gebhart/patrepeval huggingface dataset:
15‐deoxy‐Δ 12,14 ‐prostglandin J 2 (15d‐PGJ 2 ) increases oxidative stress and differentially upregulates hemeoxygenase‐1 (HO‐1) in malignant B cells (2008)

Background: 15‐deoxy Δ‐ 12,14 ‐prostaglandin J 2 (15d‐PGJ 2 ) is an endogenous ligand of peroxisome proliferator‐activator receptorγ (PPARγ ). Treatment of some B cell lymphomas with 15d‐PGJ 2 increases oxidative stress and induces apoptosis. HO‐1 is an oxidative stress‐inducible enzyme but its expression in human B cell lymphomas is unknown. We hypothesized that PPAR ligands induce HO‐1 in malignant B cells. Methods: Ramos and Granta B cell lymphoma cells and 8226 multiple myeloma cells were treated with 15d‐PGJ 2 . HO‐1 protein expression was assessed by western blot. Markers of oxidative stress included mitochondrial superoxide production and generation of reactive oxygen species (ROS). Results: Treatment of Ramos cells with 15d‐PGJ 2 strongly increased ROS and mitochondrial superoxide production and significantly reduced cell viability. Granta and 8226 cells had a similar response to 15d‐PGJ 2 treatment but they exhibited a concentration‐ and time‐dependent increase of HO‐1 expression. Interestingly, Ramos B cells did not up‐regulate HO‐1. Conclusions: The PPARγ ligand 15d‐PGJ 2 induces cell death in some B malignant cell lines and differentially regulates the induction of HO‐1. This suggests that malignant B cells have different anti‐oxidant defense mechanisms. Research supported by DE011390, ES01247, The Leukemia and Lymphoma Society and the Lymphoma Research Foundation.
Fe3O4@SiO2 Nanoparticles Functionalized with Gold and Poly(vinylpyrrolidone) for Bio-Separation and Sensing Applications (2018)

Large Fe3O4@SiO2 nanoparticles (∼200 nm) functionalized with gold and poly(vinylpyrrolidone) have been synthesized, characterized, and evaluated for bioseparation and sensing applications. The particles have been characterized using a combination of experimental techniques including ultraviolet visible spectroscopy, energy-dispersive spectroscopy, powder X-ray diffraction, Fourier transform infrared spectroscopy, electron microscopy, superconducting quantum interference device magnetrometry, and surface-enhanced Raman sensing (SERS) spectroscopy. The particles have a unique surface morphology comprised of roughened gold nodules. The surface coatings prevent oxidation and render the particles easy to functionalize in order to target a wide range of moieties. The gold coverage is not only uniform across the entire particle surface but also ultrathin so as to maintain a high percentage of the cores magnetic saturation (∼68%) when compared to that of bare magnetite. The gold nodules facilitate the generation of hot spots that enhance the electromagnetic field associated with the particle surface and are therefore useful in sensing applications like SERS, and the strong magnetic core allows for rapid separation (∼30 s) of target molecules from solution once they are bound to the particles.
Neural network analysis of rose straightness (1993)

A computer vision system has been developed to classified roses by analysis of their quality on a digital image. A neural network has been developed to estimate straightness and compare it with a Bayes classifier. / Un système de vision par ordinateur a été développé pour classifier les roses par analyse de leur qualité sur une image digitalisée. Un réseau de neurones a été mis au point pour évaluer la rectitude et la comparer avec un classificateur Bayes.
Colmade: Collaborative Masking in Auditable Decryption for BFV-based Homomorphic Encryption (2022)

This paper proposes a novel collaborative decryption protocol for the Brakerski-Fan-Vercauteren (BFV) homomorphic encryption scheme in a multiparty distributed setting, and puts it to use in designing a leakage-resilient biometric identification solution. Allowing the computation of standard homomorphic operations over encrypted data, our protocol reveals only one least significant bit (LSB) of a scalar/vectorized result resorting to a pool of N parties. By employing additively shared masking, our solution preserves the privacy of all the remaining bits in the result as long as one party remains honest. We formalize the protocol, prove it secure in several adversarial models, implement it on top of the open-source library Lattigo and showcase its applicability as part of a biometric access control scenario.
ACS Chemical Neuroscience Molecule Spotlight on Savella (2010)

