gebhart/patrepeval huggingface dataset:
Detailed Version: Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials (2007)

This is the detailed technical report that accompanies the paper “Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials” (an unpublished, technical report version of which is available online at http://www.bepress.com/ucbbiostat/paper223).\nThe version here gives full details of the models for the time-dependent analysis, and presents further results in the data analysis section. The Methods for Improving Reproductive Health in Africa (MIRA) trial is a recently completed randomized trial that investigated the effect of diaphragm and lubricant gel use in reducing HIV infection among susceptible women. 5,045 women were randomly assigned to either the active treatment arm or not. Additionally, all subjects in both arms received intensive condom counselling and provision, the "gold standard" HIV prevention barrier method.\nThere was much lower reported condom use in the intervention arm than in the control arm, making it difficult to answer important public health questions based solely on the intention-to-treat analysis.\nWe adapt an analysis technique from causal inference to estimate the "direct effects" of assignment to the diaphragm arm, adjusting for condom use in an appropriate sense.\nIssues raised in the MIRA trial apply to other trials of HIV prevention methods, some of which are currently being conducted or designed.
In Vivo Antinociceptive, Muscle Relaxant, Sedative, and Molecular Docking Studies of Peshawaraquinone Isolated from Fernandoa adenophylla (Wall. ex G. Don) Steenis (2021)

<i>Fernandoa adenophylla</i> (Wall. ex G. Don) Steenis is traditionally used to cure various diseases and can be included as an ingredient in massage oils, which are supposed to comfort muscular tension and pain. This study was designed to assess the antinociceptive, muscle relaxant, and molecular docking properties of a novel compound, namely, (5a<i>R</i>,5a1<i>R</i>,6<i>R</i>,7a<i>S</i>,14b<i>R</i>,15<i>R</i>)15-hydroxy-7a-methyl-6-(2-methylprop-1-en-1-yl)-7,7a,14b,15-tetrahydro-5<i>H</i>-t-5a,15methanobenzo[g]benzo[5,6]azuleno[1,8-<i>bc</i>]chromene-5,9,14,16(5a1<i>H</i>,6<i>H</i>)- tetraone (peshawaraquinone), isolated from the methanolic extract of <i>F. adenophylla</i> in an animal model. The chemical structure of the isolated compound was elucidated using advanced spectroscopic techniques and further confirmed by XRD analysis. Compound <b>1</b> was tested against hot plate-induced noxious stimuli at various doses (2.5, 5, 10, and 15 mg/kg i.p.). The muscle relaxation potency of compound <b>1</b> was evaluated in the inclined and traction test, while the open-field test was used for the determination of sedative potential. The isolated compound was also subjected to acute toxicity analysis. The compound was then subjected to molecular docking analysis to determine the exact mechanism of action. Compound <b>1</b> demonstrated significant (<i>p</i> < 0.05) analgesic effect in a dose-dependent manner. A noticeable muscle relaxant effect was observed with the passage of time in both experimental models. The compound <b>1</b> showed a significant (<i>p</i> < 0.05) sedative effect, and in an acute toxicity study, the compound <b>1</b> was devoid of any noxious effects. The docking studies showed preferential affinity for μ-opioid and GABAA receptors. Hence, the prospective antinociceptive and muscle relaxant and sedative properties are probably mediated through these two target interactions.
Macro-micro frequency reconfigurable antenna (2007)

In this paper, two representing diodes, the PIN diode and the varactor, are used for the Macro-micro frequency tuning. The PIN diode in the antenna is used for switching wireless service bands (Macro-tuning). As well as the varactor in the antenna is used for tuning frequency band to obtain the constant antenna gain (micro-tuning). The proposed antenna newly realizes desirable broad and fine frequency tuning at the same time for the reconfigurable wireless communication system.
Influence of Trialkylaluminum Reagents on the Propylene Polymerization Behavior of Bridged and Unbridged 2-Arylindene Metallocene Polymerization Catalysts (1999)

