gebhart/patrepeval huggingface dataset:
Modeling the impact of Plasmodium falciparum sexual stage immunity on the composition and dynamics of the human infectious reservoir for malaria in natural settings (2018)

Malaria transmission remains high in Sub-Saharan Africa despite large-scale implementation of malaria control interventions. A comprehensive understanding of the transmissibility of infections to mosquitoes may guide the design of more effective transmission reducing strategies. The impact of P. falciparum sexual stage immunity on the infectious reservoir for malaria has never been studied in natural settings. Repeated measurements were carried out at start-wet, peak-wet and dry season, and provided data on antibody responses against gametocyte/gamete antigens Pfs48/45 and Pfs230 as anti-gametocyte immunity. Data on high and low-density infections and their infectiousness to anopheline mosquitoes were obtained using quantitative molecular methods and mosquito feeding assays, respectively. An event-driven model for P. falciparum sexual stage immunity was developed and fit to data using an agent based malaria model infrastructure. We found that Pfs48/45 and Pfs230 antibody densities increased with increasing concurrent gametocyte densities; associated with 55-70% reduction in oocyst intensity and achieved up to 44% reduction in proportions of infected mosquitoes. We showed that P. falciparum sexual stage immunity significantly reduces transmission of microscopic (p < 0.001) but not submicroscopic (p = 0.937) gametocyte infections to mosquitoes and that incorporating sexual stage immunity into mathematical models had a considerable impact on the contribution of different age groups to the infectious reservoir of malaria. Human antibody responses to gametocyte antigens are likely to be dependent on recent and concurrent high-density gametocyte exposure and have a pronounced impact on the likelihood of onward transmission of microscopic gametocyte densities compared to low density infections. Our mathematical simulations indicate that anti-gametocyte immunity is an important factor for predicting and understanding the composition and dynamics of the human infectious reservoir for malaria.
Cyclocondensation Reactions between 2‐Acyl‐3‐indoleacetic Acid Derivatives and Phenylglycinol: Enantioselective Synthesis of 1‐Substituted Tetrahydro‐β‐carboline Alkaloids (2012)

Abstract Cyclocondensation reactions between a variety of 2‐acyl‐3‐indoleacetic acid derivatives and ( R )‐phenylglycinol were studied. Successful results were obtained from N ‐alkyl keto acid derivatives. The resulting tetracyclic lactams provide straightforward access to enantiopure 1‐substituted tetrahydro‐β‐carboline alkaloids.
Quantitative texture analysis: robustness of radiomics across two digital mammography manufacturers’ systems (2017)

The robustness of radiomic texture analysis across different manufacturers of mammography imaging systems is investigated. We quantified feature robustness across mammography manufacturers using a dataset of 111 women who underwent consecutive screening mammography on both general electric and Hologic systems. In each mammogram, a square region of interest (ROI) directly behind the nipple was manually selected. Radiomic features describing parenchymal patterns were automatically extracted on each ROI. Feature comparisons were conducted between manufacturers (and breast densities) using newly developed robustness metrics descriptive of correlation, equivalence, and variability. By examining the distribution of these metric values, we propose the following selection criteria to guide feature evaluation in this dataset: (1) [Formula: see text] of feature ratios [Formula: see text], (2) standard deviation of feature ratios [Formula: see text], (3) correlation of features [Formula: see text], and (4) [Formula: see text]. Statistically significant correlation coefficients ranged from 0.13 to 0.68 in comparisons between the two mammographic systems tested. Features describing spatial patterns tended to exhibit high correlation coefficients, while intensity- and directionality-based features had comparatively poor correlation. Our proposed robustness metrics may be used to evaluate other datasets, for which different ranges of metric values may be appropriate.
Optimization and in vivo evaluations of a series of small, potent, and specific renin inhibitors containing a novel Leu-Val replacement (1987)

Further structure-activity relationships (SAR) for a novel dipeptide series inhibitors are reported. These inhibitors retain the Phe8-His9 portion of angiotensinogen and employ a unique Leu10-Val11 replacement [(LVR), ref 2]. SAR at the Leu10 side chain revealed that the LVR derived from cyclohexylalanine provided a nearly 10-fold boost in potency for the final inhibitor. In addition SAR work was carried out to delineate the relationships between binding potency and (1) the size, shape, and charge of the side chain at the His9 position; (2) the size and topology of the side chain at the Phe8 site; and (3) the size of the Phe8 N-protecting group. One of the more potent inhibitors, 12, was shown to provide a substantial antihypertensive effect in a sodium depleted monkey model when administered intravenously. Metabolism work, in Sprague-Dawley rats, provided insights into the susceptibility of 12 to significant hepatic clearance and provided encouraging evidence for intestinal absorption.
P‐162: Accelerated Lifetime Testing of White OLED Panels for Lighting (2016)

