gebhart/patrepeval huggingface dataset:
A Biomarker Panel for Chronic Graft-Versus-Host Disease (2015)

Chronic GVHD (cGVHD) remains the major contributor to morbidity and mortality for survivors of allogeneic hematopoietic cell transplant (HCT), but it remains a clinical diagnosis. We used a proteomics discovery approach comparing plasma pools from onset of de novo cGVHD (N=17), progressive cGVHD (N=18), and matched time-point samples from 19 patients without GVHD. Of 105 proteins that showed at least 1.3-fold change in the quantification ratio, we further selected 24 proteins based on their involvement in relevant pathway networks, and the availability of ELISA. In addition, two markers (CXCL9 and ST2) were measured based on previously noted associations with cGVHD or refractory acute GVHD. Levels of these 26 proteins were measured by ELISA in plasma from an independent set of 178 patients with cGVHD, and from 33 controls without cGVHD. Logistic regression was used to evaluate the association between cGVHD and biomarkers after log transformation. All analyses were adjusted for significant clinical variables considering age, sex, stem cell source, conditioning (nonmyeloablative vs. others), donor (matched sibling vs. others), and time from HCT to sample collection. To determine the best combination model, we used forward selection with a 0.05 significance threshold, confirmed by backward selection. ROC curves were generated for the best single biomarker, and the combination model. The analysis of nonrelapse mortality (NRM) divided the panel weighted sum on the median value among cGVHD cases (N = 178), and compared cases above and below the median. Of the 26 proteins tested, 9 were associated with cGVHD with p-values < 0.05 (Table 1). Together ST2, CXCL9, MMP3, and OPN compose a biomarker panel for diagnosis of cGVHD with an AUC of 0.89 (Fig 1). We next compared the biomarker panel between groups with different cGVHD severity (none, mild/moderate, severe) (Fig 2). Severity of cGVHD was associated with the biomarker panel (p<0.0001 compared to control, and p=0.007 compared to each other [adjusted]). NRM was compared between groups with high vs. low biomarker levels, showing that the biomarker panel predicted NRM [Hazard Ratio=11.4, p=0.002 (adjusted)] (Fig 3). We conclude that ST2, CXCL9, MMP3, and OPN represent a biomarker panel for reliable, non-invasive diagnosis of cGVHD as well as for correlation with cGVHD severity, and prediction of NRM. Once further validated, these biomarkers could help identify patients with cGVHD at risk for poor outcomes with current treatment approaches.Table 1Area under ROCP-valueAdjusted P-valueCombinationST20.832<0.0001<0.0001YesMMP30.787<0.0001<0.0001YesTRAILR30.7160.00020.0002OPN0.708<0.0001<0.0001YesSELP0.6610.0080.005CKIT0.6540.0070.01COMP0.6430.0090.002CXCL90.6280.020.01YesCD1460.6160.030.04Combination0.885<0.0001<0.0001 Open table in a new tab Figure 2View Large Image Figure ViewerDownload Hi-res image Download (PPT)Figure 3View Large Image Figure ViewerDownload Hi-res image Download (PPT)
Abstract 12947: In Vivo Efficacy of a Novel, Inhaled Pdgfra/b Inhibitor, Gb002, in The Rat Monocrotaline and Pneumonectomy Model of Pulmonary Arterial Hypertension (2019)

Introduction: The PDGF pathway has been demonstrated to be involved in vascular remodeling in pulmonary arterial hypertension (PAH). GB002 is a novel, potent, clinical stage inhibitor of PDGFRα/β d...
73 GASTRIC ELECTRICAL STIMULATION AND SACRAL ELECTRICAL STIMULATION: ARE TWO DEVICES BETTER THAN ONE?: (2006)

