gebhart/patrepeval huggingface dataset:
Coordinated adaptations define the ontogenetic shift from worm- to fish-hunting in a venomous cone snail (2023)

Marine cone snails have attracted researchers from all disciplines but early life stages have received limited attention due to difficulties accessing or rearing juvenile specimens. Here, we document the culture of Conus magus from eggs through metamorphosis to reveal dramatic shifts in predatory feeding behaviour between post-metamorphic juveniles and adult specimens. Adult C. magus capture fish using a set of paralytic venom peptides combined with a hooked radular tooth used to tether envenomed fish. In contrast, early juveniles feed exclusively on polychaete worms using a unique "sting-and-stalk" foraging behaviour facilitated by short, unbarbed radular teeth and a distinct venom repertoire that induces hypoactivity in prey. Our results demonstrate how coordinated morphological, behavioural and molecular changes facilitate the shift from worm- to fish-hunting in C. magus, and showcase juvenile cone snails as a rich and unexplored source of novel venom peptides for ecological, evolutionary and biodiscovery studies.
Free fatty acids are produced in and secreted from target cells very early in cytotoxic T lymphocyte-mediated killing (1991)

Conjugation of CTL with their cognate targets elicits a number of early changes within the target cell that are thought to play an important role in the lytic mechanism. We now report that at times earlier than 5 min after conjugation with allospecific CTL, free fatty acids (FFA) are produced in and then secreted from alloantigen-bearing target cells. Using murine CTL clones with different alloantigen specificities, stimulation of FFA production from target cells was found to be Ag specific. FFA production does not appear to be specific for any particular FFA species. Indeed, a wide spectrum of cis unsaturated as well as saturated FFA are produced. FFA production is well correlated with, and specific for, CTL-mediated target cell lysis. Other means of perturbing or lysing target cells, including freeze/thaw disruption, detergent solubilization, or increasing membrane permeabilization with ionomycin, do not stimulate FFA production. In particular, FFA production is not stimulated by treatment with pore-forming granules under conditions that cause more than 90% target cell lysis. These results suggest that FFA production plays an important role in CTL-mediated lysis because stimulation of FFA release specifically requires an event that is CTL induced, occurs very early after conjugation, and is strongly correlated with CTL-mediated lysis.
Comparison of OP-1 Putty (rhBMP-7) to Iliac Crest Autograft for Posterolateral Lumbar Arthrodesis (2005)

This study represents the first clinical trial to demonstrate the safety and similarity of OP-1 Putty as a replacement for autogenous bone graft in the posterolateral fusion environment with a minimum of 2-year follow-up. OP-1 Putty was able to achieve osteoinduction leading to a radiographically solid fusion in the absence of autogenous iliac crest bone graft in 55% of the patients at 24 and 36 months. These results compare favorably to the historical fusion rates reported for uninstrumented arthrodesis in this challenging clinical scenario.
Dynamic Time Warping For Acoustic Response Interpolation: Possibilities And Limitations (2009)

Publication in the conference proceedings of EUSIPCO, Glasgow, Scotland, 2009
Electrocorticography and stereo EEG provide distinct measures of brain connectivity: Implications for network models (2020)

Abstract Brain network models derived from graph theory have the potential to guide functional neurosurgery, and to improve rates of post-operative seizure freedom for patients with epilepsy. A barrier to applying these models clinically is that intracranial EEG electrode implantation strategies vary by center, region and country, from cortical grid &amp; strip electrodes (ECoG), to purely stereotactic depth electrodes (SEEG), to a mixture of both. To determine whether models derived from one type of study are broadly applicable to others, we investigate the differences in brain networks mapped by ECoG and SEEG in a cohort of patients who underwent surgery for temporal lobe epilepsy and achieved a favorable outcome. We show that networks derived from ECoG and SEEG define distinct relationships between resected and spared tissue, which may be driven by sampling bias of temporal depth electrodes in patients with predominantly cortical grids. We propose a method of correcting for the effect of internodal distance that is specific to electrode type and explore how additional methods for spatially correcting for sampling bias affect network models. Ultimately, we find that smaller surgical targets tend to have lower connectivity with respect to the surrounding network, challenging notions that abnormal connectivity in the epileptogenic zone is typically high. Our findings suggest that effectively applying computational models to localize epileptic networks requires accounting for the effects of spatial sampling, particularly when analyzing both ECoG and SEEG recordings in the same cohort, and that future network studies of epilepsy surgery should also account for differences in focality between resection and ablation. We propose that these findings are broadly relevant to intracranial EEG network modeling in epilepsy and an important step in translating them clinically into patient care. Author summary Bernabei et al. report that electrocorticography and stereo EEG provide different quantifications of epileptogenic zone connectivity due to differences in electrode type and implant patterns. After correcting for sampling differences between modalities, they find that more focal forms of epilepsy surgery target regions of weaker connectivity compared to the remaining epileptic network.
Steady-state analysis of the parallel resonant converter with LLCC-type commutation network (1991)

