gebhart/patrepeval huggingface dataset:
RAGE: A beneficial role in pulmonary fibrosis (2006)

Idiopathic pulmonary fibrosis (IPF) is a severely debilitating disease with a poor prognosis. There are currently no effective therapies for IPF, thus the identification of new therapeutic targets is needed. The receptor for advanced glycation end products (RAGE) is a cell surface receptor whose activation has been linked to many diseases. Although expressed at the highest levels in the lungs of adult animals, the role of RAGE has not been examined in pulmonary disease. This study examined the potential role of RAGE in IPF pathogenesis. Methods: RAGE expression was examined in two mouse models of pulmonary fibrosis and in human IPF lungs. Pulmonary histology and hydroxyproline levels of RAGE null mice was also compared with that of wild‐type mice. In addition, cultured human pulmonary fibroblasts were treated with RAGE ligands and α‐smooth muscle actin expression was examined. Results: Membrane RAGE and its soluble (decoy) isoform, sRAGE, are significantly depleted in both murine and human fibrotic lungs. In contrast to other diseases in which RAGE signaling promotes pathology, histologic and hydroxyproline studies on aged RAGE null mice indicate that they spontaneously develop pulmonary fibrosis‐like alterations. In vitro studies suggest that RAGE signaling may inhibit myofibroblastic phenotypes in pulmonary fibroblasts. Conclusions: Combined with data from mouse models of pulmonary fibrosis and human IPF tissues, these data indicate that loss of RAGE/sRAGE plays an important role in the pathogenesis of IPF.
Coherency effects on the mixing thermodynamics of cubicTi1−xAlxN/TiN(001) multilayers (2016)

In this work, we discuss the mixing thermodynamics of cubic (B1) ${\mathrm{Ti}}_{1\ensuremath{-}x}{\mathrm{Al}}_{x}\mathrm{N}/\mathrm{TiN}(001)$ multilayers. We show that interfacial effects suppress the mixing enthalpy compared to bulk ${\mathrm{Ti}}_{1\ensuremath{-}x}{\mathrm{Al}}_{x}\mathrm{N}$. The strongest stabilization occurs for compositions in which the mixing enthalpy of bulk ${\mathrm{Ti}}_{1\ensuremath{-}x}{\mathrm{Al}}_{x}\mathrm{N}$ has its maximum. The effect is split into a strain and an interfacial (or chemical) contribution, and we show that both contributions are significant. An analysis of the local atomic structure reveals that the Ti atoms located in the interfacial layers relax significantly different from those in the other atomic layers of the multilayer. Considering the electronic structure of the studied system, we demonstrate that the lower Ti-site projected density of states at ${\ensuremath{\epsilon}}_{\mathrm{F}}$ in the ${\mathrm{Ti}}_{1\ensuremath{-}x}{\mathrm{Al}}_{x}\mathrm{N}/\mathrm{TiN}$ multilayers compared to the corresponding monolithic bulk explains a decreased tendency toward decomposition.
Evolution of Quantitative MALDI-TOF Mass Spectrometry for Clinical Applications (2015)

The nearly simultaneous discoveries of electrospray ionization (ESI)2 (1) and MALDI (2) 27 years ago removed the volatility barrier for mass spectrometry (MS). ESI-MS developed very rapidly, at least partly due to the ease of interfacing with commercially available quadrupole and trap instruments widely used for analytical applications. TOF is particularly well suited to MALDI with pulsed ion sources compatible with pulsed laser desorption, but applications developed more slowly, at least in part because higher-performance instruments were not initially available. The potential of MALDI has stimulated development of improved TOF instrumentation particularly tailored for this ionization technique.

Laser ionization MS has been extensively studied for >60 years, but until the introduction of an appropriate matrix for absorbing the laser energy was introduced, biological applications were very limited (3). Karas and Hillenkamp (2) found that the use of a suitable matrix could reduce the required photon intensity for desorption by an order of magnitude and coined the description of the process as “matrix-assisted laser desorption ionization.” Further development of the time-of-flight instrument enabled the observation of proteins of masses >100 kDa, such as β-d-galactosidase at approximately 117 kDa reported by Hillenkamp (4) at the Bordeaux International Mass Spectrometry meeting in 1988. This signaled the beginning of a new era in biological MS. The resolving power obtained in this initial work was rather low, and it was quickly realized that a major limitation was due to ion fragmentation in flight. The first practical MALDI-TOF mass spectrometer for high m / z was built by Beavis and Chait within a few months of the discovery of MALDI (5). This was a simple linear TOF with a static single field source, drift tube, and detector. A major advantage of the linear analyzer is that ions dissociating in flight arrive at nearly …
The Impact of Visceral Mass on Survival in Chronic Hemodialysis Patients (2007)