Trialkylaluminum reagents such as triisobutylaluminum (TIBA) and trimethylaluminum (TMA) influence the propylene polymerization behavior of methylaluminoxane (MAO)-activated dimethylsilyl[bis(2-phenylindenyl)]zirconium dichloride (1). TIBA selectively decreases the productivity of the meso diastereomer of 1 (1-meso). This is manifested in an increase in the isotacticity of polypropylene blends prepared from mixtures of 1-rac and 1-meso compared to polymer blends prepared in the absence of TIBA. In contrast, added trimethylaluminum decreases the productivity of both 1-rac and 1-meso. Similar trends in reactivity with AlR3 are observed for unbridged bis(2-phenylindenyl)zirconium dichloride (2) compared to a mixture of the bridged catalysts containing 57% 1-rac. Mechanical testing indicates that polypropylene from 2 has superior elastomeric properties to reactor blends prepared from mixtures of 1-rac and 1-meso in the presence and absence of trialkylaluminum reagents. Reactor blends prepared without AlR3 exhibit poorer recovery at 100% and 300% strain than that of the elastomeric polypropylene from 2. The reactor blends prepared in the presence of TIBA exhibit pronounced yielding and necking during testing, characteristic of a softened plastic.
MicroRNA-29 controls Th1 bias of CD4+ T cells in multiple sclerosis (167.5) (2011)

Abstract Multiple sclerosis (MS) is an inflammatory disease of the central nervous system initiated by autoreactive CD4+ T cells of a T-helper (Th)1 and Th17 phenotype. Identifying novel factors that control Th differentiation will lead to a better understanding of MS pathogenesis and the development of new therapeutic strategies. MicroRNAs (miRs) are small non-coding RNAs that negatively regulate post-transcriptional gene expression. Dicer-deficient CD4+ T cells that lack miRs produce more of the Th1-associated cytokine IFN-γ; however, the specific miR(s) responsible for controlling Th1 programming have not been defined. Using in silico target prediction algorithms, we identified miR-29 as a factor that could potentially regulate multiple genes in the Th1 pathway. We confirmed that miR-29 directly targets T-bet and IFN-γ, and gain- and loss-of-function experiments demonstrated the ability of miR-29 to modulate Th1 polarization. Importantly, we found that naïve CD4+ T cells from MS patients express lower basal levels of miR-29 than controls. We further established an inverse relationship between basal expression of miR-29 and expression of T-bet/IFN-γ following activation of MS patient T cells. These results identify miR-29 as a novel regulator of Th1 differentiation and function, and implicate low miR-29 as an MS susceptibility factor. Restoring miR-29 may therefore be a powerful therapeutic modality in MS and other Th1-driven autoimmune diseases.
MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors (2022)

Many critical advances in research utilize techniques that combine high-resolution with high-content characterization at the single cell level. We introduce the MICS (MACSima Imaging Cyclic Staining) technology, which enables the immunofluorescent imaging of hundreds of protein targets across a single specimen at subcellular resolution. MICS is based on cycles of staining, imaging, and erasure, using photobleaching of fluorescent labels of recombinant antibodies (REAfinity Antibodies), or release of antibodies (REAlease Antibodies) or their labels (REAdye_lease Antibodies). Multimarker analysis can identify potential targets for immune therapy against solid tumors. With MICS we analysed human glioblastoma, ovarian and pancreatic carcinoma, and 16 healthy tissues, identifying the pair EPCAM/THY1 as a potential target for chimeric antigen receptor (CAR) T cell therapy for ovarian carcinoma. Using an Adapter CAR T cell approach, we show selective killing of cells only if both markers are expressed. MICS represents a new high-content microscopy methodology widely applicable for personalized medicine.
Correction: Expanding plastics recycling technologies: chemical aspects, technology status and challenges (2022)

Correction for ‘Expanding plastics recycling technologies: chemical aspects, technology status and challenges’ by Houqian Li et al. , Green Chem. , 2022, 24 , 8899–9002, https://doi.org/10.1039/D2GC02588D.
Practical use of a framework for network science experimentation (2014)

