gebhart/patrepeval huggingface dataset:
Interactions of Bacterial Quorum Sensing Signals with Model Lipid Membranes: Influence of Membrane Composition on Membrane Remodeling (2022)

We report the influence of membrane composition on the multiscale remodeling of multicomponent lipid bilayers initiated by contact with the amphiphilic bacterial quorum sensing signal <i>N</i>-(3-oxo)-dodecanoyl-l-homoserine lactone (3-oxo-C12-AHL) and its anionic headgroup hydrolysis product, 3-oxo-C12-HS. We used fluorescence microscopy and quartz crystal microbalance with dissipation (QCM-D) to characterize membrane reformation that occurs when these amphiphiles are placed in contact with supported lipid bilayers (SLBs) composed of (i) 1,2-dioleoyl-<i>sn</i>-glycero-3-phosphocholine (DOPC) containing varying amounts of cholesterol or (ii) mixtures of DOPC and either 1,2-dioleoyl-<i>sn</i>-glycero-3-phosphoethanolamine (DOPE, a conical zwitterionic lipid) or 1,2-dioleoyl-<i>sn</i>-glycero-3-phospho-l-serine (DOPS, a model anionic lipid). In general, we observe these mixed-lipid membranes to undergo remodeling events, including the formation and subsequent collapse of long tubules and the formation of hemispherical caps, upon introduction to biologically relevant concentrations of 3-oxo-C12-AHL and 3-oxo-C12-HS in ways that differ substantially from those observed in single-component DOPC membranes. These differences in bilayer reformation and their associated dynamics can be understood in terms of the influence of membrane composition on the time scales of molecular flip-flop, lipid packing defects, and lipid phase segregation in these materials. The lipid components investigated here are representative of classes of lipids that comprise both naturally occurring cell membranes and many useful synthetic soft materials. These studies thus represent a first step toward understanding the ways in which membrane composition can impact interactions with this important class of bacterial signaling molecules.
Three-Parameter Kinematic Theory for Shear Behavior of Continuous Deep Beams (2014)

peer reviewed
Towards the development of a high-sensitivity cryogenic phased array feed (2014)

A cryogenic phased array feed operating at L-band is in development for the Green Bank Telescope (GBT). The feed consists of electrically small feed elements optimized for active impedance matching to cooled front end low noise amplifiers (LNAs), down-converters, a real-time streaming data acquisition system, and beamforming algorithms applied in post-processing. A prototype cryogenic array feed was recently tested on the GBT. This results will be an important step towards the development of a new receiver instrument, the focal L-band array for the GBT (FLAG).
Epstein‐Barr Virus in Head and Neck Cancer Assessed by Quantitative Polymerase Chain Reaction (2004)

In the overwhelming majority of head and neck cancers in this North American cohort, EBV did not appear to contribute to growth of a dominant clonal population with integrated EBV genome and was unlikely to be a genetic etiological agent in tumor development. The low quantities of EBV detected in a minority of head and neck cancers may be related to the presence of EBV genome in rare lymphoid or epithelial cells adjacent to the primary head and neck cancer.
Factors Affecting Surfactant Modification of Solid Media for Removal of Oxo Ions (2013)

In search of new, inexpensive, and green materials that exhibit ion-exchange properties suitable for removal of oxo anions from water, researchers have examined approaches that involve surface modification of existing commercially available sorbent media with positively charged surfactants. When compared to ion-exchange media, these approaches have demonstrated satisfactory promise in the removal of oxo anions for a fraction of the cost of commercially available ion-exchange media. The concept involves reversing the negative surface charge to a positive one using surfactants with positively charged groups similar to those found in ion-exchange resins. The efficiency of the ion-exchange process is closely related to a number of factors that could affect the surfactant modification of solid sorbent media for removal of oxo ions. The most important factors are: (1) the specific surface area of the sorbent media; (2) the surface charge/ion exchange capacity of the sorbent media; (3) the porosity and pore size distribution of the sorbent media; and (4) the surfactant properties. During research, the importance of some of these factors is often neglected, which may lead to unrealistic performance results for the media. Therefore, it is important to identify critical factors that could potentially lead to unrealistic experimental results and other misconceptions related to the performance of oxo anion removal from water by surfactant-modified media.
Special-Use Domain Names Problem Statement (2017)

