gebhart/patrepeval huggingface dataset:
Photodynamic Inhibition of Herpes Simplex Virus 1 Infection by Tricationic Amphiphilic Porphyrin with a Long Alkyl Chain (2023)

Photodynamic therapy (PDT) is broadly used to treat different tumors, and it is a rapidly developing approach to inactivating or inhibiting the replication of fungi, bacteria, and viruses. Herpes simplex virus 1 (HSV-1) is an important human pathogen and a frequently used model to study the effects of PDT on enveloped viruses. Although many photosensitizers (PSs) have been tested for their antiviral properties, analyses are usually limited to assessing the reduction in viral yield, and thus the molecular mechanisms of photodynamic inactivation (PDI) remain poorly understood. In this study, we investigated the antiviral properties of TMPyP3-C<sub>17</sub>H<sub>35</sub>, a tricationic amphiphilic porphyrin-based PS with a long alkyl chain. We show that light-activated TMPyP3-C<sub>17</sub>H<sub>35</sub> can efficiently block virus replication at certain nM concentrations without exerting obvious cytotoxicity. Moreover, we show that the levels of viral proteins (immediate-early, early, and late genes) were greatly reduced in cells treated with subtoxic concentrations of TMPyP3-C<sub>17</sub>H<sub>35</sub>, resulting in markedly decreased viral replication. Interestingly, we observed a strong inhibitory effect of TMPyP3-C<sub>17</sub>H<sub>35</sub> on the virus yield only when cells were treated before or shortly after infection. In addition to the antiviral activity of the internalized compound, we show that the compound dramatically reduces the infectivity of free virus in the supernatant. Overall, our results demonstrate that activated TMPyP3-C<sub>17</sub>H<sub>35</sub> effectively inhibits HSV-1 replication and that it can be further developed as a potential novel treatment and used as a model to study photodynamic antimicrobial chemotherapy.
Wrist-partitioned inverse kinematic accelerations and manipulator dynamics (2005)

An efficient algorithm is presented for the calculation of the inverse kinematic accelerations for a 6 degree-of-freedom manipulator with a spherical wrist. The inverse kinematic calculation is shown to work synergistically with the inverse dynamic calculation, producing kinematic parameters needed in the recursive Newton-Euler dynamics formulation. Additional savings in the dynamics computation are noted for a class of kinematically well-structured manipulators such as spherical-wrist arms and for manipulators with simply-structured inertial parameters.
Measurement of Trabecular Bone Mineral Density in the Thoracic Spine Using Cardiac Gated Quantitative Computed Tomography (2004)

Cardiac gated CT, primarily intended for measurement of coronary vascular calcium, can be used to measure thoracic BMD with high precision. Thoracic BMD measurements using this method are highly correlated with QCT measurements in the lumbar spine.
Intratumor Heterogeneity and Therapy Resistance: Contributions of Dormancy, Apoptosis Reversal (Anastasis) and Cell Fusion to Disease Recurrence (2020)

A major challenge in treating cancer is posed by intratumor heterogeneity, with different sub-populations of cancer cells within the same tumor exhibiting therapy resistance through different biological processes. These include therapy-induced dormancy (durable proliferation arrest through, e.g., polyploidy, multinucleation, or senescence), apoptosis reversal (anastasis), and cell fusion. Unfortunately, such responses are often overlooked or misinterpreted as "death" in commonly used preclinical assays, including the in vitro colony-forming assay and multiwell plate "viability" or "cytotoxicity" assays. Although these assays predominantly determine the ability of a test agent to convert dangerous (proliferating) cancer cells to potentially even more dangerous (dormant) cancer cells, the results are often assumed to reflect loss of cancer cell viability (death). In this article we briefly discuss the dark sides of dormancy, apoptosis, and cell fusion in cancer therapy, and underscore the danger of relying on short-term preclinical assays that generate population-based data averaged over a large number of cells. Unveiling the molecular events that underlie intratumor heterogeneity together with more appropriate experimental design and data interpretation will hopefully lead to clinically relevant strategies for treating recurrent/metastatic disease, which remains a major global health issue despite extensive research over the past half century.
Communicating Josephson qubits (2003)