<h3>Introduction</h3> Gastric electrical stimulation (GES) is available as a humanitarian use device for patients with the symptoms of gastroparesis and is effective in reducing gastrointestinal symptoms. We have previously shown that patients with gastric motor disorders often have coexisting abnormalities of the genitourinary system (Gastroenterology 1997;112:A737), which may now be treated with sacral electrical stimulation (SES), resulting in similar improvements in genitourinary symptoms. <h3>Patients</h3> We compared the results of therapy with GES and SES in 13 patients who were implanted with both devices. Patients were 11 F, 2 M, mean age of 41 years, who had documented gastroparesis as well as bladder or other pelvic floor dysfunction. All 13 patients had received their GES before the SES. <h3>Methods</h3> Patients were evaluated at baseline and latest follow-up (median 4 years for GES and 2 years for SES), according to previously standardized scores of GI (GI: 0-4, TSS max 20) and GU (GU: 0-3, UTSS, max 12) function. Results were compared by paired t-tests and reported as mean 6 SE. <h3>Results</h3> All 13 patients improved both GI and GU symptoms and the improvement in all parameters as nausea, vomiting, anorexia, bloating, abdominal pain and gastric total symptom score (TSS), leakage, urgency, voiding difficulty, number of pads used, and urinary total symptom score (UTSS) was statistically significant (see table below). <h3>Conclusions</h3> The combination of GES and SES appears to be both safe and effective for patients with concomitant gastroparesis and bladder dysfunction and the existence of a one stimulator does not preclude another.
Executable task models (2005)

Current task modeling techniques have a shortcoming in that they only use the model at design time. This means that the information contained in the model has to be embedded into the application and makes the task model static. In this paper we propose using the task model at runtime, in order to simplify producing applications which adapt to the actions of the user. In particular, we extend the ConcurTaskTree (CTT) notation to allow dynamic execution of a task model. A key feature of our extension is that it gives semantics for the use of information exchange operators. Our second contribution is an implementation of our dynamic task model. We present a prototype application which shows how the interactions with the task model at runtime allow us to produce a dynamic and context aware user interface.
Fast Repetition Rate (FRR) Fluorometer For Making In Situ Measurements Of Primary Productivity (2005)

Understanding the ocean carbon cycle and predicting how climate-induced changes in ocean circulation will affect ocean productivity requires that (a) primary productivity be measured with high spatial and temporal resolution, and (b) natural variability in primary productivity be parameterized with regardto environmental factors such as nutrient availabuity, irradiance, and temperature. Instrumentation to measure primary productivity from the stimulated in vivo fluoresence of phytoplankton chlorophyll is currendy being developed at Brookhaven National Laboratory. The instrumentation is based on fast repetition rate (FRR) fluorometry, and provides a robust technique for deriving the photosynthetic rates in situ. Moreover, the FRR methodology directly measures several photosynthetic parameters such as effective absorption cross- section, photo-conversion efficiency, and turnover time of photosynthesis, and relate them to primary productivity. Since photosynthetic parameters are affected by environmental factors such as fight and nutrient availability, the relationship between these parameters and primary productivity can be established. By understanding such relationships, prognostic models of primary productivity can be developed and parameterized.
A low-power reconfigurable analog-to-digital converter (2001)

A low-power CMOS reconfigurable analog-to-digital converter that can digitize signals over a wide range of bandwidth and resolution with adaptive power consumption is described. The converter achieves the wide operating range by (1) reconfiguring its architecture between pipeline and delta-sigma modes; (2) varying its circuit parameters, such as size of capacitors, length of pipeline, and oversampling ratio, among others; and (3) varying the bias currents of the opamps in proportion to the converter sampling frequency, accomplished through the use of a phase-locked loop (PLL). This converter also incorporates several power-reducing features such as thermal noise limited design, global converter chopping in the pipeline mode, opamp scaling, opamp sharing between consecutive stages in the pipeline mode, an opamp chopping technique in the delta-sigma mode, and other design techniques. The opamp chopping technique achieves faster closed-loop settling time and lower thermal noise than conventional design. At a converter power supply of 3.3 V, the converter achieves a bandwidth range of 0-10 MHz over a resolution range of 6-16 bits, and parameter reconfiguration time of twelve clock cycles. Its PLL lock range is measured at 20 kHz to 40 MHz. In the delta-sigma mode, it achieves a maximum signal-to-noise ratio of 94 dB and second and third harmonic distortions of 102 and 95 dB, respectively, at 10 MHz clock frequency, 9.4 kHz bandwidth, and 17.6 mW power. In the pipeline mode, it achieves a maximum DNL and INL of /spl plusmn/0.55 LSBs and /spl plusmn/0.82 LSBs, respectively, at 11 bits, at a clock frequency of 2.6 MHz and 1 MHz tone with 24.6 mW of power.
Elaboration of High-grade Chloramine from Ternary and Quaternary Ammoniacal Combinations and Hypochlorite at 100 Chlorometric Degrees (1999)