A novel converter topology known as LLCC-type parallel resonant converter (PRC-LLCC), in which the tank circuit consists of two inductors and two capacitors, is introduced. Using the state-plane approach, the steady-state analysis of the PRC-LLCC operating in the continuous conduction model is carried out. It is shown that by using the state variable transformation technique the steady-state response of the converter can be represented by two state-plane diagrams. Using these diagrams and the circuit equations, a set of control characteristic curves which are useful for converter design is derived. Based on these curves, a design procedure along with a specific design example is given. The correctness of the analysis results is verified via computer simulations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Differential Pacing for Distinguishing Block From Persistent Conduction Through an Ablation Line (2000)

An accurate assessment of isthmus block or persistent isthmus conduction is possible with this technique of differential pacing.
Cycling Behavior in Near-Identical Cell Systems (2003)

A generic pattern of collective behavior of symmetric networks of coupled identical cells is cycling behavior. In networks modeled by symmetric systems of differential (difference) equations, cycling behavior appears in the form of solution trajectories (orbits) that linger around symmetrically related steady-states (fixed points) or periodic solutions (orbits) or even chaotic attractors. In this last case, it leads to what is called "cycling chaos". In particular, Dellnitz et al. [1995] demonstrated the existence of cycling chaos in continuous-time three-cell systems modeled by Chua's circuit equations and Lorenz equations, while Palacios [2002, 2003] later demonstrated the existence of cycling chaos in discrete-time cell systems. In this work, we consider two issues that follow-up from these previous works. First of all, we address the generalization of existence of cycling behavior in continuous-time systems with more than three cells. We demonstrate that increasing the number of cells, while maintaining the same network connectivity used by Dellnitz et al. [1995], is not enough to sustain the nature of a cycle, in which only one cell is active at any given time. Secondly, we address the existence of cycling behavior in networks with near-identical cells, where the internal dynamics of each cell is governed by an identical model equation but with possibly different parameter values. We show that, under a new connectivity scheme, cycling behavior can also occur in networks with near-identical cells.
Leucocyte filtration during cardiopulmonary bypass hardly changed leucocyte counts and did not influence myeloperoxidase, complement, cytokines or platelets (1998)

In some patients, coronary artery bypass surgery induces postoperative organ dysfunction despite an apparently adequate revascularization and good haemodynamic performance. This complication may be caused by activation of the body's inflammatory systems on blood contact with large foreign surfaces in the extracorporeal circuit. Activated leucocytes may play an important role in organ damage, and it is conceivable that leucocyte removal by filtration may decrease the potential side-effects of cardiopulmonary bypass (CPB). The aim of the present study was to investigate possible effects of leucocyte filtration during the whole CPB period in elective coronary artery bypass surgery on biochemical and clinical parameters. Forty patients were randomized to extracorporeal circulation using a leucocyte-depleting filter (group L, n = 20) or to extracorporeal circulation with no leucocyte filter (group C, n = 20). In the leucocyte-depleted group, the mean total white blood cell counts increased from 6.3 (95% confidence interval, 5.5-7.0) x 10(9)/l to 7.0 (5.7-8.3) x 10(9)/l during extracorporeal circulation and in the control group from 6.3 (5.2-7.3) x 10(9)/l to 8.5 (7.2-9.8) x 10(9)/l. The intergroup difference was not statistically significant (p = 0.84). A substantial increase in concentrations of interleukin-6, myeloperoxidase and complement activation products were observed in both groups without statistically significant intergroup differences. It is concluded that the leucocyte-depletion filter did not cause a significant reduction of circulating white blood cells during CPB, and there were no significant differences between the groups with respect to the inflammatory markers studied.
The Burden of Hypopituitarism in Adults after Pituitary Surgery (1997)

peer reviewed
Incremetal Spatio-Temporal Feature Extraction and Retrieval for Large Video Database (2007)