In chronic hemodialysis, patient survival is positively correlated with body weight and body mass index (BMI). This relationship extends even to obese patients with a BMI >30 kg/m2. We have put forward the hypothesis that this survival benefit may be due to a lower average synthesis rate of uremic toxins (expressed as amount per time per unit of body weight) in larger patients, because the relative contribution of the high metabolic rate organs (HMRO) to body weight in these patients is lower and HMRO are most likely to be the prime source of uremic toxins. In addition, the average uremic toxin concentration in larger patients may be lower because of the larger distribution volume. Based on these assumptions, a better survival in patients with a lower HMRO to body weight fraction (HMRO%BW) can be predicted. To test this hypothesis we estimated gender- and race-specific HMRO mass by means of recently published regression models in 2,004 incident hemodialysis patients. Cox proportional hazards models were used to assess the association between age, serum albumin concentration, eKt/V, and HMRO% BW and mortality. High HMRO%BW was significantly associated with increased mortality (hazard ratio 1.323 [95% CI: 1.186 to 1.477]). Mean survival time was longest in the low HMRO%BW tertile (1,031 days [95%CI: 974 to 1,087]), 935 days [95%CI: 886 to 984] in the middle, and 876 days [95%CI: 825 to 926] in the high HMRO%BW tertile (p<0.0001; log rank test). These results support the hypothesis predicting that a low HMRO mass per unit of weight confers a beneficial effect on survival.
Distributed Linear Parameter Estimation: Asymptotically Efficient\n Adaptive Strategies (2011)

The paper considers the problem of distributed adaptive linear parameter\nestimation in multi-agent inference networks. Local sensing model information\nis only partially available at the agents and inter-agent communication is\nassumed to be unpredictable. The paper develops a generic mixed time-scale\nstochastic procedure consisting of simultaneous distributed learning and\nestimation, in which the agents adaptively assess their relative observation\nquality over time and fuse the innovations accordingly. Under rather weak\nassumptions on the statistical model and the inter-agent communication, it is\nshown that, by properly tuning the consensus potential with respect to the\ninnovation potential, the asymptotic information rate loss incurred in the\nlearning process may be made negligible. As such, it is shown that the agent\nestimates are asymptotically efficient, in that their asymptotic covariance\ncoincides with that of a centralized estimator (the inverse of the centralized\nFisher information rate for Gaussian systems) with perfect global model\ninformation and having access to all observations at all times. The proof\ntechniques are mainly based on convergence arguments for non-Markovian mixed\ntime scale stochastic approximation procedures. Several approximation results\ndeveloped in the process are of independent interest.\n
Effect of Dispersive Condition and Size for the Activation of ZnS Photocatalysts with Stratified Morphology (2011)

Abstract not Available.
Psychosocial Issues in Pediatric Organ Transplantation: The Parents' Perspective (1986)

The process of organ transplantation for a child has a profound impact on the entire family. Parents are faced with a number of psychosocial stresses many of which are unique in a pediatric hospital setting. We report the information provided by parents who have participated in a support group established for those with children undergoing heart and liver transplantation. Descriptive information gathered throughout the past 4 years in this group suggests that there are three specific stages that these families must endure: preoperative, perioperative, and long-term postoperative. The major psychosocial obstacles for families at each stage of the transplant process are described in detail. This information provides the health care professional with a basic framework to understand and provide guidance to the families of transplant patients.
Optimal focusing through plane interfaces using time-reversal methods (1992)

For several years, time-reversal methods were developed in this laboratory, theoretically and experimentally, to optimize focusing of an ultrasonic pressure field on a target in homogeneous and heterogeneous media. In this work, the problem is analyzed in the case of focusing through a plane interface separating two media with different sound speeds and densities. The principle consists in considering the target as an active source of an acoustic field measured by a mirror. Then, the mirror time-reverses this field, and an acoustic wave back propagates and is focused on the initial target position. A theoretical approach and numerical simulations are presented using one or two plane infinite time-reversal mirrors working on the reflected and/or transmitted components of the field generated by the source. It is shown that it can be more efficient to time reverse the reflected or transmitted field, depending on the velocity contrast between the two media. The problem of mirrors of finite size is also discussed, resulting in a broader focusing peak. Finally, the time-reversal method is compared to the standard Fermat’s surface technique, that reduces to a time-delay computation according to Snell’s law. It will be shown how the time-reversal method, that takes into account the whole information coming from the medium, improves the focalization on the initial target position.
CC-90009: A Cereblon E3 Ligase Modulating Drug That Promotes Selective Degradation of GSPT1 for the Treatment of Acute Myeloid Leukemia (2021)