Savella (milnacipran), a selective serotonin and noradrenaline reuptake inhibitor, was approved by the FDA on January 14th, 2009, for the treatment of fibromyalgia.
High resolution contrast-enhanced magnetic resonance angiography of carotid arteries using an array coil on a cardiovascular scanner (2000)

3D contrast-enhanced MR angiography (CE-MRA) of the carotid arteries is technically challenging despite its increasing clinical use. Spatial resolution remains to be limited by the contrast agent bolus concentration's transient nature, rapid venous enhancement, and voxel size of the acquisition matrix. in order for carotid CE-MRA to be considered an adequate alternative or replacement to X-ray angiography, it is our perspective that isotropic high resolution carotid CE-MRA is crucial which can reveal details of pathology in reformat and maximum-intensity-projection post processing. Also in carotid CE-MRA an accurate timing for image acquisition is essential. This has been addressed with real-time fluoroscopic triggering, smart-prep time-resolved acquisition, and test bolus techniques. The purpose of this study is to use smart-prep CE-MRA technique with a combined head-neck-cervical spine neurovascular array coil on a dedicated 1.5 T cardiovascular scanner, to acquire isotropic high resolution CE-MRA from the aortic arch through circle of Willis within a single bolus contrast acquisition in a routine clinical setting.
FERMI (2011)

The demand for increased spectral efficiencies is driving the next generation broadband access networks towards deploying smaller cells (femtocells) with sophisticated air interface technologies (Orthogonal Frequency Division Multiple Access or OFDMA). The projected dense deployment of femtocells however, makes interference and hence resource management both critical and extremely challenging. In this paper, we design and implement one of the first resource management systems, FERMI, for OFDMA-based femtocell networks. As part of its design, FERMI (i) provides resource isolation in the frequency domain (as opposed to time) to leverage power pooling across cells to improve capacity; (ii) uses measurement-driven triggers to intelligently distinguish clients that require just link adaptation from those that require resource isolation; (iii) incorporates mechanisms that enable the joint scheduling of both types of clients in the same frame; and (iv) employs efficient, scalable algorithms to determine a fair resource allocation across the entire network with high utilization and low overhead. We implement FERMI on a prototype four-cell WiMAX femtocell testbed and show that it yields significant gains over conventional approaches.
ChemInform Abstract: SIMPLE ROUTE TO 6,7,8,9‐TETRAHYDRODIBENZO(B,F)THIEPIN‐11(10H)‐ONES (1984)

Abstract Die Kondensation von Thiophenolen (I) mit Z‐Oxocyclohexylessigsäureethylester (II) führt zu Sulfiden (III), die nach Verseifung zu Hexahydrodibenzothiepinen (V) cyclisiert werden.
Joint Multiple Testing Procedures for Graphical Model Selection with Applications to Biological Networks (2009)

Gaussian graphical models have become popular tools for identifying relationships between genes when analyzing microarray expression data. In the classical undirected Gaussian graphical model setting, conditional independence relationships can be inferred from partial correlations obtained from the concentration matrix (= inverse covariance matrix) when the sample size n exceeds the number of parameters p which need to estimated. In situations where n &lt; p, another approach to graphical model estimation may rely on calculating unconditional (zero-order) and first-order partial correlations. In these settings, the goal is to identify a lower-order conditional independence graph, sometimes referred to as a ‘0-1 graphs’. For either choice of graph, model selection may involve a multiple testing problem, in which edges in a graph are drawn only after rejecting hypotheses involving (saturated or lower-order) partial correlation parameters. Most multiple testing procedures applied in previously proposed graphical model selection algorithms rely on standard, marginal testing methods which do not take into account the joint distribution of the test statistics derived from (partial) correlations. We propose and implement a multiple testing framework useful when testing for edge inclusion during graphical model selection. Two features of our methodology include (i) a computationally efficient and asymptotically valid test statistics joint null distribution derived from influence curves for correlation-based parameters, and (ii) the application of empirical Bayes joint multiple testing procedures which can effectively control a variety of popular Type I error rates by incorpo- rating joint null distributions such as those described here (Dudoit and van der Laan, 2008). Using a dataset from Arabidopsis thaliana, we observe that the use of more sophisticated, modular approaches to multiple testing allows one to identify greater numbers of edges when approximating an undirected graphical model using a 0-1 graph. Our framework may also be extended to edge testing algorithms for other types of graphical models (e.g., for classical undirected, bidirected, and directed acyclic graphs).
Air cavity low-loss transmission lines for high speed serial link applications (2011)