In this paper we present a novel framework for semantic retrieval of video database. Each frame of video clips, characterized by its HSV (hue-saturation-value) color feature, is first projected onto the spatial principle components via CCIPCA (candid covariance-free incremental principal component analysis). Temporal Chebyshev polynomials for video clips of various lengths are captured subsequently. The similarity of two video clips is finally presented in a reasonable and computable form. The framework works incrementally and is suitable for videos of data streams in sequential order. Extensive experiments demonstrate that the framework can obtain promising results on video similarity comparison, and also with a comparably computational speedup.
The GABARAP Co-Secretome Identified by APEX2-GABARAP Proximity Labelling of Extracellular Vesicles (2020)

The autophagy-related ATG8 protein GABARAP has not only been shown to be involved in the cellular self-degradation process called autophagy but also fulfils functions in intracellular trafficking processes such as receptor transport to the plasma membrane. Notably, available mass spectrometry data suggest that GABARAP is also secreted into extracellular vesicles (EVs). Here, we confirm this finding by the immunoblotting of EVs isolated from cell culture supernatants and human blood serum using specific anti-GABARAP antibodies. To investigate the mechanism by which GABARAP is secreted, we applied proximity labelling, a method for studying the direct environment of a protein of interest in a confined cellular compartment. By expressing an engineered peroxidase (APEX2)-tagged variant of GABARAP-which, like endogenous GABARAP, was present in EVs prepared from HEK293 cells-we demonstrate the applicability of APEX2-based proximity labelling to EVs. The biotinylated protein pool which contains the APEX2-GABARAP co-secretome contained not only known GABARAP interaction partners but also proteins that were found in APEX2-GABARAP's proximity inside of autophagosomes in an independent study. All in all, we not only introduce a versatile tool for co-secretome analysis in general but also uncover the first details about autophagy-based pathways as possible biogenesis mechanisms of GABARAP-containing EVs.
An Extremely Mild Method for the Construction ofE-1,3-Dienes (1992)

A novel route to simple E-1,3-dienes using a vinylogous Peterson olefination is described. The allylic hydroxysilanes 2 are prepared by a chromium-mediated coupling of 1-bromo-3-trimethylsilylpropene to a selection of aldehydes.
Direct Catalytic Enantioselective Aza‐Diels—Alder Reactions. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Modular Biomaterial Scaffold‐Based Vaccine Elicits Durable Adaptive Immunity to Subunit SARS‐CoV‐2 Antigens (2021)

The coronavirus disease 2019 (COVID-19) pandemic demonstrates the importance of generating safe and efficacious vaccines that can be rapidly deployed against emerging pathogens. Subunit vaccines are considered among the safest, but proteins used in these typically lack strong immunogenicity, leading to poor immune responses. Here, a biomaterial COVID-19 vaccine based on a mesoporous silica rods (MSRs) platform is described. MSRs loaded with granulocyte-macrophage colony-stimulating factor (GM-CSF), the toll-like receptor 4 (TLR-4) agonist monophosphoryl lipid A (MPLA), and SARS-CoV-2 viral protein antigens slowly release their cargo and form subcutaneous scaffolds that locally recruit and activate antigen-presenting cells (APCs) for the generation of adaptive immunity. MSR-based vaccines generate robust and durable cellular and humoral responses against SARS-CoV-2 antigens, including the poorly immunogenic receptor binding domain (RBD) of the spike (S) protein. Persistent antibodies over the course of 8 months are found in all vaccine configurations tested and robust in vitro viral neutralization is observed both in a prime-boost and a single-dose regimen. These vaccines can be fully formulated ahead of time or stored lyophilized and reconstituted with an antigen mixture moments before injection, which can facilitate its rapid deployment against emerging SARS-CoV-2 variants or new pathogens. Together, the data show a promising COVID-19 vaccine candidate and a generally adaptable vaccine platform against infectious pathogens.
Spatial bias and temporal lag in tactile space perception (2006)

