of the desmoplastic reaction. In situ hybridization studies localized transcripts coding for collagens type I and III to spindle-shaped stromal cells, whereas transcripts for MMP-2, MMP-9, TIMP-1 and TIMP-2 were found in both stromal and tumor cells. However, MMP-2 transcripts appeared to be more abundant in stromal cells, TIMP-1 and TIMP-2 transcripts were evenly distributed over tumor and stromal cells and relatively more MMP-9 transcripts were found in tumor cells. We conclude that, in human pancreatic cancer, MMP-2, MMP-9, TIMP-1 and TIMP-2 may be involved in processes leading to the strong desmoplastic reaction observed in these tumors. Both stromal and tumor cells appear to be the source of MMPs and TIMPs in human pancreatic cancer.
Crystal structure of β-Cu<sub>2</sub>P<sub>2</sub>O<sub>7</sub> (1968)

The crystal structure of β-CU 2 P 2 O 7 has been determined by X-ray methods. The crystals are monoclinic with a = 6.827(8) Å, b = 8.118(10) Å, c = 4.576(6) Å, β = 108.85(10)°, Z = 2, and space group C2/m. This structure is analogous to that of the mineral thortveitite and the high temperature forms of the pyrophosphates of Zn, Mg, and Mn. The cations are octahedrally coordinated to oxygen atoms with equatorial Cu—O bonds of 2.00 Å and 1.94 Å while the axial bond lengths are 2.58 Å. The anion has inner P—O bonds of 1.542 Å and average terminal bonds of 1.509 Å. In addition to the usual refinement with anisotropic thermal parameters, the structure has been refined in terms of a disordered structure generated from the low temperature α form of CU 2 P 2 O 7 . This disordered model agrees as well with the data (R = 0.12) as the structure based on the thortveitite structure with large anisotropic motion assigned to the atoms.
Communication metrics for software development (1997)

We present empirical evidence that metrics on communication artifacts generated by groupware tools can be used to gain significant insight into the development process that produced them. We describe a testbed for developing and testing communication metrics, a senior level software engineering project course at Carnegie Mellon University, in which we conducted several studies and experiments from 1991 to 1996 with more than 300 participants. Such a testbed is an ideal environment for empirical software engineering, providing sufficient realism while allowing for controlled observation of important project parameters. We illustrate the value of communication metrics with three proof-of-concept experiments and propose a statistical framework based on structural equations for validating communication metrics.
Software power optimizations in an embedded system (2002)

The topic of reducing power dissipation in embedded systems has received considerable attention in the recent years. Techniques have been reported to minimize energy dissipation through (a) selection of better algorithms for the application e.g. DSP algorithms that require fewer number of operations to perform a task such as filtering (b) minimizing state transitions and switching activity in the hardware implementation, and (c) reducing the operating supply voltage by changing the architecture of the system e.g. through the use of pipelining. However, power dissipation is often neglected when developing the software for embedded systems. Software optimization techniques can be used to reduce the cost, size, and power dissipation in embedded systems without adding to system overheads. In this paper, we view the power dissipation as consisting of two parts, the power dissipated in the application-specific integrated circuits (hardware power) and the power dissipated by the CPU, memory and associated busses (software power). We provide a trace-based technique to estimate software power and study the effect of different code optimization techniques on software power, performance and code size.
A service for queue prediction and job statistics (2010)

Science Gateways often execute computations on clusters managed by batch schedulers. These schedulers queue computations until resources are available and then execute them. Clusters are typically scarce resources so the amount of time a computation waits before it begins to execute can be significant. Gateways can potentially reduce the turn around time of their computations and improve their user experience if they use estimates of how long computations will wait in a queue before beginning to execute. This paper describes a service that provides such estimates as well as current and historical job information. An instance of this service has been deployed on TeraGrid and is available to TeraGrid science gateways.