High-grade chloramine is prepared in batch and in continuous mode starting from mixed ammoniacal solutions and hypochlorite at hundred chlorometric degrees.
Two-mode fibre spatial-mode converter using periodiccore deformation (1994)

Efficient conversion between the LP01 and LP11 modes in a two-mode fibre is achieved by periodically ablating the fibre surface with a CO2 laser and then annealing the fibre with an electric arc. The resulting periodic core deformation produces 99% mode conversion over a 37 nm bandwidth around 1540 nm and 0.38 dB insertion loss.
Priority-based receiver-side relay election in wireless ad hoc sensor networks (2006)

Receiver-side relay election has been recently proposed as an alternative to transmitter-side relay selection in wireless ad hoc networks. In this paper we study different prioritization schemes among potential relay nodes to achieve a better delay and contention resolution performance. We consider a priority criteria based on least remaining distance to the destination and propose a generalized mapping function to introduce relative priority among the eligible relay nodes. We show that, a suitable mapping can be found to achieve an optimum relay election performance, which also outperforms the random forwarding approach. Our intuition is guided by an analytic framework and verified by network simulation.
Near-Infrared-Induced Heating of Confined Water in Polymeric Particles for Efficient Payload Release (2014)

Near-infrared (NIR) light-triggered release from polymeric capsules could make a major impact on biological research by enabling remote and spatiotemporal control over the release of encapsulated cargo. The few existing mechanisms for NIR-triggered release have not been widely applied because they require custom synthesis of designer polymers, high-powered lasers to drive inefficient two-photon processes, and/or coencapsulation of bulky inorganic particles. In search of a simpler mechanism, we found that exposure to laser light resonant with the vibrational absorption of water (980 nm) in the NIR region can induce release of payloads encapsulated in particles made from inherently non-photo-responsive polymers. We hypothesize that confined water pockets present in hydrated polymer particles absorb electromagnetic energy and transfer it to the polymer matrix, inducing a thermal phase change. In this study, we show that this simple and highly universal strategy enables instantaneous and controlled release of payloads in aqueous environments as well as in living cells using both pulsed and continuous wavelength lasers without significant heating of the surrounding aqueous solution.
Human erythropoietin-specific sites of monoclonal antibody-mediated neutralization (1993)

Recombinant human erythropoietin (rhuEpo)-specific mouse monoclonal antibodies (MoAbs) have been produced and characterized. All antibodies were specifically reactive with rhuEpo in enzyme-linked immunosorbent assay (ELISA). Epitope exclusion studies showed three distinct epitope regions, A, B, and C, recognized by neutralizing MoAbs. An additional epitope region D was recognized by non-neutralizing MoAbs. Antibodies defining an epitope region competed with each other for binding sites, but did not compete with antibodies defining a different epitope region. Group B antibodies were able to compete for the receptor binding site on rhuEpo with a soluble human Epo-receptor-lg fusion protein. No single peptide sequences were found to specifically interact either with group B MoAbs or with the rhuEpo-receptor. Therefore, it is suggested that epitope region B and the receptor binding site share binding determinants that are primarily composed of conformational epitopes. Because group A and group C antibodies did not compete with the receptor for binding to the receptor binding site of the rhuEpo molecule, it is suggested that neutralization via epitope regions A and C is mediated through binding inhibition caused by conformational changes, transmuting the binding site(s) for the receptor. Conversely, binding to the receptor seems to induce conformational changes in the hormone molecule, eliminating epitopes for group A and C antibodies.
Capacitor-couple ESD protection circuit for deep-submicron low-voltage CMOS ASIC (1996)

Capacitor-couple technique used to lower snapback-trigger voltage and to ensure uniform ESD current distribution in deep-submicron CMOS on-chip ESD protection circuit is proposed. The coupling capacitor is realized by a poly layer right under the wire-bonding metal pad without increasing extra layout area to the pad. A timing-original design model has been derived to calculate the capacitor-couple efficiency of this proposed ESD protection circuit. Using this capacitor-couple ESD protection circuit, the thinner gate oxide of CMOS devices in deep-submicron low-voltage CMOS ASIC can be effectively protected.
Ligands to the melanocortin receptors (2001)