This paper reports on the design, optimization, processing and measurement of an air-cavity transmission line structure on FR-4 boards for high-speed chip-to-chip links. The proposed structure has air as the insulating material, thereby minimizing the dielectric loss. Full-wave electromagnetic simulation is used to predict the performance of the proposed air-cavity structure. Compared to conventional transmission lines on an FR4 substrate, the effective dielectric constant is reduced by 25% from 2.75 to 2.07, and the dielectric loss is reduced by 26% from 0.48 dB/cm (1.22 dB/inch) to 0.35 dB/cm (0.9 dB/inch) at 20 GHz. Simulation also shows that conductor surface roughness contributes significant loss, which is confirmed by the measurement results. An active low power electrical link demonstration is also reported herein. The transmitter (TX) utilizes a 1-tap feed-forward-equalization (FFE) for pre-cursor cancellation and the receiver (RX) a 1-tap decision-feedback-equalization (DFE) for post-cursor cancellation. The TX and RX frontends implement a current-sharing scheme to reduce the overall link power consumption. The circuitry and interconnect were co-designed to achieve 6.25 Gb/s at ~0.6 mW/Gb/s (or 0.6 pJ/bits) in 0.13 μm 1.2V CMOS process.
Relaxometry of lens homogenates. II. temperature dependence and comparison with other proteins (1989)

We have extended our earlier work (C.F. Beaulieu, J.I. Clark, R.D. Brown III, M. Spiller, and S.H. Koenig, Magn. Reson. Med. 8, 45 (1988] on the magnetic field dependence of 1/T1 (NMRD profiles) of calf lens nuclear homogenates, at 25 degrees C, to 5 degrees C, and to other protein systems as well. These include concentrated solutions of myoglobin and bovine serum albumin, both globular proteins, the first compact and roughly spherical, the other extended, flexible, and with weak internal bonding; chicken lens homogenate, for which the dominant crystallins (lens proteins) are approximately 70% alpha-helical compared with calf crystallins, which are essentially all beta-sheet; and hen egg white, both native and heat-denatured. Our earlier conjectures regarding a reversible change in protein organization of the calf lens crystallins as a function of solute protein concentration is given added support. Our findings suggest that cytoplasmic homogenate can be characterized as a heterogeneous and polymorphic solution of crystallins. At high concentrations the NH moieties of the protein backbone become accessible to solvent with water (not NH proton) exchange rates greater than 10(4) s-1. This conclusion is based on two aspects of the observed NMRD profiles. At low crystallin concentration, the profiles of calf and chicken lens homogenates are similar in form to those of myoglobin and native hen egg white, a form that has been studied previously for a range of diamagnetic globular proteins and has been demonstrated to arise from the rotational thermal motion of the solute molecules. At high crystallin concentrations, the NMRD profiles of the lens homogenates develop a monotonic background (high rates at low fields), much like that of the heat-denatured egg-white sample and those of most tissues. In addition, there is a set of peaks in the central part of the profiles of the concentrated crystallins, seen also in the denatured egg white and some tissues but not in the myoglobin sample, which is known to arise from cross-relaxation interactions between the water protons and (through the intermediary of the NH proton) the 14N quadrupolar levels. The magnitude of these peaks, which is larger by an order of magnitude for native calf lens homogenates than for any tissue, requires that the majority of the NH moieties be accessible to water. Finally, going to 5 degrees C for the native calf lens homogenate takes the sample below the temperature of reversible phase separation, and it becomes opaque.(ABSTRACT TRUNCATED AT 400 WORDS)
A small, portable RNA device for the control of exon skipping in mammalian cells (2018)