We propose a scheme to implement a quantum information transfer protocol with a superconducting circuit and Josephson charge qubits. The information exchange is mediated by an $L\ensuremath{-}C$ resonator used as a data bus. The main decoherence sources are analyzed in detail.
Restoration of Endothelium‐dependent Vasodilatory Responses in T2D Resistance Arteries by a Pharmacologic Activator of Endothelial K Ca Channels (2015)

Endothelial dysfunction is a common early pathogenic event in patients with type 2 diabetes (T2D). In isolated hearts from diabetic Goto-Kakizaki (GK) rats, we have reported that SKA-31, a positive modulator of endothelial Ca2+-activated K+ (KCa) channels, enhances total coronary flow. In the current study, we examined the effects of SKA-31 on cannulated, myogenically active cremaster arteries from 24 week old wild-type (WT) and T2D GK rats, along with small intra-thoracic arteries from patients. At 70 mmHg intraluminal pressure, inhibition of myogenic tone by 0.3 μM acetylcholine (ACh) or 0.1 μM bradykinin (BK) (39.5±3.5% and 30.3±5.4%, respectively) was weaker in GK arteries than that observed in WT arteries (ACh = 59.2±3.9%, BK = 50.5±4.1%). In contrast, inhibition of tone by 10 μM SNP, a smooth muscle relaxant, was comparable in both arteries (GK = 56.2±3.3%, WT = 51.5±5.9%). Following exposure to a threshold concentration of SKA-31 (0.3 μM), vasodilatory responses to ACh (55.2±4.3%) and BK (49.2±5.5%) were significantly augmented in GK arteries, whereas only modest effects were observed in WT arteries. SKA-31 exposure also enhanced vasodilatory responses to ACh (0.3 μM) and BK (0.1 μM) in human arteries, but did not alter responses to either SNP or pinacidil. Electrophysiologically, KCa current densities were similar in isolated endothelial cells from WT and GK vessels. In summary, these data demonstrate that SKA-31 is able to restore endothelium-dependent vasodilatory responses in a rat model of T2D exhibiting endothelial dysfunction and metabolic syndrome, and has similar effects in resistance arteries from T2D patients. Supported in part by research funding to APB from the CIHR.
Estimation of plasma serotonin using isopycnic centrifugation (2000)

The valid measurement of the concentration of serotonin (5-HT) in blood plasma is important when using the platelet as a model for the serotonergic neuron. The assay is hampered by the release of 5-HT by (residual) platelets during the preparation for assay. We developed an isopycnic method that separates cells gently and completely from plasma by centrifuging a diluted Percoll density-gradient to which whole blood was added. In this study this method was compared with the usual differential centrifugation method. The isopycnic method on average resulted in nine times lower levels of plasma 5-HT. This difference was linearly related to the number of residual platelets in plasma after differential centrifuging. The proportion of intra-individual variation decreased three-fold. Therefore, the use of a Percoll density-gradient may lead to a more precise and more accurate estimate of the level of plasma 5-HT. Copyright 2000 John Wiley & Sons, Ltd.
Experimental investigations of a new concept of wave energy converter hybridizing piezoelectric and dielectric elastomer generators (2021)

Abstract A novel concept of a surge wave energy converter for nearshore applications is investigated experimentally. The centimetre-sized prototype developed in this work represents a proof of concept of a submerged system, which entails a hybrid transduction solution for the electrical conversion of wave energy, that uses piezoelectric elements (PZEs) and dielectric elastomer generators (DEG). The idea is to exploit the horizontal pressure gradient and horizontal water velocity underneath the waves to compress the PZE and inflate each half wave period a soft variable capacitance, which composes the DEG. The electrical charges created by the PZE are used to polarize the DEG, which is able to multiply the input energy. This hybridization is conceived to allow the system to generate electrical energy from waves without conventional high voltage supplies, thus reducing production costs and allowing standalone clean electrical generation. The article provides the preliminary fluid-mechanical measurements performed in a wave flume with a first version of the prototype and supported by a model comprising the fluid/structure interaction, the materials response, and the electrical operations. An estimation of the output energy of a small-sized prototype in constant charge mode is computed, and perspectives for optimizing the system are presented.
Secure M-commerce Transactions: A Third Party Based Signature Protocol (2007)