The policy defined in RFC 6761 for IANA registrations in the Special-
Use Domain Names registry has been shown, through experience, to
present challenges that were not anticipated when RFC 6761 was
written. This memo presents a list, intended to be comprehensive, of
the problems that have since been identified. In addition, it reviews
the history of domain names and summarizes current IETF publications
and some publications from other organizations relating to Special-Use
Domain Names. This document should be considered required reading for
IETF participants who wish to express an informed opinion on the topic
of Special-Use Domain Names.
Line-narrowing approaches to solid state NMR imaging: pulsed gradients and second averaging (1990)

Abstract There are questions in materials sciences which can be addressed by NMR imaging. However, not all materials exhibit sufficient molecular motion to reduce dipolar couplings to the level at which the familiar techniques of medical NMR imaging are appropriate. For the more general case of these less mobile materials, line-narrowing methods, specialized to imaging, are appropriate. We have earlier demonstrated that such imaging sequences adequately overcome the fundamental dipolar broadening in engineering polymers; however, these sequences are subject to certain practical limitations which we address. We present a class of homonuclear line-narrowing imaging methods which intercalate short gradient pulses ( ca. 5 ps) into the RF pulse sequence. Such a strategy improves spatial resolution and signal sensitivity by reducing extraneous broadening from off-resonance effects. In a further implementation, the chemical shift and susceptibility terms in the spin hamiltonian are suppressed by ‘second averaging’ about a particular axis, while the hamiltonian for the gradient pulses is aligned along that axis: the result is a further improvement in spatial resolution. Prospects for the future of solid state NMR imaging are considered.
<title>Coherent Optical Implementation Of Generalized Two-Dimensional Transforms</title> (1978)

A coherent optical method capable of performing arbitrary two-dimensional linear transformations has recently been studied, in which transform coefficients are given by two-dimensional inner products of the input image and a set of basis functions. Since the inner product of two functions is equal to the value of their correlation when there is zero shift between the functions, it is possible to use an optical correlator to solve for the coefficients of the transform. By using random phase masks in the input and the filter planes of the correlator, we have been able to pack many coefficients close together in the output plane, and thus take better advantage of the space-bandwidth product of the optical system. Both the input random phase mask and the spatial filter are computer-generated holographic elements, created by a computer-controlled laser beam scanner. The system can be &quot;programmed&quot; to perform arbitrary two-dimensional linear transformations. For demonstration, the set of two-dimensional Walsh functions was chosen as a transform basis. When the resolution of the Walsh functions was limited to 128 x 128, up to 256 transform coefficients were obtained in parallel. The signal-to-noise and accuracy of the transform coefficients were compared to the theory.
Recombinant human hexamer-dominant IgM monoclonal antibody to Ganglioside GM3 for treatment of melanoma (2008)