Constructing a veridical spatial map by touch poses at least two problems for a perceptual system. First, as the hand is moved through space, the locations of features may be displaced if there is an uncorrected lag between the moment the hand encounters a feature and the time that feature is encoded on a spatial map. Second, due to the sequential nature of the process, some form of memory, which itself may be subject to spatial distortions, is required for integration of spatial samples. We investigated these issues using a task involving active haptic exploration with a stylus swept back and forth in the horizontal plane at the wrist. Remembered locations of tactile targets were shifted towards the medial axis of the forearm, suggesting a central tendency in haptic spatial memory, while evidence for a displacement of perceived locations in the direction of sweep motion was consistent with processing delays.
Effect of macrophage activation on killing ofListeria monocytogenes.Roles of reactive oxygen or nitrogen intermediates, rate of phagocytosis, and retention of bacteria in endosomes (1992)

The role of macrophage activation in the killing of L. monocytogenes is unclear. Some studies suggest that activation for enhanced production of reactive oxygen and nitrogen intermediates may not be of central importance. Recent data have indicated an important role for interferon-gamma (IFN-gamma) induced retention of L. monocytogenes in endosomes. Data from the present study indicate that proteose peptone-elicited macrophages from DBA2/J, CD-1, and C3H/HeN mice are listericidal. Activation of these cells in vitro for 20 h by IFN-gamma (20 or 500 U/ml) increased H2O2 or nitrite production, but did not increase the number of L. monocytogenes killed during a subsequent 6-h or 7-h culture. Incubation of macrophages with IFN-gamma plus lipopolysaccharide (LPS) caused greater activation and increased the number of Listeria killed during a 6-h or 7-h culture. However, this seems primarily attributable to enhanced phagocytosis. Proteose peptone-elicited macrophages were significantly more effective than resident macrophages in preventing the escape of L. monocytogenes from endosomes into the cytoplasm. This capability was not significantly enhanced by IFN-gamma in vitro, but was enhanced by IFN-gamma plus LPS. This correlates well with the effects of these activation stimuli on killing of L. monocytogenes by proteose peptone-elicited macrophages. These results indicate that enhanced retention of L. monocytogenes in endosomes is induced by proteose peptone elicitation and that further macrophage activation in vitro by IFN-gamma does not improve listericidal activity.
Rheological Characterization of Novel, Delayed-Transition Metal Crosslinked Fracturing Fluids: Correlation With First Field Applications (2009)

Abstract The extent of crosslinking produced by a polymeric fracturing gel can significantly contribute to the success or failure of a hydraulic fracturing treatment. In certain cases, excessive crosslinking while the fluid is in the tubulars can result in friction pressures that are too high, and these may prohibit the treatment from achieving the design goals. With titanium (Ti) or zirconium (Zr) crosslinked gels, which are prone to irreversible shear degradation, early crosslinking in the tubulars can substantially reduce the final gel strength, even to the degree that near-wellbore proppant transport is compromised, and the treatment may screen out. On the other hand, a Ti or Zr crosslinked gel that crosslinks substantially after exiting the perforations may not have sufficient proppant-transport capability to complete the treatment successfully. Varying treatment conditions such as mix-water composition and temperature, tubular shear rate and transit time, and reservoir temperature pose difficult challenges to routinely achieving the optimal crosslinking state. Conditions such as offshore wellbore temperature and viscous heating in smaller-diameter tubing can further complicate the task. Various chemical means have been employed to tune the crosslinking temperature for specific treating conditions. These methods involve addition of chemicals to control the crosslinking kinetics, such as pH buffers; adjustment of crosslinker concentration; and competing ligands to temporarily bind the metal crosslinker. Blended crosslinkers containing a single Group 4 (Ti, Zr) metal with different organic ligands with different binding strengths have been employed to achieve crosslinking at two temperature ranges so that early viscosity for proppant transport can be developed. Mixed metal crosslinkers such as aluminum (Al) and Zr have also been formulated for this same purpose. This paper examines the disadvantages of these strategies, and describes the development and application of a high-temperature fracturing fluid system that has overcome the issues described.
Contrast Solution Properties and Scan Parameters Influence the Apparent Diffusivity of Computed Tomography Contrast Agents in Articular Cartilage (2021)