In this paper, we present a novel joint signature protocol suited to applications run on UMTS and heterogeneous networks. The protocol enables a mobile user to securely delegate his/her signing power to an assisted server so that the assisted server can perform signature generation and verification on behalf of the user. By shifting computational expensive cryptographic operations to a third party, i.e. the assisted server, the protocol is able to eliminate public key operations for the mobile end, while providing message origin authentication, integrity, and non-repudiation services to both delegated (i.e. the mobile user) and delegating (i.e. the third party) entities. The protocol is suited to m-commerce applications, in which a mobile user with a resource restrictive device wishes to access Internet-based security-sensitive services. The security of the proposed protocol is analyzed and its performance against other related work is evaluated.
Degradation of the sulfonylurea herbicide LGC‐42153 in flooded soil (2003)

LGC-42153, 2-fluoro-1-[3-(4,6-dimethoxypyrimidin-2-ylcarbamoylsulfamoyl)pyridin-2-yl] propyl methoxyacetate, is a new sulfonylurea herbicide for use in rice. Its breakdown and metabolism was studied in soil under flooded conditions using two radioactive tracer compounds labelled at either the propyl group or the pyrimidine ring. The half-life of LGC-42153 was approximately 3.0 days. The mass balance over 120 days ranged from 94.0 to 104.2% of applied radiocarbon, and no significant amount of volatiles or [14C]carbon dioxide were observed. Solvent non-extractable radiocarbon reached about 11-14% of applied radiocarbon at 120 days after treatment. The major metabolic reaction was the cleavage of the carboxyl ester bond to give 1-(4,6-dimethoxypyrimidin-2-yl)-3-[2-(1-hydroxy-2-fluoropropyl)pyridine-3-sulfonyl]urea, which underwent hydrolysis of the sulfonylurea bridge giving 2-(1-hydroxy-2-fluoro)propyl-3-pyridinesulfonamide and 4,6-dimethoxy-2-aminopyrimidine.
Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts (2023)

Our data provide novel insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumors. We show the key role of microglial phenotypic states in supporting GBM tumor growth and response to treatment. Our data place PDOXs as relevant models to assess the functionality of the TME and changes in the GBM ecosystem upon treatment.
Is Zirconia a Viable Alternative to Titanium for Dental Implantology? (2022)

Aim To review the literature using a systematic approach to answer the question: 'Are zirconia dental implants an alternative to titanium dental implants?' This was evaluated by assessing the evidence for survival rate, success rate and marginal bone loss of the two implant materials. Methods Relevant studies were identified after searching PUBMED, EMBASE and the Cochrane library. Two reviewers assessed the papers using the specified inclusion criteria, title and abstracts. Studies that were not related to the outcomes of: survival rate, success rate or marginal bone loss of zirconia dental implants were excluded. Results From a total of 1617 titles and abstracts, 33 potentially relevant full text papers were identified. Of these, 18 met the criteria for inclusion in the review. The review revealed heterogeneity between the studies in terms of surgical characteristics, implant characteristics, defining success and measuring marginal bone loss therefore making comparisons between studies difficult. However, in the three randomised control studies included in this review, which compared zirconia implants to titanium implants, the survival rate was lower for zirconia implants, but the success rate and marginal bone loss were found to be similar. Conclusion Overall, initial studies indicate that zirconia dental implants could be a viable alternative to titanium implants but need further well-designed studies need to be carried out to assess their long-term survival rate, success rate and marginal bone loss. At present, zirconia implants should be used with caution but can be an alternative option if a patient has an absolute contraindication to titanium.
Supplementary Table S3 from An LKB1–SIK Axis Suppresses Lung Tumor Growth and Controls Differentiation (2023)

&lt;p&gt;Summaries of GSEA and ssGSEA analyses of human lung adenocarcinoma data sets using previously published signatures of mucinous adenocarcinoma.&lt;/p&gt;
Cerebral Syphilitic Gumma Suspected to have Developed during Primary Syphilis and Treated with Antibiotics in an HIV-Negative Patient (2018)

