gebhart/patrepeval huggingface dataset:
Optogenetic Stimulation Using Anion Channelrhodopsin (GtACR1) Facilitates Termination of Reentrant Arrhythmias With Low Light Energy Requirements: A Computational Study (2021)

Optogenetic defibrillation of hearts expressing light-sensitive cation channels (e.g., ChR2) has been proposed as an alternative to conventional electrotherapy. Past modeling work has shown that ChR2 stimulation can depolarize enough myocardium to interrupt arrhythmia, but its efficacy is limited by light attenuation and high energy needs. These shortcomings may be mitigated by using new optogenetic proteins like <i>Guillardia theta</i> Anion Channelrhodopsin (GtACR1), which produces a repolarizing outward current upon illumination. Accordingly, we designed a study to assess the feasibility of GtACR1-based optogenetic arrhythmia termination in human hearts. We conducted electrophysiological simulations in MRI-based atrial or ventricular models (<i>n</i> = 3 each), with pathological remodeling from atrial fibrillation or ischemic cardiomyopathy, respectively. We simulated light sensitization via viral gene delivery of three different opsins (ChR2, red-shifted ChR2, GtACR1) and uniform endocardial illumination at the appropriate wavelengths (blue, red, or green light, respectively). To analyze consistency of arrhythmia termination, we varied pulse timing (three evenly spaced intervals spanning the reentrant cycle) and intensity (atrial: 0.001-1 mW/mm<sup>2</sup>; ventricular: 0.001-10 mW/mm<sup>2</sup>). In atrial models, GtACR1 stimulation with 0.005 mW/mm<sup>2</sup> green light consistently terminated reentry; this was 10-100x weaker than the threshold levels for ChR2-mediated defibrillation. In ventricular models, defibrillation was observed in 2/3 models for GtACR1 stimulation at 0.005 mW/mm<sup>2</sup> (100-200x weaker than ChR2 cases). In the third ventricular model, defibrillation failed in nearly all cases, suggesting that attenuation issues and patient-specific organ/scar geometry may thwart termination in some cases. Across all models, the mechanism of GtACR1-mediated defibrillation was voltage forcing of illuminated tissue toward the modeled channel reversal potential of -40 mV, which made propagation through affected regions impossible. Thus, our findings suggest GtACR1-based optogenetic defibrillation of the human heart may be feasible with ≈2-3 orders of magnitude less energy than ChR2.
SMART Mobility. Multi-Modal Freight Capstone Report (2020)

The U.S. Department of Energy’s Systems and Modeling for Accelerated Research in Transportation (SMART) Mobility Consortium is a multiyear, multi-laboratory collaborative, managed by the Energy Efficient Mobility Systems Program of the Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office, dedicated to further understanding the energy implications and opportunities of advanced mobility technologies and services. The first three-year research phase of SMART Mobility occurred from 2017 through 2019, and included five research pillars: Connected and Automated Vehicles, Mobility Decision Science, Multi-Modal Freight, Urban Science, and Advanced Fueling Infrastructure. A sixth research thrust integrated aspects of all five pillars to develop a SMART Mobility Modeling Workflow to evaluate new transportation technologies and services at scale. This report summarizes the work of the Multi-Modal Freight Pillar. The Multi Modal Freight Pillar’s objective is to assess the effectiveness of emerging freight movement technologies and understand the impacts of the growing trends in consumer spending and e-commerce on parcel movement considering mobility, energy, and productivity. For information about the other Pillars and about the SMART Mobility Modeling Workflow, please refer to the relevant pillar’s Capstone Report.
[2002 Nobel Prize in Physiology and Medecine: from nematodes to programmed cell death]. (2002)

Qu'est-ce qu'un ver de terre de 1 mm de la famille des nematodes (Caenorhabditis elegans pour les intimes) peut avoir a faire avec la medecine et le cancer ? Et pourtant le jury du Karolinska, qui vient de decerner le prix Nobel de physiologie et medecine a trois specialistes de cet organisme, ne s'y est pas trompe. Il a reconnu en S. Brenner l'extraordinaire visionnaire qui lui a fait [...]
PPARδ-mediated antiinflammatory mechanisms inhibit angiotensin II-accelerated atherosclerosis (2008)