Acute myeloid leukemia (AML) is marked by significant unmet clinical need due to both poor survival and high relapse rates where long-term disease control for most patients with relapsed or refractory AML remain dismal. Inspired to bring novel therapeutic options to these patients, we envisioned protein degradation as a potential therapeutic approach for the treatment of AML. Following this course, we discovered and pioneered a novel mechanism of action which culminated in the discovery of CC-90009. CC-90009 represents a novel protein degrader and the first cereblon E3 ligase modulating drug to enter clinical development that specifically targets GSPT1 (G1 to S phase transition 1) for proteasomal degradation. This manuscript briefly summarizes the mechanism of action, scientific rationale, medicinal chemistry, pharmacokinetic properties, and efficacy data for CC-90009, which is currently in phase 1 clinical development.
Singlet lifetime measurements in an all-proton chemically equivalent spin system by hyperpolarization and weak spin lock transfers (2015)

Correction for 'Singlet lifetime measurements in an all-proton chemically equivalent spin system by hyperpolarization and weak spin lock transfers' by Y. Zhang et al., Phys. Chem. Chem. Phys., 2015, 17, 24370-24375.
Antimicrobial potential of bacteriocins in poultry and swine production (2017)

The routine use of antibiotics in agriculture has contributed to an increase in drug-resistant bacterial pathogens in animals that can potentially be transmitted to humans. In 2000, the World Health Organization identified resistance to antibiotics as one of the most significant global threats to public health and recommended that the use of antibiotics as additives in animal feed be phased out or terminated, particularly those used to treat human infections. Research is currently being carried out to identify alternative antimicrobial compounds for use in animal production. A number of studies, mostly in vitro, have provided evidence indicating that bacteriocins, which are antimicrobial peptides of bacterial origin, may be promising alternatives to conventional antibiotics in poultry and swine production. This review provides an update on bacteriocins and their potential for use in the poultry and swine industries.
Development of a multiple-scattering acoustic sensor for process monitoring: Application to monitoring milk coagulation (2017)

Diverse industrial processes can be monitored by tracking changes in a fluid media. Having inline nondestructive information about the state of the process permits to have optimal results at reasonable costs. The suitability of low-power-ultrasound techniques has been widely investigated. However, sometimes this techniques have a poor signal-to-noise ratio or excessive sensitivity to temperature changes. In the present work, multiple-scattering of an ultrasonic signal is generated to enhancing the process-tracing ability. A pulse-echo system is used. The acoustic signal travels through a rod array, which is immersed in the changing medium. Useful information is taken from the echoes correlation. As a test case, this system has been proved for tracing milk coagulation, which is necessary in the cheese-manufacturing process.
Systemically Administered Hemostatic Nanoparticles for Identification and Treatment of Internal Bleeding (2019)

Internal bleeding is an injury that can be difficult to localize and effectively treat without invasive surgeries. Injectable polymeric nanoparticles have been developed that can reduce clotting times and blood loss, but they have yet to incorporate sufficient diagnostic capabilities to assist in identifying bleeding sources. Herein, polymeric nanoparticles were developed to simultaneously treat internal bleeding while incorporating tracers for visualization of the nanoparticles by standard clinical imaging modalities. Addition of 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine perchlorate (DiD; a fluorescent dye), biotin functionality, and gold nanoparticles to hemostatic polymeric nanoparticles resulted in nanoparticles amenable to imaging with near-infrared (NIR) imaging, immunohistochemistry, and X-ray computed tomography (CT), respectively. Following a lethal liver resection injury, visualization of accumulated nanoparticles by multiple imaging methods was achieved in rodents, with the highest accumulation observed at the liver injury site, resulting in improved survival rates. Tracer addition to therapeutic nanoparticles allows for an expansion of their applicability, during stabilization by first responders to diagnosis and identification of unknown internal bleeding sites by clinicians using standard clinical imaging modalities.
Disparity scaling in the presence of accommodation-vergence conflict (2010)

To construct percepts from binocular information, the visual system must scale the retinal disparities with an estimate of fixation distance. Conventional 3d displays provide conflicting information about fixation distance: frequently, one distance is specified by the disparities, while another is specified by the display's physical distance. Simulated depth cues include the eyes' vergence, and horizontal and vertical disparities. Physical distance cues include focal cues which are retinal blur and accommodation. We have previously examined the influence of mismatches between simulated depth cues and focus cues on 3d percepts (Watt et al., 2005) using conventional displays. In that study, observers could have conceivably used high-level information such as knowledge of the monitor translation. We developed a fixed-viewpoint, volumetric display that allows one to present 3d images at three focal distances simultaneously (Akeley et al., 2004; Banks et al., 2005). Here we examine the utility of that display in minimizing the perceptual consequences of mismatches between simulated depth cues and focus cues. The volumetric display minimizes the contribution of high-level information. The stimulus was an “open-book” hinge textured with random dots. Observers indicated whether the hinge angle was greater or less than 90 deg. In one set of conditions, stimuli were presented on a conventional monitor at one of three physical distances and one of three simulated distances. In another set, the stimuli were presented on the volumetric display (Akeley et al., 2004). From the observers' judgments we determined the “equivalent distance”, the distance estimate that appeared to be used to scale the disparities. Physical and simulated distance cues both affected judgments, indicating that focal cues influence depth percepts. The influence of physical display distance was less in the volumetric display suggesting that high-level cues also affect distance estimates used to scale disparities.
An Information-Theoretic Approach for Computational Material Modeling (2008)