Cerebral syphilitic gumma is classified as tertiary syphilis. It has become rare owing to antiluetic treatment, but there are some cases reported recently which developed in less than 1 year after the suspected syphilis infection. We report herein on the case of a 41-year-old HIV- negative man who attended our hospital due to convulsions, diagnosed noninvasively as having cerebral syphilitic gumma, and treated effectively during suspected primary syphilis following supposed infection 9 months previously.
Incidence of coronary artery by-pass graft following percutaneous transluminal coronary angioplasty. (1987)

Two hundred fifty eight patients had percutaneous transluminal coronary angioplasty. Of those, 48 cases underwent surgical revascularization for unsuccessful angioplasty. Sex was not a risk factor. Timely surgical revascularization reversed acute ischemia and/or myocardial infarction or limited the size of the infarction in 32 of the 48 patients or 67%. Revascularization procedures were performed in six out of forty-eight patients who had previous aortocoronary by-pass surgery and attempted PTCA, none had any complications. Death occurred in one out of forty-eight patients, or 2%. Femoral-femoral by-pass devices, in addition to intra-aortic balloon devices, should be available in the cardiac catheterization laboratory. Patients with multi-vessel disease are at greater risk of angioplasty and surgery. Sixteen out of 23 patients (70%) who had emergency revascularization procedures had multi-vessel disease. In one patient with borderline renal function, emergency surgery after PTCA with a large amount of renograffin dye injected caused renal failure and led to permanent dialysis.
Utilisation de stics pour la mise en place d'une veille agro-climatique sur internet (2005)

National audience
Effects of Repeated, Long-Duration Hyperoxic Water Immersions on Neuromuscular Endurance in Well-Trained Males (2019)

Repeated, resting, long-duration hyperoxic WIs caused significant reductions to muscular endurance but not to indirect measures of oxygen kinetics in load bearing and non-load bearing muscles.
Renal Blood Monitoring System Using Bio-impedance Measurement:Pilot Study (2020)

The electrical bio-impedance signal obtained from kidney reflects the nature of renal blood circulation. This paper proposed a novel approach that can be used to diagnose the acute kidney allograft rejection, the method based on non-invasive electrical impedance measurement from cutaneous electrodes on skin surface. An appropriate biophysical model has been proposed for the dynamic calculation of electrical resistivity change of kidney, which allows determining the amount of blood per 100 G of kidney tissue. The results of multichannel mapping with different electrode systems had shown electrical impedance signal due to renal blood circulation as well as the effect of the blood filling of the surrounding tissues of the kidney. Achieve an optimal location of the electrode system relative to the projection of the kidney onto the surface of the skin as well as taking into the account the surrounding tissues contribution can improve the measurement accuracy.
Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin (2022)

Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.
Dedication (2003)

In December 2001 Klaus Baberschke celebrated his 65th birthday. In connection with this occasion a four day scientific workshop was held at Wandlitz near Berlin as well as a colloquium at the Freie Universität Berlin. Klaus Baberschke has worked and taught successfully at the FUB for more than 30 years and still continues to do so. 24 invited and 35 contributed papers were presented on subjects related to the role of spin--orbit coupling in condensed matter physics, a topic to which Klaus Baberschke has made many outstanding contributions, starting from g-factors, to crystal field effects and to recent applications of XMCD sum rules. The papers in this special volume reflect some of the many interests of Klaus and also his attitude towards research: high quality and clarity of presentation. They give an outstanding summary of the current state of the art in theory and experiment in this special field of magnetic properties in low dimensional systems. The truly international workshop participation also testifies to the strong scientific links Klaus has enjoyed across the world, an important ingredient for high quality research in the fast evolving field of low dimensional magnetism. The organizers have benefited from many years of successful collaboration and illuminating discussions with Klaus. The work will go on.
Vibrational Spectroscopy of N-Methyliminodiacetic Acid (MIDA)-Protected Boronate Ester: Examination of the B–N Dative Bond (2011)