ABSTRACT The inability to detect early degenerative changes to the articular cartilage surface that commonly precede bulk osteoarthritic degradation is an obstacle to early disease detection for research or clinical diagnosis. Leveraging a known artifact that blurs tissue boundaries in clinical arthrograms, contrast agent diffusivity can be derived from computed tomography arthrography (CTa) scans. We combined experimental and computational approaches to study protocol variations that may alter the CTa-derived apparent diffusivity. In experimental studies on bovine cartilage explants, we examined how contrast agent dilution and transport direction (absorption vs. desorption) influence the apparent diffusivity of untreated and enzymatically digested cartilage. Using multiphysics simulations, we examined mechanisms underlying experimental observations and the effects of image resolution, scan interval and early scan termination. The apparent diffusivity during absorption decreased with increasing contrast agent concentration by an amount similar to the increase induced by tissue digestion. Models indicated that osmotically induced fluid efflux strongly contributed to the concentration effect. Simulated changes to spatial resolution, scan spacing and total scan time all influenced the apparent diffusivity, indicating the importance of consistent protocols. With careful control of imaging protocols and interpretations guided by transport models, CTa-derived diffusivity offers promise as a biomarker for early degenerative changes.
An Ion Pairing Approach to Enhance Oral Bioavailability of Alendronate (2015)

Aim: Alendronate (AL) is a nitrogen-containing bisphosphonate drug that exhibits limited oral bioavailability due to predominantly hydrophilic molecular properties. To enhance oral absorption of this important osteoporosis drug, a novel ion-pairing strategy using the cationic polymer polyethylenimine (PEI) was explored as an initial step of an alternate oral drug delivery strategy that attempts to prepare polymer-encapsulated ion pair nanoparticles. Methodology: Electrostatically stabilized AL/PEI association complexes were fabricated by combining AL and PEI solutions prepared in 0.05 M acetate buffer, pH 5.0, at different AL/PEI Short Research Article El-Hamid et al.; JSRR, 5(4): 344-351, 2015; Article no.JSRR.2015.101 345 charge ratios under stirring. The free fraction of AL after complexation with PEI was quantified spectrophotometrically at λ=300 nm using ferric chloride. Particle size distribution and zeta potential of ion pairs formed at different molar AL/PEI ratios were measured by dynamic laser light scattering. Results: The complexation efficiency of PEI was low until an AL/PEI charge ratio of1:1.7. Increasing PEI concentrations effectively decreased the free fraction of AL implying formation of stable ion pairs between the negatively charged AL and the positively charged polymer. The lowest fraction of free AL was 18.7% measured at an AL/PEI charge ratio of 1:33. The mean hydrodynamic diameter of nanoassemblies decreased with increasing AL/PEI charge ratio reaching a limiting value of 71±1.4 nm at AL/PEI=1:33. Corresponding zeta potential measured for these association complexes was +37±2.8 mV. Conclusion: AL/PEI charge ratio greater than 1:1.7 facilitates effective formation of electrostatically stabilized ion pairs that carry a significant positive surface charge indicative of substantial colloidal stability in aqueous solution. The small size of AL/PEI complexes fabricated at 1:33 favors these ion pairs for subsequent encapsulation into biocompatible polymers suitable for oral drug delivery.
Supplemental Table 2 from A Synthetic Lethal Screen Reveals Enhanced Sensitivity to ATR Inhibitor Treatment in Mantle Cell Lymphoma with ATM Loss-of-Function (2023)

&lt;p&gt;Supplemental Table 2. SiRNA sequences (Supplemental data)&lt;/p&gt;