This paper presents an information-theoretic approach for computational material modeling, which characterizes materials by effectively utilizing all the known information including prior and empirical information. The approach is built within the framework of recursive Bayesian estimation where various inverse analysis techniques, such as Singular Value Decomposition (SVD) and Kalman Filter (KF) can be implemented. Numerical examples first investigate the validity of the proposed approach via parametric studies. The proposed approach has been then successfully applied to the identification of a composite specimen using a triaxial testing machine.
Transcriptional Analysis of an E2F Gene Signature as a Biomarker of Activity of the Cyclin-Dependent Kinase Inhibitor PHA-793887 in Tumor and Skin Biopsies from a Phase I Clinical Study (2010)

A transcriptional signature of the pan-cyclin-dependent kinase (Cdk) inhibitor PHA-793887 was evaluated as a potential pharmacodynamic and/or response biomarker in tumor and skin biopsies from patients treated in a phase I clinical study. We first analyzed the expression of a number of known E2F-dependent genes that were predicted to be modulated after Cdk2 and Cdk4 inhibition in xenograft tumor and skin samples of mice treated with the compound. This panel of 58 selected genes was then analyzed in biopsies from seven patients treated with PHA-793887 in a phase I dose escalation clinical trial in solid tumors. Quantitative real-time PCR or microarray analyses were done in paired skin and tumor biopsies obtained at baseline and at cycle 1. Analysis by quantitative real-time PCR of the signature in skin biopsies of patients treated at three different doses showed significant transcriptional downregulation with a dose-response correlation. These data show that PHA-793887 modulates genes involved in cell cycle regulation and proliferation in a clinical setting. The observed changes are consistent with its mechanism of action and correlate with target modulation in skin and with clinical benefit in tumors.
Distributed State Estimation and Energy Management in Smart Grids: A Consensus${+}$Innovations Approach (2014)

This paper reviews signal processing research for applications in the future electric power grid, commonly referred to as smart grid. Generally, it is expected that the grid of the future would differ from the current system by the increased integration of distributed generation, distributed storage, demand response, power electronics, and communications and sensing technologies. The consequence is that the physical structure of the system becomes significantly more distributed. The existing centralized control structure is not suitable any more to operate such a highly distributed system. Hence, in this paper, we overview distributed approaches, all based on consensus +innovations, for three common energy management functions: state estimation, economic dispatch, and optimal power flow. We survey the pertinent literature and summarize our work. Simulation results illustrate tradeoffs and the performance of consensus +innovations for these three applications.
Influence of the Architecture and Surface Effects on the Electronic Transport in Materials for Lithium Batteries (2011)

Abstract not Available.
Neprosin, a Selective Prolyl Endoprotease for Bottom-up Proteomics and Histone Mapping (2017)

Trypsin dominates bottom-up proteomics, but there are reasons to consider alternative enzymes. Improving sequence coverage, exposing proteomic "dark matter," and clustering post-translational modifications in different ways and with higher-order drive the pursuit of reagents complementary to trypsin. Additionally, enzymes that are easy to use and generate larger peptides that capitalize upon newer fragmentation technologies should have a place in proteomics. We expressed and characterized recombinant neprosin, a novel prolyl endoprotease of the DUF239 family, which preferentially cleaves C-terminal to proline residues under highly acidic conditions. Cleavage also occurs C-terminal to alanine with some frequency, but with an intriguingly high "skipping rate." Digestion proceeds to a stable end point, resulting in an average peptide mass of 2521 units and a higher dependence upon electron-transfer dissociation for peptide-spectrum matches. In contrast to most proline-cleaving enzymes, neprosin effectively degrades proteins of any size. For 1251 HeLa cell proteins identified in common using trypsin, Lys-C, and neprosin, almost 50% of the neprosin sequence contribution is unique. The high average peptide mass coupled with cleavage at residues not usually modified provide new opportunities for profiling clusters of post-translational modifications. We show that neprosin is a useful reagent for reading epigenetic marks on histones. It generates peptide 1-38 of histone H3 and peptide 1-32 of histone H4 in a single digest, permitting the analysis of co-occurring post-translational modifications in these important N-terminal tails.