An accelerated test method for evaluating the long‐term lifetime and color shift of white OLED panels based on device‐degradation models was proposed. We successfully estimated the lifetime and color shift of white OLED panels at standard drive conditions with a short test period.
The process trellis architecture for real-time monitors (1990)

The process trellis is a parallel software architecture for building heuristic real-time monitors. These programs, for example Intelligent Cardiovascular Monitors, must process massive quantities of data in real time. It is natural to turn to parallelism to meet these computational requirements. The process trellis software architecture is intended to simplify the creation and maintenance of heuristic real-time monitors. To do this it must be 1) modular, 2) efficient and 3) predictable.
The SYNTAX score predicts early mortality risk in the elderly with acute coronary syndrome having primary PCI. (2011)

The SXscore predicts 30-day mortality in elderly patients with ACS undergoing primary PCI. In patients discharged alive, the CSS predicts risk of MACCE at 1 year.
A scalable multi-FPGA framework for real-time digital signal processing (2009)

FPGAs have emerged as the preferred platform for implementing real-time signal processing applications. In the sub-45nm technologies, FPGAs offer significant cost and design-time advantages over application-specific custom chips and consume significantly less power than general-purpose processors while maintaining, or improving performance. Moreover, FPGAs are more advantageous than GPUs in their support for control-intensive applications, custom bit-precision operations, and diverse system interface protocols. Nonetheless, a significant inhibitor to the widespread adoption of FPGAs has been the expertise required to effectively realize functional designs that maximize application performance. While there have been several academic and commercial efforts to improve the usability of FPGAs, they have primarily focused on easing the tasks of an expert FPGA designer rather than increasing the usability offered to an application developer. In this work, the design of a scalable algorithmic-level design framework for FPGAs, AlgoFLEX, is described. AlgoFLEX offers rapid algorithmic level composition and exploration while maintaining the performance realizable from a fully custom, albeit difficult and laborious, design effort. The framework masks aspects of accelerator implementation, mapping, and communication while exposing appropriate algorithm tuning facilities to developers and system integrators. The effectiveness of the AlgoFLEX framework is demonstrated by rapidly mapping a class of image and signal processing applications to a multi-FPGA platform.
Biological Properties of (1 → 3)-β- d -Glucan-Based Synthetic Oligosaccharides (2010)

Despite the fact that β-glucans are well-established immunomodulators, the problems with batch-to-batch heterogeneity remains problematic. The aim of this study was to prepare and evaluate new type of synthetic oligosaccharides. A new family of oligo-(1 → 3)-β-d-glucans modified on the reducing end was synthesized using a controlled and specific inversion of configuration at C-2 starting from already formed oligo-(1 → 3)-β-d-glucans. The designed glycosides are characterized by the presence of four or five glucopyranose entities and a mannose residue at the reducing end. To study of the impact of well-defined structural modulations, we used murine and human models to evaluate their immunostimulating potential. These novel oligosaccharides showed strong and long-lasting stimulation of phagocytosis and significant potentiation of synthesis and/or secretion of interleukin (IL-2, IL-4, IL-5, IL-6), tumor necrosis factor-α, and vascular endothelial growth factor. In addition, the oligosaccharides tested showed significant effects on expression of several genes in human fibroblasts and breast cancer cells. From our results it is clear that these synthetic oligosaccharides represent a better alternative to natural β-glucans.
First Human Dosing Experience with TRV130, a Biased Ligand at the Mu Opioid Receptor (P02.013) (2013)

OBJECTIVE: To evaluate the safety, tolerability, PK and PD of TRV130.
Supplementary Data from Genomic Alterations in <i>PIK3CA</i>-Mutated Breast Cancer Result in mTORC1 Activation and Limit the Sensitivity to PI3Kα Inhibitors (2023)

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ChemInform Abstract: STEREOSPECIFIC SYNTHESIS OF THE BICYCLO(2.2.2) PORTION OF GRANATICIN; SYNTHESIS OF SARUBICIN A (1985)

Abstract Die auf dem angegebenen Weg stereospezifisch durchführbare Synthese der Verbindung (VIII) entspricht einer formalen Totalsynthese von Sarubicin A (IX), da dieses nach Literaturmethode in einem Schritt aus (VIII) zugänglich ist.
Factors Affecting the Operational Thermal Resistance of Electronic Components (1999)