Activation of the nuclear hormone receptor peroxisome proliferator-activated receptor delta (PPARdelta) has been shown to improve insulin resistance, adiposity, and plasma HDL levels. However, its antiatherogenic role remains controversial. Here we report atheroprotective effects of PPARdelta activation in a model of angiotensin II (AngII)-accelerated atherosclerosis, characterized by increased vascular inflammation related to repression of an antiinflammatory corepressor, B cell lymphoma-6 (Bcl-6), and the regulators of G protein-coupled signaling (RGS) proteins RGS4 and RGS5. In this model, administration of the PPARdelta agonist GW0742 (1 or 10 mg/kg) substantially attenuated AngII-accelerated atherosclerosis without altering blood pressure and increased vascular expression of Bcl-6, RGS4, and RGS5, which was associated with suppression of inflammatory and atherogenic gene expression in the artery. In vitro studies demonstrated similar changes in AngII-treated macrophages: PPARdelta activation increased both total and free Bcl-6 levels and inhibited AngII activation of MAP kinases, p38, and ERK1/2. These studies uncover crucial proinflammatory mechanisms of AngII and highlight actions of PPARdelta activation to inhibit AngII signaling, which is atheroprotective.
Energy Efficiency Indicators for Assessing Construction Systems Storing Renewable Energy: Application to Phase Change Material-Bearing Façades (2015)

Assessing the performance or energy efficiency of a single construction element by itself is often a futile exercise. That is not the case, however, when an element is designed, among others, to improve building energy performance by harnessing renewable energy in a process that requires a source of external energy. Harnessing renewable energy is acquiring growing interest in Mediterranean climates as a strategy for reducing the energy consumed by buildings. When such reduction is oriented to lowering demand, the strategy consists in reducing the building’s energy needs with the use of construction elements able to passively absorb, dissipate, or accumulate energy. When reduction is pursued through M&amp;E services, renewable energy enhances building performance. The efficiency of construction systems that use renewable energy but require a supplementary power supply to operate can be assessed by likening these systems to regenerative heat exchangers built into the building. The indicators needed for this purpose are particularly useful for designers, for they can be used to compare the efficiency or performance to deliver an optimal design for each building. This article proposes a series of indicators developed to that end and describes their application to façades bearing phase change materials (PCMs).
Oligopeptides as Catalysts for Asymmetric Epoxidation (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Full utilization and fairness on high speed bus networks (2002)

Many existing protocols indicate that full utilization and fairness might be incompatible in high-speed high-latency MANs or LANs. The purpose of this paper is to understand the relationship between full utilization and fairness. A new protocol called FUFA (fully utilized and fair) is designed to demonstrate some of the basic properties. We define full utilization and fairness precisely, and show that both are achieved together in the proposed protocol. The main idea is that each station takes account of the idle slots propagated previously to interpret the information from downstream (i.e., estimated aggregate number of data segments in the queue downstream and the estimated number of active downstream stations). This allows the active downstream stations to be served in a round robin fashion according to the updated information.
Transcatheter Arterial Chemoembolization with or without Radiofrequency Ablation in the Management of Patients with Advanced Hepatic Malignancy (2002)

Transcatheter arterial chemoembolization (TACE) is efficacious against hepatic malignancies by rendering tumors ischemic while delivering high-dose chemotherapy. The added benefit of radiofrequency ablation (RFA) has not been determined. We sought to review our experience with TACE with or without RFA in the treatment of hepatocellular carcinoma and colorectal liver metastases in patients not amenable to resection. TACE and RFA were undertaken in 13 patients with hepatocellular carcinoma (n = 7) or colorectal liver metastases (n = 6). Concurrently 24 patients underwent TACE alone for hepatocellular carcinoma (n = 15) or colorectal liver metastases (n = 9). Patients undergoing TACE with or without RFA were similar in age, gender, and diagnosis. Overall follow-up was 9.1 months +/- 7.1. One-year survival was greater in patients undergoing TACE with RFA than with TACE alone (100% vs 67%, P = 0.04). Mean survival was longer after TACE with RFA compared with TACE alone (25.3 months +/- 15.9 vs 11.4 months +/- 7.3, P < 0.05). No patients suffered significant complications. The addition of RFA to TACE improves survival in patients with unresectable primary or metastatic hepatic malignancies. RFA with TACE should be in the armamentarium of surgeons caring for patients with malignant liver lesions.
Lactobacillus rhamnosus GG and Streptococcus thermophilus induce suppressor of cytokine signalling 3 (SOCS3) gene expression directly and indirectly via interleukin-10 in human primary macrophages (2011)