This review will give a brief overview of the pharmacology of the melanocortin receptors (MCRs) as a background. The review will not handle the patents or patent applications dealing with cloning of the different subtypes of the receptor, since this has been recently reviewed [1]. This review will focus on different ligands acting either as agonists or antagonists to the different subtypes of the receptor, i.e., MC1R, MC3R, MC4R and MC5R. Just recently a number of patent applications have reached the public domain, which describe small peptides or low molecular weight organic compounds binding and acting on the MCRs.
Entropy rate superpixel segmentation (2011)

We propose a new objective function for superpixel segmentation. This objective function consists of two components: entropy rate of a random walk on a graph and a balancing term. The entropy rate favors formation of compact and homogeneous clusters, while the balancing function encourages clusters with similar sizes. We present a novel graph construction for images and show that this construction induces a matroid - a combinatorial structure that generalizes the concept of linear independence in vector spaces. The segmentation is then given by the graph topology that maximizes the objective function under the matroid constraint. By exploiting submodular and mono-tonic properties of the objective function, we develop an efficient greedy algorithm. Furthermore, we prove an approximation bound of ½ for the optimality of the solution. Extensive experiments on the Berkeley segmentation benchmark show that the proposed algorithm outperforms the state of the art in all the standard evaluation metrics.
Tomographic inversion by matrix transformation (2006)

We have developed a new method to build seismic velocity models for complex structures. In our approach, we use a spatially non‐uniform parameterization of the velocity model in tomography and use a uniform grid representation of the same velocity model in ray tracing to generate the linear system of tomographic equations. Subsequently, a matrix transformation is applied to the system of equations to produce a new linear system of tomographic equations using the non‐uniform parameterization. In this way, we improve the stability of tomographic inversion without adding computational cost. We demonstrate the effectiveness of our process with a 3D synthetic data example.
Tendon healing induced by chemically modified mRNAs (2017)

Tendon disorders are frequent both in human and veterinary medicine with high re-injury rates and unsatisfactory therapeutic treatments. Application of naked, chemically-modified mRNA (cmRNA), encoding for therapeutic proteins, is an innovative approach to address tendon healing. In the current study, we demonstrated that injection of naked cmRNA, diluted in a glucose-containing solution, into tendons resulted in high protein expression in healthy and experimentally-injured tendons. Injection of bone morphogenetic protein 7 (BMP-7)-encoding cmRNA resulted in a significantly higher expression of BMP-7 protein and reduced formation of collagen type III, compared to vehicle control. Moreover, in a large animal model, reporter protein expression was detectable not only in healthy, but also in experimentally-injured, severely inflamed tendons. Summarising, these results demonstrated the potential of cmRNAs encoding for therapeutic proteins as a new class of drugs for the treatment of tendon disorders.
Electron Temperature Derived from Measurements of Complex Plasma Impedance (2008)

Abstract : In earlier work, using a network analyzer, we have shown the existence of collisionless resistance (CR) in the sheath of spherical probe when driven by a small RF signal. For any position in the sheath, the CR was shown to be inversely proportional to the plasma density gradient there; but to exist only when the applied frequency corresponds to the plasma frequency (omega sub pe), or density, at that position. We have recently begun a study of the low-to-intermediate frequency response of the probe to the RF signal. At sufficiently low frequencies, the CR is beyond cutoff, i.e., since the earlier work shows that the existence of CR depends on the plasma density gradient, there is a cutoff which is proportional to the applied bias level and which will occur at the plasma frequency at the surface of the probe. Since electron density at the probe surface decreases as a function of applied (negative) bias, the CR will extend to lower frequencies as the magnitude of negative bias increases. Therefore, to eliminate both CR and ion current contributions, the frequencies we consider are much greater than the ion plasma frequency (omega sub pi), but less than the plasma frequency at the probe surface (omega sub pe (r sub 0)), where r sub 0 is the probe radius. We show that, in this frequency regime, the complex impedance measurements made with a network analyzer can be used to determine electron temperature. We present an overview of the theory used along with comparisons to data sets made using three stainless steel spherical probes of different sizes in different experimental environments and different plasma parameter regimes. We compare the results of the temperature measurements to those made by conventional Langmuir probe sweeps; the method shown here requires not curve fitting as is the usual procedure with Langmuir probes when a Maxwell Boltzmann electron distribution function is assumed.
A Process Integration Approach to the Assessment of CO<sub>2</sub> Fixation through Dry Reforming (2015)