Splicing is an essential and highly regulated process in mammalian cells. We developed a synthetic riboswitch that efficiently controls alternative splicing of a cassette exon in response to the small molecule ligand tetracycline. The riboswitch was designed to control the accessibility of the 3' splice site by placing the latter inside the closing stem of a conformationally controlled tetracycline aptamer. In the presence of tetracycline, the cassette exon is skipped, whereas it is included in the ligand's absence. The design allows for an easy, context-independent integration of the regulatory device into any gene of interest. Portability of the device was shown through its functionality in four different systems: a synthetic minigene, a reporter gene and two endogenous genes. Furthermore, riboswitch functionality to control cellular signaling cascades was demonstrated by using it to specifically induce cell death through the conditionally controlled expression of CD20, which is a target in cancer therapy.
MCG simulations of myocardial infarctions with a realistic heart-torso model (1998)

Data from simulations of the anterior myocardial infarction (AMI) and inferior myocardial infarction (IMI) are presented. One infarct located in the anterior section of the left ventricle and a second one in the inferior wall of the left ventricle were modeled. A high-resolution finite element model of a heart and torso was used in this study. Differences in the normal and infarcted fields were computed. Our data suggest that the infarcted region contribution to the total magnetic field can be accounted for by an equivalent current dipole. It might also be possible to detect an infarct from these difference fields constructed for different cases of myocardial infarction. More simulations are needed to determine the relations between infarct sizes and locations and magnetic fields. These relations might then be used to detect various cases of myocardial infarction.
Dynamic Disruptions in Nuclear Envelope Architecture and Integrity Induced by HIV-1 Vpr (2001)

Human immunodeficiency virus-1 (HIV-1) Vpr expression halts the proliferation of human cells at or near the G2 cell-cycle checkpoint. The transition from G2 to mitosis is normally controlled by changes in the state of phosphorylation and subcellular compartmentalization of key cell-cycle regulatory proteins. In studies of the intracellular trafficking of these regulators, we unexpectedly found that wild-type Vpr, but not Vpr mutants impaired for G2 arrest, induced transient, localized herniations in the nuclear envelope (NE). These herniations were associated with defects in the nuclear lamina. Intermittently, these herniations ruptured, resulting in the mixing of nuclear and cytoplasmic components. These Vpr-induced NE changes probably contribute to the observed cell-cycle arrest.
5G-ENSURE D2.4: Security Architecture (draft) (2016)

This deliverable (D2.4) of the 5G-ENSURE project describes a draft security architecture for 5G networks. The focus lies on a logical and functional architecture and omits (most) aspects related to physical/deployment architecture. This focus is motivated by general trends such as network de-perimetrization as well as 5G systems’ strong dependency on software defined networking and virtualization in general. Furthermore, this focus has reduced the otherwise strong interdependency between this architecture task and the trust modelling and risk analysis tasks in 5G-ENSURE. Still, each of these three tasks have at the time of writing produced initial draft documents, which will then be re-used in a second iteration of all three tasks, producing updated, final versions.
In Situ Tumor Ablation Creates an Antigen Source for the Generation of Antitumor Immunity (2004)

Abstract Tumor-destructing techniques, like radiofrequency ablation (RFA), allow eradication of large tumors. Potentially, in situ tumor destruction also can provide the immune system with an antigen source for the induction of antitumor immunity. Antigen-presenting cells could take up antigens in the periphery after which they induce specific immune responses. Recent data show that especially antigen-presenting dendritic cells are crucial for the induction of potent immune responses. However, virtually nothing is known regarding the induction of immune responses after in situ tumor destruction in mice or humans. We used the well-defined murine B16-OVA melanoma cell line to develop a novel tumor model to explore: (a) the immunologic consequences of in situ tumor destruction; and (b) the efficacy of a combination approach of tumor destruction and immunostimulation. Applying this model system we demonstrate that following RFA, a weak but detectable immune response develops, directed against OVA, but also against a broader range of B16 antigens. Adoptive transfer experiments further indicate that antitumor reactivity can be transferred to naïve mice by splenocytes. To augment the response observed, we administered a blocking monoclonal antibody against cytotoxic T-lymphocyte-associated antigen 4 at the time of tumor destruction. Interestingly, this strongly enhanced antitumor immunity, resulting in long-lasting tumor protection. These results illustrate that in situ tumor destruction can provide a useful antigen source for the induction of antitumor immunity, provided that additional immunostimulatory signals are coadministered.
Differential branching fraction and angular analysis of the B + → K + μ + μ − decay (2013)