In the present study we have characterized T helper type 2 (Th2) [interleukin (IL)-10]/Th1 (IL-12) cytokine expression balance in human primary macrophages stimulated with multiple non-pathogenic Gram-positive bacteria used in the food industry and as probiotic substances. Bacteria representing Lactobacillus, Bifidobacterium, Lactococcus, Leuconostoc, Propionibacterium and Streptococcus species induced anti-inflammatory IL-10 production, although quantitative differences between the bacteria were observed. S. thermophilus was able to induce IL-12 production, while the production of IL-12 induced by other bacteria remained at a low level. The highest anti-inflammatory potential was seen with bifidobacteria, as evidenced by high IL-10/IL-12 induction ratios. All studied non-pathogenic bacteria were able to stimulate the expression of suppressor of cytokine signalling (SOCS) 3 that controls the expression of proinflammatory cytokine genes. Lactobacillus and Streptococcus species induced SOCS3 mRNA expression directly in the absence of protein synthesis and indirectly via bacteria-induced IL-10 production, as demonstrated by experiments with cycloheximide (CHX) and anti-IL-10 antibodies, respectively. The mitogen-activated protein kinase (MAPK) p38 signalling pathway played a key role in bacteria-induced SOCS3 gene expression. Enhanced IL-10 production and SOCS3 gene expression induced by live non-pathogenic Lactobacillus and Streptococcus is also likely to contribute to their immunoregulatory effects in vivo.
Supplementary Figure 6 from Interleukin-6/STAT3 Pathway Signaling Drives an Inflammatory Phenotype in Group A Ependymoma (2023)

&lt;p&gt;IL-6 is the driving cytokine for immune suppressive phenotype observed in 811 CM monocytes.&lt;/p&gt;
Pyrimido[1,2‐b]‐1,2,4,5‐tetrazin‐6‐ones as HCMV Protease Inhibitors: A New Class of Heterocycles with Flavin‐Like Redox Properties. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Visualizing and manipulating hyperstabilization of T cell microvilli contacts by engineered chimeric antigen receptors (2021)

Abstract T cells typically recognize their ligands using a defined cell biology – the scanning of their membrane microvilli to palpate their environment – while that same membrane scaffolds T cell receptors (TCRs) that can signal upon ligand binding. Chimeric antigen receptors (CARs) present both a therapeutic promise as well as a tractable means to study the interplay between receptor affinity, microvillar dynamics and T cell function. CARs are often built using single-chain variable fragments (scFvs) with far greater affinity than that of natural TCRs. We used high resolution lattice lightsheet (LLS) and total internal reflection fluorescence (TIRF) imaging to visualize microvillar scanning in the context of variations in CAR design. This demonstrated that conventional CARs hyper-stabilized microvillar contacts relative to TCRs. Reducing the affinity and/or avidity of binding brought synapse microvillar dynamics into natural ranges, normalized synapse resolution and improved downstream effector function. This work highlights the importance of understanding the underlying cell biology when designing receptors for optimal antigen engagement.
Slackline Training for Balance and Strength Promotion (2010)