N-methyliminodiacetic acid (MIDA)-protected boronate esters are a new class of reagents that offer great promise in iterative Suzuki-Miyaura cross-coupling reactions. Compared to earlier reagents, MIDA esters are easily handled and are benchtop stable under air indefinitely. The success of this new species is tied to its unique molecular architecture. Compared to the simpler B-N containing molecules ammonia borane and trimethylamine borane, MIDA esters are much larger, and the sp(3) hybridized boron atom is secured by two five membered rings, making this molecular class stable for spectroscopic study. Here, we present infrared, Raman, and surface enhanced Raman (SERS) spectra of methylboronic acid MIDA ester. Comparisons of the spectroscopic results to those from electronic structure calculations suggest that the B-N stretching mode in this molecule lies in the range 560-650 cm(-1), making it among the lowest energy vibrations observed to date that can be primarily attributed to B-N stretching.
The pedestrian watchmaker: Genetic clocks from engineered oscillators (2009)

The crucial role of time-keeping has required organisms to develop sophisticated regulatory networks to ensure the reliable propagation of periodic behavior. These biological clocks have long been a focus of research; however, a clear understanding of how they maintain oscillations in the face of unpredictable environments and the inherent noise of biological systems remains elusive. Here, we review the current understanding of circadian oscillations using Drosophila melanogaster as a typical example and discuss the utility of an alternative synthetic biology approach to studying these highly intricate systems.
Exercise endurance time as a function of percent maximal power production (1987)

To develop and validate a mathematical model of the relationship between endurance time (T) and power production, 15 male subjects were first tested for maximal power on an instrumented cycle ergometer at 60 rpm. On subsequent days, they were tested for T at various percentages of maximal power. Curves of T as a function of percent maximal power were curvilinear, and could be made to overlap among subjects by individual abscissa scaling, which resulted in the appearance of horizontal stretching or compression of the curves. The degree of stretching-compression was defined by a statistically obtained scaling factor (F) which served to quantify each subject's endurance ability at fractions of maximal power. F was used to transform percent of maximal power to a scaled power variable (Psc). A curve of the form T = a(Psc)b was developed on 10 of the subjects and validated on the remaining five. Correlation between predicted and actual T was 0.967 for the fitting group and 0.980 for the validation group. A maximal power test and a single endurance test at 40 to 50% of maximal power were found to establish individual endurance-power curves fairly well, with a correlation of 0.828 between actual and predicted T. The combination of F and maximal power for a given physical activity provide a useful profile of an individual's ability to perform at constant exercise intensity.
Glenohumeral Pressure With Surface Replacement Arthroplasty Versus Hemiarthroplasty (2014)

It is not known whether significant differences in the glenohumeral center of pressure and contact pressure exist between surface replacement arthroplasty and hemiarthroplasty compared with the native joint. Twelve fresh-frozen cadaveric shoulders were dissected free of soft tissue, and the joint capsule was removed. The scapula was potted with the glenoid parallel to the ground. A pressure-sensitive sensor was placed in the glenohumeral joint, and each specimen was tested in sequence: intact, surface replacement, and hemiarthroplasty. Loading was done with a 440-N compression load at 0.5 Hz with the shoulder in 4 different positions. The center of pressure and contact pressure were measured at each position. The glenohumeral contact pressure with surface replacement was not different from intact pressure in 2 arm positions. Pressure with hemiarthroplasty was significantly different compared with the intact shoulder at all 4 arm positions and compared with the surface replacement group at 2 arm positions (P≤.05). Change in the anterior-posterior center of pressure from intact was significantly smaller with surface replacement compared with hemiarthroplasty with the humerus at 0° flexion/0° abduction and at 0° flexion/90° abduction (1.11±0.89 mm vs 2.38±1.62 mm, P=.02, and 0.68±0.50 mm vs 2.37±2.0 mm, P=.01, respectively). Change in the superior-inferior center of pressure was significantly smaller with surface replacement vs hemiarthroplasty at 0° flexion/0° abduction and at 90° flexion/90° abduction (0.98±1.16 mm vs 2.33±1.38 mm, P=.02, and 1.50±1.28 mm vs 2.90±1.92 mm, P=.04, respectively). Compared with hemiarthroplasty, surface replacement arthroplasty more closely replicated the contact pressure and center of pressure in the intact glenohumeral joint.