In 2006, the US Army Research Laboratory (ARL) and the UK Ministry of Defence (MoD) established a collaborative research alliance with academia and industry, called the International Technology Alliance (ITA)<sup>1</sup> In Network and Information Sciences, to address fundamental issues concerning Network and Information Sciences that will enhance decision making for coalition operations and enable rapid, secure formation of ad hoc teams in coalition environments and enhance US and UK capabilities to conduct coalition warfare. Research conducted under the ITA was extended through collaboration between ARL and IBM UK to characterize and dene a software stack and tooling that has become the reference framework for network science experimentation in support for validation of theoretical research. This paper discusses the composition of the reference framework for experimentation resulting from the ARL/IBM UK collaboration and its use, by the Network Science Collaborative Technology Alliance (NS CTA)<sup>2</sup> , in a recent network science experiment conducted at ARL. It also discusses how the experiment was modeled using the reference framework, the integration of two new components, the Apollo Fact-Finder<sup>3</sup> tool and the Medusa Crowd Sensing<sup>4</sup> application, the limitations identified and how they shall be addressed in future work.
Novel η1-N,η2-C,C-Binding Mode between Pyridinyl-Functionalized Cyclopentadienyl Ligands and Iridium (2005)

The reaction between 2-(2,3,4,5-tetramethyl-cyclopenta-1,3-dienyl)-pyridine 1 and IrCl3 was performed in an attempt to synthesize a cyclometalated system with decreased pi conjugation in the ligand. An unexpected reduction and rearrangement of bis-pyridinyl-cyclopentadienyl cyclometalated Ir(III) intermediate 2 took place yielding bis-pyridinyl-fulvene Ir(I) complex 4, which exhibits a novel bis-eta1-N,eta2-C,C-binding mode between the pyridinyl-functionalized fulvene ligand and iridium. The iridium atom in 4 is not sandwiched between two cyclopentadienyl moieties; rather, the two cyclopentadienyl groups adopt a pi-pi stacking arrangement with a centroid-centroid distance of 3.494 A. The Cl/P(wedge)O ligand-exchange reaction between 4 and 2-[(diphenylphosphanyl)-methyl]-1,1,1,3,3,3-hexafluoro-propan-2-ol 5 led to loss of one pyridinyl-functionalized fulvene ligand and produced complex 6, in which the remaining pyridinyl-functionalized fulvene ligand exhibits the mono-eta1-N,eta2-C,C-binding mode.
A suitable parametrization to simulate slug flows with the Volume-Of-Fluid method (2012)

Diffuse–interface methods, such as the Volume-Of-Fluid method, are often used to simulate complex multiphase flows even if they require significant computation time. Moreover, it can be difficult to simulate some particular two-phase flows such as slug flows with thin liquid films. Suitable parametrization is necessary to provide accuracy and computation speed. Based on a numerical study of slug flows in capillary tubes, we show that it is not trivial to optimize the parametrization of these methods. Some simulation problems described in the literature are directly related to a poor model parametrization, such as an unsuitable discretization scheme or too large time steps. The weak influence of the mesh irregularity is also highlighted. It is shown how to capture accurately thin liquid films with reasonably low computation times.
Matrix sparsification and non-negative factorization for task partitioning in computational sensing and imaging (2017)

We address the mathematical foundations of a special case of the general problem of partitioning an end-to-end sensing algorithm for implementation by optics and by a digital processor for minimal electrical power dissipation. Specifically, we present a non-iterative algorithm for factoring a general <i>k</i> &times; <i>k</i> real matrix <strong>A</strong> (describing the end-to-end linear pre-processing) into the product <strong>BC</strong>, where C has no negative entries (for implementation in linear optics) and B is maximally sparse, i.e., has the fewest possible non-zero entries (for minimal dissipation of electrical power). Our algorithm achieves a sparsification of <strong>B</strong>: i.e., the number s of non-zero entries in <strong>B</strong>: of<i> s</i> &le; 2<i>k</i>, which we prove is optimal for our class of problems.
Naming and discovery in networks: architecture and economics (2009)