The prevalence of sustaining a sport injury is high in adults. Deficits in postural control/muscle strength represent important injury-risk factors. Thus, the purpose of this study was to investigate the impact of a specific type of balance training, i. e. slackline training, followed by detraining on balance and strength performance. Twenty-seven adults participated in this study and were assigned to an intervention (age 22.8±3.3 yrs) or a control group (age 23.9±4.4 yrs). The intervention group participated in 4 weeks of slackline training on nylon webbings. Detraining lasted 4 weeks. Tests included the measurement of (A) total centre of pressure displacements during one-legged standing on a balance platform and during the compensation of a perturbation impulse, (B) maximal torque and rate of force development (RFD) of the plantar flexors on an isokinetic device, and (C) jumping height on a force platform. After training, no significant interaction effects were observed for variables of static/dynamic postural control, maximal torque, and jumping height. Training-induced improvements were found for RFD. After the withdrawal of the training stimulus, RFD slightly decreased. Given that the promotion of balance and strength is important for injury prevention, changes in RFD only might not be sufficient to produce an injury-preventive effect.
DNA‐Reinigung in Tröpfchen auf einem magnetischen “Lab‐on‐a‐Chip” (2006)

Vereinigen, Mischen, Teilen und Transport – diese grundlegenden Schritte durchlaufen DNA-haltige Tröpfchen bei einer DNA-Reinigungsmethode auf einem Chip. Das System extrahiert Genmaterial aus rohen Zellproben geringer Konzentration mithilfe der Aktuation von magnetischen Mikropartikeln in den Tröpfchen über einer Spulenanordnung (siehe Bild).
Saturation-bandwidth tradeoffs in grid frequency regulation for wind generation with energy storage (2011)

Selection of linear feedback to operate with plants having actuator saturation limits has long been important in control design research, with one approach represented in the work of Saberi and his co-workers. The work here seeks to tailor this “saturation-accommodating” design method to problems motivated by integrating into the grid renewable energy sources, such as wind turbines, and energy storage technologies, such as batteries, ultra-capacitors, or flywheels. We examine the problem of grid frequency control, in which large numbers of actuators (generators or storage devices) offer distributed control action by varying power output. We tailor Saberi's method to enhance controller utilization and regulation performance when actuators fall into two classes: (i) low bandwidth, “slow” actuators with broad saturation limits (e.g., power control available by varying blade pitch in wind generators); and (ii) high bandwidth, “faster” actuators with narrow saturation limits (e.g., power control available from battery or ultra-capacitor energy storage).
MicroRNA Expression Profiling of Bone Marrow–Derived Proangiogenic Cells (PACs) in a Mouse Model of Hindlimb Ischemia: Modulation by Classical Cardiovascular Risk Factors (2020)

This study describes for the first time the effects of CRFs on the modulation of miR profile in PACs related to PAD and ischemia-induced neovascularization. We found that several angiogenesis-modulating miRs are similarly altered in different CRF conditions. Our findings constitute a solid framework for the identification of miRs that could be targeted in PACs in order to improve their angiogenic function and for the future development of novel therapies to improve neovascularization and reduce tissue damage in patients with severe PAD.
Photoactivation of Extracellular‐Signal‐Regulated Kinase Signaling in Target Cells by Femtosecond Laser (Laser Photonics Rev. 12(7)/2018) (2018)

Photostimulation In article number 1700137, Minglie Hu, Hao He, and co-workers demonstrate that a single-time short flash of femtosecond-laser stimulation on any target cells can activate the extracellular signal-regulated kinase (ERK) signaling pathway directly, without any optogenetics or exogenous materials. This optical activation is non-invasive, controllable, and precise in both spatial and temporal dimensions.
The Appearance and Modulation of Osteocyte Marker Expression during Calcification of Vascular Smooth Muscle Cells (2011)

This study has demonstrated the up-regulation of key osteocytic molecules during the vascular calcification process. A fuller understanding of the functional role of osteocyte formation and specifically sclerostin and E11 expression in the vascular calcification process may identify novel potential therapeutic strategies for clinical intervention.
Therapeutic inhibition of the SRC-kinase HCK facilitates T cell tumor infiltration and improves response to immunotherapy (2022)

