gebhart/patrepeval huggingface dataset:
Authors' Reply: AMP-Activated Protein Kinase as a Target for Preconditioning in Transplantation Medicine (2010)

In their response, Roselló-Catafau et al. underscore the potential of adenosine monophosphate-activated protein kinase (AMPK) to limit cellular injury during hypothermia or ischemia/reperfusion in the context of transplantation, as reviewed recently by us (1). The authors underline the importance of nitric oxide, whose production can be stimulated not only by activation of AMPK but also by insulin-like growth factor (IGF)-1 and the use of Institute Georges Lopez preservation solution (IGL-1) when compared with University of Wisconsin solution (2, 3). This might be due to the substitution of polyethylene glycol (a lipid antioxidant) for hydroxylethyl starch in IGL-1. Specifically, Roselló-Catafau et al. propose to optimize static cold preservation by the addition of both AMPK activators and IGF-1 to the IGL-1 preservation solution (4, 5). Although this indeed seems a logical strategy, some points need consideration. First, it is unclear at which time point during the transplantation procedure, activation of AMPK should occur to benefit optimally from its anticipated protective effects. So far, protective effects of AMPK activators have been shown from administration to the donor before harvesting the organ (6, 7) or by addition to the preservation solution at the time of cold preservation (5). Although the most convenient way to use pharmacologic agents that activate AMPK might be to add these compounds to the preservation solution, pretreatment of the donor may represent the optimal strategy because of inhibition of cellular metabolism in the donor organ before cooling. However, we are not aware of a study that compared both conditions, and thus, it is unclear whether activation of AMPK during preservation represents the optimal treatment strategy. Second, combining AMPK activators and IGF-1 in the preservation solution needs explicit investigation. Although some studies report a synergistic action of AMPK activators and IGF-1 (8), a large number of studies describe antagonistic actions of both compounds (9–12). Taken together, it is clear that AMPK- and IGF-1-mediated signal transduction pathways interact with each other. Clarification of cross-talk between AMPK- and IGF-1-mediated signal transduction pathways in different organs might be of major relevance for transplantation medicine. Because this interaction may vary between cell types, identification of the optimal application of AMPK activators in (clinical) transplantation remains a challenging task ahead. Hjalmar R. Bouma Marlies E. Ketelaar Benito A. Yard Rutger J. Ploeg Robert H. Henning 1Department of Clinical Pharmacology Graduate School of Medicine University Medical Center Groningen University of Groningen Groningen, The Netherlands 2Vth Medical Department University Hospital Mannheim Mannheim, Germany 3Department of Surgery/Division of Abdominal and Transplant Surgery University Medical Center Groningen Groningen, The Netherlands.
A Bottom‐Up Proteomic Approach to Identify Substrate Specificity of Outer‐Membrane Protease OmpT (2017)

Identifying peptide substrates that are efficiently cleaved by proteases gives insights into substrate recognition and specificity, guides development of inhibitors, and improves assay sensitivity. Peptide arrays and SAMDI mass spectrometry were used to identify a tetrapeptide substrate exhibiting high activity for the bacterial outer-membrane protease (OmpT). Analysis of protease activity for the preferred residues at the cleavage site (P1, P1') and nearest-neighbor positions (P2, P2') and their positional interdependence revealed FRRV as the optimal peptide with the highest OmpT activity. Substituting FRRV into a fragment of LL37, a natural substrate of OmpT, led to a greater than 400-fold improvement in OmpT catalytic efficiency, with a k<sub>cat</sub> /K<sub>m</sub> value of 6.1×10<sup>6</sup> L mol<sup>-1</sup> s<sup>-1</sup> . Wild-type and mutant OmpT displayed significant differences in their substrate specificities, demonstrating that even modest mutants may not be suitable substitutes for the native enzyme.
A Clinician's Tool for Analyzing Non-compliance (2011)