Recently, significant research has been dedicated to the field of mitigating CO2 emissions. Chemical sequestration (fixation) of CO2 into value-added products (e.g., methanol, Fischer–Tropsch liquids, propylene) is an emerging option. The fixation of CO2 via the dry reforming (DR) of natural gas involves the conversion of two greenhouse gases (carbon dioxide and methane) into a useful intermediate (synthesis gas). Synthesis gas can be subsequently converted into various chemicals and fuels. Nevertheless, syngas produced from DR is typically characterized by a H2:CO ratio lower than that typically required for conversion into high-value hydrocarbons. In addition, DR catalysts continuously deactivate as a result of extensive coke formation. This paper focuses on quantifying the potential for CO2 fixation using dry reforming and the integration of different reforming technologies. The results highlight the strong inverse relationship between CO2 chemical fixation and the required syngas H2:CO ratio. Combined reforming involving DR and steam reforming greatly benefits from the presence of waste heat sources because heat generation is the major source of CO2 generation. A process case study is presented to illustrate the importance of a process viewpoint with respect to DR.
Cloning and Functional Characterization of a Novel ATP-sensitive Potassium Channel Ubiquitously Expressed in Rat Tissues, including Pancreatic Islets, Pituitary, Skeletal Muscle, and Heart (1995)

ATP-sensitive K+ (KATP) channels play a crucial role in coupling metabolic energy to the membrane potential of cells. We have isolated a cDNA encoding a novel member (uKATP-1) of the inward rectifier K+ channel family from a rat pancreatic islet cDNA library. Rat uKATP-1 is a 424-amino acid residue protein (M(r) = 47,960). Electrophysiological studies of uKATP-1 expressed in Xenopus laevis oocytes show that uKATP-1 is a weak rectifier and is blocked with Ba2+ ions. Single-channel patch clamp study of clonal human kidney epithelial cells (HEK293) transfected with uKATP-1 cDNA reveals that uKATP-1 closes in response to 1 mM ATP and has a single channel conductance of 70 +/- 2 picosiemens (n = 6), indicating that uKATP-1 is an ATP-sensitive inward rectifier K+ channel. In addition, uKATP-1 is activated by the KATP channel opener, diazoxide. RNA blot analysis shows that uKATP-1 mRNA is expressed ubiquitously in rat tissues, including pancreatic islets, pituitary, skeletal muscle, and heart, suggesting that uKATP-1 may play a physiological role as a link between the metabolic state and membrane K+ permeability of cells in almost every normal tissue. Since uKATP-1 shares only 43-46% amino acid identity with members of previously reported inward rectifier K+ channel subfamilies, including ROMK1, IRK1, GIRK1, and cKATP-1, uKATP-1 is not an isoform of these subfamilies and, therefore, represents a new subfamily of the inward rectifier K+ channel family having two transmembrane segments.
Analysis of the Impact of CT Based Attenuation Correction, Scatter Compensation and 3D- Beam Modeling on SPECT Image Quality (2005)

Non uniform photon attenuation and Compton scatter degrade nuclear medicine SPECT images by removing true counts or adding unwanted counts, respectively. For quantitative SPECT, iterative reconstruction algorithms, such as OSEM, allow 3D collimator modeling and compensation of the effects of scatter and attenuation. In this work, we investigate, through ROI and SPM analysis of phantom and computer simulation studies, how a combination of compensation strategies affects image quality and quantitative accuracy. Phantoms were imaged with a SPECT and a CT scanner. With these acquisitions, semi-quantitative analysis was performed for the following reconstruction strategies: OSEM-3D without attenuation and scatter compensation; OSEM-3D CTAC (with attenuation correction); and OSEM-3D with attenuation and scatter compensation (CTACSC). For the simulated dataset, the SNR was 50.5 with CTACSC compared to 27.5 without any compensation and OSEM-3D CTACSC produced reconstructed images with contrast within 0.23% of the true image with a standard error of 21 counts. Without compensation, the error increases to 2382 counts. The implementation and design of the OSEM-3D CTACSC approach proved effective, with improved visual quality and quantitative accuracy of the SPECT images.