Although immunotherapy has revolutionized cancer treatment, many immunogenic tumors remain refractory to treatment. This can be largely attributed to an immunologically "cold" tumor microenvironment characterized by an accumulation of immunosuppressive myeloid cells and exclusion of activated T cells. Here, we demonstrate that genetic ablation or therapeutic inhibition of the myeloid-specific hematopoietic cell kinase (HCK) enables activity of antagonistic anti-programmed cell death protein 1 (anti-PD1), anti-CTLA4, or agonistic anti-CD40 immunotherapies in otherwise refractory tumors and augments response in treatment-susceptible tumors. Mechanistically, HCK ablation reprograms tumor-associated macrophages and dendritic cells toward an inflammatory endotype and enhances CD8<sup>+</sup> T cell recruitment and activation when combined with immunotherapy in mice. Meanwhile, therapeutic inhibition of HCK in humanized mice engrafted with patient-derived xenografts counteracts tumor immunosuppression, improves T cell recruitment, and impairs tumor growth. Collectively, our results suggest that therapeutic targeting of HCK activity enhances response to immunotherapy by simultaneously stimulating immune cell activation and inhibiting the immunosuppressive tumor microenvironment.
Lectins as Tools for the Purification of Liver Endothelial Cells (2003)

Successful procedures for the isolation and culture of large-vessel endothelial cells (EC), were first reported in the early seventies (1,2). Since then, microvascular EC have been isolated from various organs, such as adrenal gland (3), brain (4), skin (5), retina (6), and myocardium (7). The initial steps of the conventional methods for EC isolation involve mechanical and/or enzymatic dissociation of the tissues, followed by filtration and pelleting of cells. A number of special techniques have been developed to eliminate contaminating cell types and enrich endothelial cells in mixed cell populations. These include: manual removal of nonendothelial cell types; use of selective media; plating cells on gelatin or fibronectin-coated dishes, and Percoll gradient centrifugation (8,9). The main problem with the conventional methods is that they are labor intensive and often do not produce pure EC populations. A more advanced approach is to use fluorescent-activated cell sorting (FACS) which allows sorting based on specific surface antigens or metabolic differences. Auerbach et al. used FACS for EC isolation, using an antibody against angiotensin converting enzyme (10). Later, Voyta et al. sorted EC, based on their uptake of acetylated low-density lipoprotein (11). Cell separation techniques using magnetic affinity are based on similar principles as the FACS, but do not involve expensive equipment. In this chapter, we describe liver endothelial cell isolation, using lectin-coated magnetic beads (12).
Service Function Chaining using Virtual Networks with BGP VPNs (2018)

This document describes how service function chains (SFC) can be
applied to traffic flows using routing in a virtual (overlay) network
to steer traffic between service nodes. Chains can include services
running in routers, on physical appliances or in virtual machines.
Service chains have applicability at the subscriber edge, business
edge and in multi-tenant datacenters. The routing function into SFCs
and between service functions within an SFC can be performed by
physical devices (routers), be virtualized inside hypervisors, or run
as part of a host OS. A BGP control plane for route distribution is
used to create virtual networks implemented using IP MPLS, VXLAN or
other suitable encapsulation, where the routes within the virtual
networks cause traffic to flow through a sequence of service nodes
that apply packet processing functions to the flows. Two techniques
are described: in one the service chain is implemented as a sequence
of distinct VPNs between sets of service nodes that apply each service
function; in the other, the routes within a VPN are modified through
the use of special route targets and modified next-hop resolution to
achieve the desired result. In both techniques, service chains can be
created by manual configuration of routes and route targets in routing
systems, or through the use of a controller which contains a
topological model of the desired service chains. This document also
contains discussion of load balancing between network functions,
symmetric forward and reverse paths when stateful services are
involved, and use of classifiers to direct traffic into a service
chain.
Global abundance of microbial rhodopsins (2012)

Photochemical reaction centers and rhodopsins are the only phototrophic mechanisms known to have evolved on Earth. The minimal cost of bearing a rhodopsin-based phototrophic mechanism in comparison to maintaining a photochemical reaction center suggests that rhodopsin is the more abundant of the two. We tested this hypothesis by conducting a global abundance calculation of phototrophic mechanisms from 116 marine and terrestrial microbial metagenomes. On average, 48% of the cells from which these metagenomes were generated harbored a rhodopsin gene, exceeding the reaction center abundance by threefold. Evidence from metatranscriptomic data suggests that this genomic potential is realized to a substantial extent, at least for the small-sized (>0.8 μm) of microbial fractions.