2406 Ganglioside GM3 is the most common ganglioside found on human melanoma cells. It is expressed at much higher densities and frequencies on melanoma cells than on normal cells. A human B-lymphoblastoid cell line that was established by immortalization of human B-cells by Epstein-Barr virus produces a human IgM antibody to GM3 (L612). L612 binds to GM3 and kills GM3-positive human melanoma cells in the presence of complement. L612 has been shown to be effective in some patients with late-stage melanoma. L612 consists of hexameric IgM (~20%), pentameric IgM (~74%), and other minor IgM molecules. Because hexameric IgMs have been shown to activate complement more effectively than pentameric IgMs, we tested whether hexameric L612 plays a dominant role in the antitumor activity. Chinese hamster ovary (CHO) cells were transfected with L612 heavy (H)- and light (L)-chain genes, with or without the joining (J)-chain gene, that resulted in generation of pentamer dominant- and hexmaner dominant-IgM, respectively. Recombinant IgM secreted from CHO cells without the joining chain (designated CA19) was ~80% hexameric, whereas recombinant IgM secreted from CHO cells transfected with joining-chain genes (designated CJ45) was ~90% pentameric. CA19 and CJ45 were compared for their anti-melanoma activities by in vitro and in vivo experiments. Both CA19 and CJ45 IgMs caused complement-dependent cytotoxicity (CDC) against GM3 rich M-1 human and B16F10 mouse melanoma cell lines, but the amount of CA19 required for 50% specific cytotoxicity was 5 to 10 times smaller as compared to that of CJ45. Neither L612 nor its two recombinant forms (CA19 and CJ45) induced CDC against a GM3-negative A549 lung cancer cells, showing an antigen-specific binding and killing by these antibodies.  The in vivo antitumor effects of the recombinant IgMs were evaluated using B16F10 cell line in a nude rat xenograft model. The nude rat’s complement had been shown to be as effective as human complement with respect to induction of CDC by these human IgM antibodies against the mouse melanoma. Intravenous injection of CA19 compared with CJ45 or native L612 elicited more profound antitumor activity in nude rats bearing B16F10 xenograft. Compared to vehicle, CA19, CJ45, and L612 prolonged survival by 238%, 162%, and 155%, respectively. These results suggest that a hexamer-dominant human IgM against GM3 may provide a more potent treatment option for GM3-positive melanoma.
Modeling of Reactive Filling in Complex Cavities*** (1991)

Abstract The flow of reacting monomers into thin planar cavities of irregular geometry is analyzed. The Hele-Shaw approximations are used to simplify the momentum and mass balances. At each time step, the flow domain is mapped onto a rectangular domain using elliptic expressions. The transformed governing equations are solved using finite-differences. The transient three-dimensional energy and species balances are solved using an explicit marching scheme coupled to the flow. Viscosity is modeled as a function of temperature and extent of reaction. Castro's model is used to compare several fountain flow approximations. A simplified algorithm was found to capture the essence of the fountain flow kinematics. The fountain flow approximations described here can also be used in thermoplastic injection molding modeling. Results for a rectangular end gated mold and for an irregular mold geometry are presented.
Thrombocytopenia in neonates and the risk of intraventricular hemorrhage: a retrospective cohort study (2011)

Although IVH ≥ grade 2 occurs more often in neonates with thrombocytopenia, this relation is independent of the severity of thrombocytopenia. Prospective studies should be conducted to assess the true risk of hemorrhage depending on underlying conditions. Randomized controlled trials are urgently needed to determine a safe lower threshold for platelet transfusions.
Detection and retrieval of cysts in joint ultrasound B-mode and elasticity breast images (2010)

Distinguishing cysts from other tumors is a routine clinical practice for diagnosing breast cancer. It has shown that more accurate diagnosis can be achieved by combining elasticity images with traditional B-mode ultrasound images. In this paper, we propose a fully automatic system to detect cysts jointly in both B-mode and elasticity images. It is based on database-guided techniques that learn the knowledge of cyst appearance automatically from B-mode and elasticity images in a database. Further, for a detected cyst in a query image, the cysts with similar image appearance in the database are retrieved to improve diagnostic accuracy and confidence. In the experiment, we show that our system achieves high sensitivity and specificity in cyst diagnosis.
Laser photodecomposition of sintered YBa2Cu3O6+x: Ejected species population distributions and initial kinetic energies for the laser ablation wavelengths 351, 248, and 193 nm (1991)