We describe a computer program to assist a clinician with assessing the e cacy of treatments in experimental studies for which treatment assignment is random but subject compliance is imperfect.The major diculty i n s u c h studies is that treatment e cacy is not identi able", that is, it cannot be estimated from the data, even when the number of subjects is in nite, unless additional knowledge is provided.Our system combines Bayesian learning with Gibbs sampling using two inputs: 1 the investigator's prior probabilities of the relative sizes of subpopulations and 2 the observed data from the experiment.The system outputs a histogram depicting the posterior distribution of the average treatment e ect, that is, the probability that the average outcome e.g., survival would attain a given level, had the treatment been taken uniformly by the entire population.This paper describes the theoretical basis for the proposed approach and presents experimental results on both simulated and real data, showing agreement with the theoretical asymptotic bounds.
Size‐, Water‐, and Defect‐Regulated Potassium Manganese Hexacyanoferrate with Superior Cycling Stability and Rate Capability for Low‐Cost Sodium‐Ion Batteries (2019)

Potassium manganese hexacyanoferrate (KMHCF) is a low-cost Prussian blue analogue (PBA) having a rigid and open framework that can accommodate large alkali ions. Herein, the synthesis of KMHCF and its application as a high-performance cathode in sodium-ion batteries (NIBs) is reported. High-quality KMHCF with low amounts of crystal water and defects and with homogeneous microstructure is obtained by controlling the nucleation and grain growth by using a high-concentration citrate solution as a precipitation medium. The obtained KMHCF exhibits superior cycling and rate performance as a NIB cathode, showing 80% capacity retention after 1000 cycles at 1 C and a high capacity of 95 mA h g<sup>-1</sup> at 20 C. Unlike conventional single-cation batteries, the hybrid NIB with KMHCF as cathode and Na as anode in Na-ion electrolyte displays three reversible plateaus that involve stepwise insertion/extraction of both K<sup>+</sup> and Na<sup>+</sup> in the PBA framework. In later cycling, the K<sup>+</sup> -Na<sup>+</sup> cointercalated phase is partially converted into a cubic sodium manganese hexacyanoferrate (NaMHCF) phase due to the increasing replacement of Na<sup>+</sup> for K<sup>+</sup> .
Thermal Stabilisation of Polymer–Fullerene Bulk Heterojunction Morphology for Efficient Photovoltaic Solar Cells (2014)

A novel stable bisazide molecule that can freeze the bulk heterojunction morphology at its optimized layout by specifically bonding to fullerenes is reported. The concept is demonstrated with various polymers: fullerene derivatives systems enable highly thermally stable polymer solar cells.
Supplementary Figure 6A-B from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 6A-B from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
Combustion Characteristics of High-Energy/High-Density Hydrocarbon Compounds (1996)

Abstract The combustion characteristics of PCU Alkene Dimers (C22H24) are evaluated as solid fuels in high speed flows, at conditions typical for ramjet operation (i.e., Mach 0.25, stagnation temperature and pressure of 300 K and 150 kPa, respectively). Samples of the dimer are binded into a solid layer with a styrene-polybutadiene copolymer (8% w/w) on the test chamber wall and convectively ignited by a gaseous flame in air. The goals of this research are of both practical and fundamental relevance: (i) determine the ability of the high energy fuel to increase practical devices’ performance, (ii) quantify and improve the combustion characteristics of the alkene dimers (i.e., ignition, flame stability, particulate formation), (iii) investigate the dynamics of the solid-gas interface combustion. To date, ignition times and rates of heat release were measured and the theoretical modelling was initiated. Preliminary results indicate that, in the present configuration, the dimer ignition times fall within the range reported in literature for other solid fuels. Large differences exist among different sets of data due primarily to nonsimilar geometrical configuration of the test. The dimer exhibits substantial rates of heat release in comparison with other solid fuels.
A Robotic Ultrasound Scanner for Automatic Vessel Tracking and Three-Dimensional Reconstruction of B-Mode Images (2015)