In less than three decades, the Internet was transformed from a research network available to the academic community into an international communication infrastructure. Despite its tremendous success, there is a growing consensus in the research community that the Internet has architectural limitations that need to be addressed in a effort to design a “future Internet”. Among the main technical limitations are the lack of mobility support, and the lack of security and trust. The Internet, and particularly TCP/IP, identifies endpoints using a location/routing identifier, the IP address. Coupling the endpoint identifier to the location identifier hinders mobility and poorly identifies the actual endpoint. On the other hand, the lack of security has been attributed to limitations in both the network and the endpoint. Authentication for example is one of the main concerns in the architecture and is hard to implement partly due to lack of identity support. 
The general problem that this dissertation is concerned with is that of designing a future Internet. Towards this end, we focus on two specific sub-problems. The first problem is the lack of a framework for thinking about architectures and their design implications. It was obvious after surveying the literature that the majority of the architectural work remains idiosyncratic and descriptions of network architectures are mostly idiomatic. This has led to the overloading of architectural terms, and to the emergence of a large body of network architecture proposals with no clear understanding of their cross similarities, compatibility points, their unique properties, and architectural performance and soundness. On the other hand, the second problem concerns the limitations of traditional naming and discovery schemes in terms of service differentiation and economic incentives. One of the recurring themes in the community is the need to separate an entity's identifier from its locator to enhance mobility and security. Separation of identifier and locator is a widely accepted design principle for a future Internet. Separation however requires a process to translate from the identifier to the locator when discovering a network path to some identified entity. We refer to this process as identifier-based discovery, or simply discovery, and we recognize two limitations that are inherent in the design of traditional discovery schemes. The first limitation is the homogeneity of the service where all entities are assumed to have the same discovery performance requirements. The second limitation is the inherent incentive mismatch as it relates to sharing the cost of discovery. This dissertation addresses both subproblems, the architectural framework as well as the naming and discovery limitations.
Ligand affinity of the 67-kD elastin/laminin binding protein is modulated by the protein's lectin domain: visualization of elastin/laminin-receptor complexes with gold-tagged ligands. (1991)

Video-enhanced microscopy was used to examine the interaction of elastin- or laminin-coated gold particles with elastin binding proteins on the surface of live cells. By visualizing the binding events in real time, it was possible to determine the specificity and avidity of ligand binding as well as to analyze the motion of the receptor-ligand complex in the plane of the plasma membrane. Although it was difficult to interpret the rates of binding and release rigorously because of the possibility for multiple interactions between particles and the cell surface, relative changes in binding have revealed important aspects of the regulation of affinity of ligand-receptor interaction in situ. Both elastin and laminin were found to compete for binding to the cell surface and lactose dramatically decreased the affinity of the receptor(s) for both elastin and laminin. These findings were supported by in vitro studies of the detergent-solubilized receptor. Further, immobilization of the ligand-receptor complexes through binding to the cytoskeleton dramatically decreased the ability of bound particles to leave the receptor. The changes in the kinetics of ligand-coated gold binding to living cells suggest that both laminin and elastin binding is inhibited by lactose and that attachment of receptor to the cytoskeleton increases its affinity for the ligand.
Dendritic Glutamate Receptor mRNAs Show Contingent Local Hotspot-Dependent Translational Dynamics (2013)

Protein synthesis in neuronal dendrites underlies long-term memory formation in the brain. Local translation of reporter mRNAs has demonstrated translation in dendrites at focal points called translational hotspots. Various reports have shown that hundreds to thousands of mRNAs are localized to dendrites, yet the dynamics of translation of multiple dendritic mRNAs has remained elusive. Here, we show that the protein translational activities of two dendritically localized mRNAs are spatiotemporally complex but constrained by the translational hotspots in which they are colocalized. Cotransfection of glutamate receptor 2 (GluR2) and GluR4 mRNAs (engineered to encode different fluorescent proteins) into rat hippocampal neurons demonstrates a heterogeneous distribution of translational hotspots for the two mRNAs along dendrites. Stimulation with s-3,5-dihydroxy-phenylglycine modifies the translational dynamics of both of these RNAs in a complex saturable manner. These results suggest that the translational hotspot is a primary structural regulator of the simultaneous yet differential translation of multiple mRNAs in the neuronal dendrite.
The Forgotten Role of Central Volume in Low Frequency Oscillations of Heart Rate Variability (2015)