A bstract The angular distribution and differential branching fraction of the decay B + → K + μ + μ − are studied with a dataset corresponding to 1.0fb −1 of integrated luminosity, collected by the LHCb experiment. The angular distribution is measured in bins of dimuon invariant mass squared and found to be consistent with Standard Model expectations. Integrating the differential branching fraction over the full dimuon invariant mass range yields a total branching fraction of $ \mathcal{B} $ ( B + → K + μ + μ − ) = (4 . 36 ± 0 . 15 ± 0 . 18) × 10 −7 . These measurements are the most precise to date of the B + → K + μ + μ − decay.
Evaluation of Amino-Oxyacetic Acid as a Palliative in Tinnitus (1990)

Amino-oxyacetic acid (AOAA) was evaluated as a palliative in tinnitus. Sixty-six patients with tinnitus presumed to be of cochlear origin were given either a placebo or 75 mg of AOAA four times a day for 1 week. Response was evaluated by both audiometric measurement of tinnitus loudness and subjective rating by patients of change or no change in tinnitus severity. Because loudness measurements and self-rating have not been shown to be independent, and since the aim of clinical treatment of tinnitus is the alleviation of subjective distress, greater weight was given to the patient's self-rating. A total of 21 % of all patients reported a subjective decrease in tinnitus severity, usually within 3 to 4 days after the start of AOAA use. Patients with tinnitus caused by presbycusis or Meniere's disease were the most likely to respond to AOAA treatment with a reduction in tinnitus severity, whereas those with drug-induced tinnitus were the least likely to respond. Nausea and dysequilibrium were the most common side effects of AOAA use. Of the 21 % of patients who responded to AOAA, 71 % developed some type of side effect. Amino-oxyacetic acid produces a reduction in the severity of tinnitus in about 20% of patients; however, the incidence of side effects makes the drug unacceptable for clinical use.
Figure 6 from A Comparative Study of Neuroendocrine Heterogeneity in Small Cell Lung Cancer and Neuroblastoma (2023)

&lt;p&gt;Similar and distinct NE score–associated therapeutic sensitivity in SCLC and neuroblastoma cell lines. &lt;b&gt;A,&lt;/b&gt; Correlation between NE scores and therapeutic sensitivity for drugs with selected targets. Therapeutic sensitivity data were previously harmonized such that a higher value represents more resistance in each study. For each of the nine selected targets, all compounds with the same target were identified from multiple studies. Pearson correlation coefficient &lt;i&gt;r&lt;/i&gt; from correlating compound data with NE scores were calculated for neuroblastoma lines (&lt;i&gt;x&lt;/i&gt;-axis values) and SCLC lines (&lt;i&gt;y&lt;/i&gt;-axis values), respectively and visualized as a scatter plot, with colors annotating the source of data, and transparency annotating the statistical significance. &lt;b&gt;B,&lt;/b&gt; Meta-analysis–summarized correlation between drug therapeutic sensitivity and NE scores in neuroblastoma (&lt;i&gt;x&lt;/i&gt;-axis) and SCLC (&lt;i&gt;y&lt;/i&gt;-axis) cell lines. Note that high NE scores are associated with resistance to inhibitors of LCK, MEK, XIAP, mTOR, HSP90, and Abl, and sensitivity to BCL inhibitors. NE scores are associated with resistance to BRD inhibitors in neuroblastoma but not SCLC whereas microtubule inhibitors resistance correlates with high NE scores in SCLC but not neuroblastoma cell lines.&lt;/p&gt;
Sustained oscillations in free-energy state and hexose phosphates in yeast. (1996)

In a population of intact cells of the yeast Saccharomyces cerevisiae the dynamics of glycolytic metabolism were investigated under the condition of sustained oscillations. At 5-s intervals cells were quenched in -40 degrees C methanol, extracted and the intracellular concentrations of glycolytic metabolites, adenine nucleotides and phosphate were analysed. Oscillations were found for the glycolytic intermediates glucose 6-phosphate, fructose 6-phosphate and fructose 1,6-bisphosphate. At variance with earlier reports on transient glycolytic oscillations, some intermediates further down the glycolytic pathway did not oscillate significantly, even though NADH did. In addition, the adenylate energy charge and the free energy of ATP hydrolysis oscillated significantly. Dynamic coupling through the latter may be responsible for this effective compartmentation of glycolytic dynamics.