Locating and evaluating the length and severity of a stenosis is very important for planning adequate treatment of peripheral arterial disease (PAD). Conventional ultrasound (US) examination cannot provide maps of entire lower limb arteries in 3-D. We propose a prototype 3D-US robotic system with B-mode images, which is nonionizing, noninvasive, and is able to track and reconstruct a continuous segment of the lower limb arterial tree between the groin and the knee. From an initialized cross-sectional view of the vessel, automatic tracking was conducted followed by 3D-US reconstructions evaluated using Hausdorff distance, cross-sectional area, and stenosis severity in comparison with 3-D reconstructions with computed tomography angiography (CTA). A mean Hausdorff distance of 0.97 ± 0.46 mm was found in vitro for 3D-US compared with 3D-CTA vessel representations. To evaluate the stenosis severity in vitro, 3D-US reconstructions gave errors of 3%-6% when compared with designed dimensions of the phantom, which are comparable to 3D-CTA reconstructions, with 4%-13% errors. The in vivo system's feasibility to reconstruct a normal femoral artery segment of a volunteer was also investigated. These results encourage further ergonomic developments to increase the robot's capacity to represent lower limb vessels in the clinical context.
Propionibacterium acnes biofilm is present in intervertebral discs of patients undergoing microdiscectomy (2017)

This study confirms that P. acnes is prevalent in herniated disc tissue. Moreover, it provides the first visual evidence of P. acnes biofilms within such specimens, consistent with infection rather than microbiologic contamination.
Diffusion-Weighted Magnetic Resonance Imaging in Distinguishing Between Mucin-Producing and Serous Pancreatic Cysts (2016)

Diffusion-weighted imaging may be a helpful tool in distinguishing between mucin-producing and serous pancreatic cysts.
Expedient Synthesis of Triazole‐Linked Glycosyl Amino Acids and Peptides. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Tunable Water‐Based Meta‐Lens (2023)

Abstract Water, the source of life, is a more abundant, low‐cost, and environment‐friendly candidate material for tunable meta‐devices compared to conventional approaches in the microwave region. Wavefront shaping can be flexibly manipulated by adjusting the shapes and temperature of water‐based meta‐atoms, but individual control of each meta‐atom is complicated and inconvenient, especially for continuous tunability. Here, we propose a design strategy based on the phase compensation mechanism to continuously tune the properties of water‐based meta‐lenses at 5 GHz. Integrated‐resonant units (IRUs) with coupled water pillars are carefully designed to effectively tailor the balance between polarization conversion efficiency and phase compensation. By changing the filling height of water in the designed meta‐lens from 10 to 60 mm, the focal length can be tuned from 228 to 424 mm. The off‐axis focusing of the meta‐lens is also demonstrated in which the deflection angle is adjustable from around 0° to 5°. This work will pave the way for designing tunable water‐based meta‐devices and facilitating their applications in microwave imaging systems.
Novel serial code concatenation strategies for error floor mitigation of low-density parity-check and turbo product codes (2013)

This paper presents a novel multiple serial code concatenation (SCC) strategy to combat the error-floor problem in iterated sparse graph-based error correcting codes such as turbo product-codes (TPC) and low-density parity-check (LDPC) codes. Although SCC has been widely used in the past to reduce the error-floor in iterative decoders, the main stumbling block for its practical application in high-speed communication systems has been the need for long and complex outer codes. Alternative, short outer block codes with interleaving have been shown to provide a good tradeoff between complexity and performance. Nevertheless, their application to next-generation high-speed communication systems is still a major challenge as a result of the careful design of long complex interleavers needed to meet the requirements of these applications. The SCC scheme proposed in this work is based on the use of short outer block codes. Departing from techniques used in previous proposals, the long outer code and interleaver are replaced by a simple block code combined with a novel encoding/decoding strategy. This allows the proposed SCC to provide a better tradeoff between performance and complexity than previous techniques. Several application examples showing the benefits of the proposed SCC are described. Particularly, a new coding scheme suitable for high-speed optical communication is introduced.
NeuroBFD: Size-independent automated classification of neurons using conditional distributions of morphological features (2018)