The hypothesis that central volume plays a key role in the source of low frequency (LF) oscillations of heart rate variability (HRV) was tested in a population of end stage renal disease patients undergoing conventional hemodialysis (HD) treatment, and thus subject to large fluid shifts and sympathetic activation. Fluid overload (FO) in 58 chronic HD patients was assessed by whole body bioimpedance measurements before the midweek HD session. Heart Rate Variability (HRV) was measured using 24-hour Holter electrocardiogram recordings starting before the same HD treatment. Time domain and frequency domain analyses were performed on HRV signals. Patients were retrospectively classified in three groups according to tertiles of FO normalized to the extracellular water (FO/ECW%). These groups were also compared after stratification by diabetes mellitus. Patients with the low to medium hydration status before the treatment (i.e. 1st and 2nd FO/ECW% tertiles) showed a significant increase in LF power during last 30 min of HD compared to dialysis begin, while no significant change in LF power was seen in the third group (i.e. those with high pre-treatment hydration values). In conclusion, several mechanisms can generate LF oscillations in the cardiovascular system, including baroreflex feedback loops and central oscillators. However, the current results emphasize the role played by the central volume in determining the power of LF oscillations.
Chemical Modulation of Protein O-GlcNAcylation via OGT Inhibition Promotes Human Neural Cell Differentiation (2017)

The enzymes that determine protein O-GlcNAcylation, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), act on key transcriptional and epigenetic regulators, and both are abundantly expressed in the brain. However, little is known about how alterations in O-GlcNAc cycling affect human embryonic stem cell (hESC) neural differentiation. Here, we studied the effects of perturbing O-GlcNAcylation during neural induction of hESCs using the metabolic inhibitor of OGT, peracetylated 5-thio-N-acetylglucosamine (Ac<sub>4</sub>-5SGlcNAc). Treatment of hESCs with Ac<sub>4</sub>-5SGlcNAc during induction limited protein O-GlcNAcylation and also caused a dramatic decrease in global levels of UDP-GlcNAc. Concomitantly, a subpopulation of neural progenitor cells (NPCs) acquired an immature neuronal morphology and expressed early neuronal markers such as β-III tubulin (TUJ1) and microtubule associated protein 2 (MAP2), phenotypes that took longer to manifest in the absence of OGT inhibition. These data suggest that chemical inhibition of OGT and perturbation of protein O-GlcNAcylation accelerate the differentiation of hESCs along the neuronal lineage, thus providing further insight into the dynamic molecular mechanisms involved in neuronal development.
COAXID – omni-directional inner diameter laser cladding optic (2011)

Laser ID materials deposition is applied for inner surface coatings of abrasively loaded tools, the generative fabrication of inner 3D structures of aero engines and gas turbines as well as the repair of local damages in oil drilling tools. The core element of the modularly designed ID cladding head presented here is a multi-jet coaxial powder nozzle. This nozzle concept permits a precise powder supply in any welding position, independently from gravity and welding direction. Thus, not only simple inner coatings are applicable, but also complex shaped metal structures can be generated in internal areas with restricted accessibility. All media supply, such as powder, shielding gas, cooling water, is safely packaged inside the processing head. The optical elements for shaping and focusing the laser beam are interchangeable and permit the use of disc an d Nd:YAG laser up to 3 kW laser power. Currently, the minimum ID caliber is 4 inches, and the maximum immersion depth amounts to 40 inches. Current developments aim at the reduction of the minimum diameter to 2 inches and increased immersion depths to more than one meter by using diode laser with high power.
Mechanisms and Consequences of Ebolavirus-Induced Lymphocyte Apoptosis (2009)

Ebolavirus (EBOV) is a member of the filovirus family and causes severe hemorrhagic fever, resulting in death in up to 90% of infected humans. EBOV infection induces massive bystander lymphocyte apoptosis; however, neither the cellular apoptotic pathway(s) nor the systemic implications of lymphocyte apoptosis in EBOV infection are known. In this study, we show data suggesting that EBOV-induced lymphocyte apoptosis in vivo occurs via both the death receptor (extrinsic) and mitochondrial (intrinsic) pathways, as both Fas-associated death domain dominant negative transgenic mice and mice overexpressing bcl-2 were resistant to EBOV-induced lymphocyte apoptosis. Surprisingly, inhibiting lymphocyte apoptosis during EBOV infection did not result in improved animal survival. Furthermore, we show for the first time that hepatocyte apoptosis likely occurs in EBOV infection, and that mice lacking the proapoptotic genes Bim and Bid had reduced hepatocyte apoptosis and liver enzyme levels postinfection. Collectively, these data suggest that EBOV induces multiple proapoptotic stimuli and that blocking lymphocyte apoptosis is not sufficient to improve survival in EBOV infection. These data suggest that hepatocyte apoptosis may play a role in the pathogenesis of EBOV infection, whereas lymphocyte apoptosis appears to be nonessential for EBOV disease progression.