We present experimental results of photoablated product and kinetic energy (KE) distributions from the ultraviolet laser ablation of a sintered YBa2Cu3O6+x wafer at the laser wavelengths 351, 248, and 193 nm. Data is presented which spans the laser fluence range beginning at the threshold for species ejection (50 mJ/cm2) to nearly that required for the formation of an above surface plasma (800 mJ/cm2). The goal of this experiment was to measure changes in the photophysical process as the incident laser fluence was increased above the threshold value. Our results show, that near the laser threshold fluence, the photoejected products consist of small atomic and oxide species. An unforeseen result for the UV laser wavelengths used, is the lack of CuO+/CuO and free oxygen (O+/O, O+2/O2) in the mass spectrum. In addition, the product distributions are dependent on the laser wavelength. Measured also, at laser threshold fluence, are the nascent photoejected cation kinetic energy distribution. Here our results show that the KE distribution is independent of both the laser fluence and the wavelength. The mean kinetic energy, 〈KE〉, exceeds 3 eV and cannot be explained by a thermal excitation process. With increasing laser fluence (50% above threshold), we detected the photodissociation of the ejected oxide species, and the appearance of the O− anion. Unlike the KE of the cation species, the O− kinetic energy is nearly thermal (&amp;lt;1 eV). With additional increases in the laser fluence, we measure the photoejection of slow KE neutral species and the simultaneous KE enhancement of the laser ablated ions (KE≳30 eV). At the highest laser fluences used in this experiment, it was noted that atomic cluster formations were enhanced. These compounds are presumably formed in the expanding ablated plume. In summary, our results show that, at threshold laser fluences, the photoejection process is via non thermal excitation. With increasing laser fluence the ejected species mass spectrum includes products from the plume photolysis and the plume chemistry.
Effects of Targeted Delivery of Metformin and Dental Pulp Stem Cells on Osteogenesis via Demineralized Dentin Matrix under High Glucose Conditions (2020)

High glucose condition inhibited osteoblast differentiation could be a main mechanism contributing to the decreased bone repair associated with diabetes. Metformin, a widely prescribed antidiabetic drug, was shown to have osteogenic properties in our previous study. Transplanted mesenchymal stromal cells (MSCs) may differentiate into osteoblasts and promote bone regeneration. Our study aimed to combine the benefits of metformin and MSCs transplantation on osteogenesis in high glucose conditions. We developed demineralized dentin matrix (DDM) as a carrier to target deliver metformin and dental pulp-derived MSCs (DPSCs). We collected clinically discarded teeth, isolated DPSCs from the dental pulp, and prepared the DDM from the dentin. The DDM was observed by scanning electron microscopy and was found to have well-distributed tubes. Then, metformin was loaded into the DDM to form the DDM-Met complex (DDM-Met); DDM-Met released metformin at a favorable concentration. The DPSCs seeded with the DDM-Met in a high glucose medium showed satisfactory attachment and viability together with increased mineralization and upregulated osteogenesis-related genes, including alkaline phosphatase (ALP), osteocalcin (OCN), runt-related transcription factor 2 (Runx2), and osteopontin (OPN). A possible mechanism of the enhanced osteogenic differentiation of DPSCs was explored, and the adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) pathway was found to play a role in the enhancement of osteogenesis. DDM-Met appeared to be a successful metformin and DPSC carrier that allowed for the local delivery of metformin and DPSCs in high glucose conditions. DDM-Met-DPSC construct has promising prospects to promote osteogenesis and enhance the much-needed diabetic bone regeneration.
Using eye contact and contextual speech recognition for hands-free surgical charting (2008)

In this paper we discuss ongoing research into applications for multimodal Attentive User Interfaces in hands-free charting during surgical procedures. Although speech recognition has matured enough that it can now be used for some software and hardware control, speech recognition solutions still have trouble filtering ldquocommand speechrdquo from ldquoambient speech.rdquo Our research builds on previous research that couples eye contact sensing with speech recognition to gauge intent. Users enable a voice activation system used for surgical time charting by fixing their gaze on a small camera before speaking command words.
[Angiogenesis: prognostic marker in prostatic cancer]. (1999)

Angiogenesis, the formation of new blood vessels, has been suggested to provide important prognostic information in prostate cancer. The aim of this study was to investigate, whether microvessel density (MVD) at diagnosis was correlated with disease-specific survival in a non-curative treated population of prostate cancer patients. MVD was immunohistochemically (factor VIII-related antigen) quantified in archival tumours obtained at diagnosis in 221 prostate cancer patients. The maximal MVD was quantified inside a 0.25 mm2 area of the tumour and the median MVD was 43 (range 16-151). MVD was statistically significantly correlated with clinicopathological characteristics and disease-specific survival. A multivariate analysis demonstrated that MVD was a significant predictor of disease-specific survival in the entire cancer population, as well as in the clinically localized cancer population. These findings suggest that quantitation of angiogenesis reflects the spontaneous clinical outcome of prostate cancer.
Optical observation of energy loss distribution and practical range of positrons from a water solution in a water‐equivalent phantom (2009)