Automated classification and characterization of digitally-traced neurons poses a challenge in constructing the neurome of human brain. The complex anatomical structure of each neuron causes observable morphological and geometrical variations between different cell types and within cell types. Given a graph model of a neuron, one of the major bottlenecks in encoding such variation followed by the within-cell and between-cell comparisons is the size of the neuron. In this work, we define size-independent statistical morphometrics as feature descriptors for each neuron. The customized morphometrics are built by extracting three raw features, which are bifurcation angle, branch fragmentation, and spatial arborization density of a neuron. Next, the local variation in each of the raw features is encoded by constructing a conditional distribution for that feature, which provides an effective and discriminatory feature assembly. In addition, the algorithm is automatic, scalable, and coordinate-independent. The comparative approach is shown to outperform the existing state-of-the-art methods.
Cascading Boost Effect on the Capacity of Nitrogen-Doped Graphene Sheets for Li- and Na-Ion Batteries (2016)

Specific capacity and cyclic performance are critically important for the electrode materials of rechargeable batteries. Herein, a capacity boost effect of Li- and Na-ion batteries was presented and clarified by nitrogen-doped graphene sheets. The reversible capacities progressively increased from 637.4 to 1050.4 mAh g<sup>-1</sup> (164.8% increase) in Li-ion cell tests from 20 to 185 cycles, and from 187.3 to 247.5 mAh g<sup>-1</sup> (132.1% increase) in Na-ion cell tests from 50 to 500 cycles. The mechanism of the capacity boost is proposed as an electrochemical induced cascading evolution of graphitic N to pyridinic and/or pyrrolic N, during which only these graphitic N adjacent pyridinic or pyrrolic structures can be taken precedence. The original and new generated pyridinic and pyrrolic N have strengthened binding energies to Li/Na atoms, thus increased the Li/Na coverage and delivered a progressive capacity boost with cycles until the entire favorable graphitic N transform into pyridinic and pyrrolic N.
Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans (2018)

Viral strain characteristics likely contribute to oral HSV-1 shedding rates.
A symptotic analysis of large heterogeneous queueing systems (1988)

As a simple example of a large heterogeneous queueing system, we consider a single queue with many servers with differing service rates. In the limit of infinitely many servers, we identify a queue control policy that minimizes the average system delay. When there are only two possible server speeds, we can analyze the convergence of this policy to optimality. Based on this result, we propose policies for large but finite systems with a general distribution of server speeds.
CCN1 secretion and cleavage regulate the lung epithelial cell functions after cigarette smoke (2014)

Despite extensive research, the pathogenesis of cigarette smoking (CS)-associated emphysema remains incompletely understood, thereby impeding development of novel therapeutics, diagnostics, and biomarkers. Here, we report a novel paradigm potentially involved in the development of epithelial death and tissue loss in CS-associated emphysema. After prolonged exposure of CS, CCN1 cleavage was detected both in vitro and in vivo. Full-length CCN1 (flCCN1) was secreted in an exosome-shuttled manner, and secreted plasmin converted flCCN1 to cleaved CCN1 (cCCN1) in extracellular matrix. Interestingly, exosome-shuttled flCCN1 facilitated the interleukin (IL)-8 and vascular endothelial growth factor (VEGF) release in response to cigarette smoke extract (CSE). Therefore, flCCN1 potentially promoted CS-induced inflammation via IL-8-mediated neutrophil recruitment and also maintained the lung homeostasis via VEGF secretion. Interestingly, cCCN1 abolished these functions. Furthermore, cCCN1 promoted protease and matrix metalloproteinase (MMP)-1 production after CSE. These effects were mainly mediated by the COOH-terminal fragments of CCN1 after cleavage. Both the decrease of VEGF and the elevation of MMPs favor the development of emphysema. cCCN1, therefore, likely contributes to the epithelial cell damage after CS. Additionally, CSE and cCCN1 both stimulated integrin-α7 expressions in lung epithelial cells. The integrin-α7 appeared to be the binding receptors of cCCN1 and, subsequently, mediated its cellular function by promoting MMP1. Consistent with our observation on the functional roles of cCCN1 in vitro, elevated cCCN1 level was found in the bronchoalveolar lavage fluid from mice with emphysematous changes after 6 mo CS exposure. Taken together, we hypothesize that cCCN1 promoted the epithelial cell death and tissue loss after prolonged CS exposure.
GelMA/bioactive silica nanocomposite bioinks for stem cell osteogenic differentiation (2021)

Leveraging 3D bioprinting for processing stem cell-laden biomaterials has unlocked a tremendous potential for fabricating living 3D constructs for bone tissue engineering. Even though several bioinks developed to date display suitable physicochemical properties for stem cell seeding and proliferation, they generally lack the nanosized minerals present in native bone bioarchitecture. To enable the bottom-up fabrication of biomimetic 3D constructs for bioinstructing stem cells pro-osteogenic differentiation, herein we developed multi-bioactive nanocomposite bioinks that combine the organic and inorganic building blocks of bone. For the organic component gelatin methacrylate (GelMA), a photocrosslinkable denaturated collagen derivative used for 3D bioprinting was selected due to its rheological properties display of cell adhesion moieties to which bone tissue precursors such as human bone marrow derived mesenchymal stem cells (hBM-MSCs) can attach to. The inorganic building block was formulated by incorporating mesoporous silica nanoparticles functionalized with calcium, phosphate and dexamethasone (MSNCaPDex), which previously proven to induce osteogenic differentiation. The newly formulated photocrosslinkable nanocomposite GelMA bioink incorporating MSNCaPDex nanoparticles and laden with hBM-MSCs was successfully processed into a 3D bioprintable construct with structural fidelity, and well dispersed nanoparticles throughout the hydrogel matrix. These nanocomposite constructs could induce the deposition of apatite<em>in vitro</em>, thus showing attractive bioactivity properties. Viability and differentiation studies showed that hBM-MSCs remained viable and exhibited osteogenic differentiation biomarkers when incorporated in GelMA/MSNCaPDex constructs and without requiring further biochemical, nor mechanical stimuli. Overall, our nanocomposite bioink has demonstrated excellent processability via extrusion bioprinting into osteogenic constructs with potential application in bone tissue repair and regeneration.
Spatial and temporal regulation of a soybean ( Glycine max ) lectin promoter in transgenic cotton ( Gossypium hirsutum ) (2002)

The activity of a soybean (Glycine max L. Merrill) lectin gene promoter was investigated in transgenic cotton plants (Gossypium hirsutum L.) with the view to using this promoter for the seed-specific alteration of gossypol, a secondary metabolite in cotton that has adverse effects on the nutritional value of cottonseed products like oil and protein-rich meal. Agrobacterium-mediated transformation generated stable transformants containing a construct with the lectin promoter fused to the β-glucuronidase reporter gene (pLeGUS). Fluorometric GUS assays and northern hybridization detected strong promoter activity during embryo development. GUS activity in developing embryos was detected as early as 10 d post-anthesis (dpa), peaking late in embryo maturation. Enzyme activity persisted in imbibed mature seed, and negligible activity remained detectable in the roots and cotyledons of 7-d-old seedlings. No GUS activity was detected in leaves and squares of mature plants. GUS transcripts increased during embryo development to peak about 35 dpa, declining to a low level in imbibed mature seed. No transcripts were detected in roots, cotyledons, leaves or squares. Histochemical GUS activity staining indicated promoter activity in all cells of the cotyledons, including the flattened cells of the gossypol glands, the presumed site of synthesis of gossypol. This study concluded that the soybean lectin gene promoter is a useful tool for the seed-specific expression of transgenes in cotton.
Performance of a Handheld PCR Instrument in the Detection of Bacillus anthracis, Francisella tularensis, and Yersinia pestis: Sensitivity, Specificity, and Effect of Interferents on Assay Results (2004)

Smiths Detection-Edgewood, Inc. (SDE) developed the Bio-Seeq to provide a portable platform for use by first responders to detect biological threats in civilian areas. The Bio-Seeq is an updated, redesigned version of a small, portable PCR instrument previously known as the HANAA, Handheld Advanced Nucleic Acid Analyzer. We have tested the performance of real-time fluorogenic PCR assay reagents for the detection of three biological threat agents, Bacillus anthracis (BA), Francisella tularensis (FT), and Yersinia pestis (YP). All three assays are sensitive, and specific for the agents they detect. Common household substances (cornstarch, coffee creamer, baking powder, and wheat flour) interfered with the sensitivity of the assay to varying degrees that were consistent across the three assays.