The energy loss distribution of beta+ particles is closely related to their maximum penetration depth distribution and annihilation point distribution. The latter is of practical importance for positron emission tomography. Experimental data related to the energy loss distribution are important for comprehensive validation of physics and simulation models of beta+ interactions. In this paper the authors present a new experimental approach that allows them to visually observe the beta+ energy loss distribution of a solution of nuclear medicine radioisotopes in a plastic scintillator using an optical camera. The authors also report a set of the first experimental results. A water solution of 18F was localized in a small hole in a plastic scintillator (BC430). Optical imaging of the scintillator yielded visual images of the energy loss distribution with a submillimeter resolution. The radial dependence in the energy distribution was quantitatively measured by analysis of the images, and exponential fitting parameters were obtained. The authors observed that the results of Monte Carlo simulation with EGS5 (version 1.0.2) and GEANT4 (version 4.9.01.p01) were consistent with those obtained experimentally. The results of the Monte Carlo simulation indicated that for a linear scale, the energy loss distribution in the scintillator was approximately the same as that in water, and the relative shape of the energy loss distribution was close to those of the maximum penetration depth distribution and annihilation point distribution. This paper also presents discussions about the further possibilities of this optical imaging approach. Thus, optical observation of the beta+ energy loss distribution in a scintillator is a promising technique for visual and quantitative experimental studies of beta+ emission from a solution of radioisotopes that are used in nuclear medicine.
Supplementary Table 1 from Characterization of Torin2, an ATP-Competitive Inhibitor of mTOR, ATM, and ATR (2023)

&lt;p&gt;PDF file - 401K&lt;/p&gt;
Faculty Opinions recommendation of Nivolumab and Ipilimumab as Maintenance Therapy in Extensive-Disease Small-Cell Lung Cancer: CheckMate 451. (2021)

PURPOSE: In extensive-disease small-cell lung cancer (ED-SCLC), response rates to first-line platinum-based chemotherapy are robust, but responses lack durability. CheckMate 451, a double-blind phase III trial, evaluated nivolumab plus ipilimumab and nivolumab monotherapy as maintenance therapy following first-line chemotherapy for ED-SCLC.METHODS: Patients with ED-SCLC, Eastern Cooperative Oncology Group performance status 0-1, and no progression after ≤ 4 cycles of first-line chemotherapy were randomly assigned (1:1:1) to nivolumab 1 mg/kg plus ipilimumab 3 mg/kg once every 3 weeks for 12 weeks followed by nivolumab 240 mg once every 2 weeks, nivolumab 240 mg once every 2 weeks, or placebo for ≤ 2 years or until progression or unacceptable toxicity. Primary end point was overall survival (OS) with nivolumab plus ipilimumab versus placebo. Secondary end points were hierarchically tested.RESULTS: Overall, 834 patients were randomly assigned. The minimum follow-up was 8.9 months. OS was not significantly prolonged with nivolumab plus ipilimumab versus placebo (hazard ratio [HR], 0.92; 95% CI, 0.75 to 1.12; P = .37; median, 9.2 v 9.6 months). The HR for OS with nivolumab versus placebo was 0.84 (95% CI, 0.69 to 1.02); the median OS for nivolumab was 10.4 months. Progression-free survival HRs versus placebo were 0.72 for nivolumab plus ipilimumab (95% CI, 0.60 to 0.87) and 0.67 for nivolumab (95% CI, 0.56 to 0.81). A trend toward OS benefit with nivolumab plus ipilimumab was observed in patients with tumor mutational burden ≥ 13 mutations per megabase. Rates of grade 3-4 treatment-related adverse events were nivolumab plus ipilimumab (52.2%), nivolumab (11.5%), and placebo (8.4%).CONCLUSION: Maintenance therapy with nivolumab plus ipilimumab did not prolong OS for patients with ED-SCLC who did not progress on first-line chemotherapy. There were no new safety signals. PMID: 33683919