The thermal resistance of electronic components is known to often differ considerably between standard test conditions and those found in service. One way to correct for this is to use multi-parameter thermal resistances. Another, presented here, is to adjust the junction-to-ambient thermal resistance to account for operational conditions. For forced convection applications, two factors are proposed; the first accounts for any upstream aerodynamic disturbance and the second addresses purely thermal interaction. Thus if an upstream powered component interacts with a downstream component, the two factors are combined. It is shown that both factors may be quantified in terms of readily measured temperatures and then used as coefficients to adjust the standard thermal resistance data for operational conditions. To overcome the misconception that the currently published single-value thermal resistances are solely a property of the electronic package, thermal resistance is redefined to include both the resistance of the package and the part of the printed circuit board (PCB) covered by the component thermal footprint. This approach is applied to a symmetrical array of board mounted 160-lead devices and data showing how the factors vary with component position, nondimensional power distribution and Reynolds number is presented. Based on data a new method of generating operational component thermal resistances is proposed. [S1043-7398(00)00603-4]
Early gene regulation of osteogenesis in embryonic stem cells (2012)

The early gene regulatory networks (GRNs) that mediate stem cell differentiation are complex, and the underlying regulatory associations can be difficult to map accurately. In this study, the expression profiles of the genes Dlx5, Msx2 and Runx2 in mouse embryonic stem cells were monitored over a 48 hour period after exposure to the growth factors BMP2 and TGFβ1. Candidate GRNs of early osteogenesis were constructed based on published experimental findings and simulation results of Boolean and ordinary differential equation models were compared with our experimental data in order to test the validity of these models. Three gene regulatory networks were found to be consistent with the data, one of these networks exhibited sustained oscillation, a behaviour which is consistent with the general view of embryonic stem cell plasticity. The work cycle presented in this paper illustrates how mathematical modelling can be used to elucidate from gene expression profiles GRNs that are consistent with experimental data.
Peering vs. transit: Performance comparison of peering and transit interconnections (2017)

The economic aspects of peering and transit interconnections between ISPs have been extensively studied in prior literature. Prior research primarily focuses on the economic issues associated with establishing peering and transit connectivity among ISPs to model interconnection strategies. Performance analysis, on the other hand, while understood intuitively, has not been empirically quantified and incorporated in such models. To fill this gap, we conduct a large scale measurement based performance comparison of peering and transit interconnection strategies. We use JavaScript to conduct application layer latency measurements between 510K clients in 900 access ISPs and multi-homed CDN servers located at 33 IXPs around the world. Overall, we find that peering paths outperformed transit paths for 91% Autonomous Systems (ASes) in our data. Peering paths have smaller propagation delays as compared to transit paths for more than 95% ASes. Peering paths outperform transit paths in terms of propagation delay due to shorter path lengths. Peering paths also have smaller queueing delays as compared to transit paths for more than 50% ASes.
The Energy of Adsorbed Hydroxyl on Pt(111) by Microcalorimetry (2011)

The energy of adsorbed hydroxyl on Pt(111) was measured by dosing D2O gas onto oxygen precovered Pt(111) at 150 K while following the heat of reaction with single-crystal adsorption calorimetry. The adsorption of D2O on oxygen precovered Pt(111) is known to produce surface OD (hydroxyl) coadsorbed with molecular D2O in a well-defined structure. The heat of reaction and sticking probability of D2O on Pt(111) were measured as a function of oxygen precoverage and D2O dose. With 0.25 monolayers (ML) of oxygen atoms, the differential heat of adsorption is nearly constant at 61.3 kJ/mol for the first ∼1/3 ML but drops to 57.9 kJ/mol by 0.50 ML and 50.5 kJ/mol by saturation (0.62 ML). Similar experiments with Oad precoverages of 0.18 and 0.07 ML gave lower saturation D2O coverages (0.55 and 0.22 ML, respectively) and lower heats of reaction by ∼3.4 and ∼4.6 kJ/mol, respectively, except at very low D2O coverage where step sites may play a role. From the integral heat of D2O adsorption, the standard enthalpy of formation of the (D2O···OD)ad complex is estimated to be −527 kJ/mol. Assuming that the adsorbed D2O molecules in this (D2O···OD)ad complex have the same enthalpy as when adsorbed as a pure D2O film on Pt(111), the enthalpy of formation of adsorbed OD is found to be −226 kJ/mol, and the Pt–OD bond enthalpy to be 263–274 kJ/mol. From these values, we estimate that the reaction D2Oad → ODad + Dad is endothermic by 29–39 kJ/mol. At D2O coverages below 0.4 ML, the sticking probability of D2O on Pt(111) at 150 K is ∼0.9 for oxygen precoverages between 0.14 and 0.25 ML.
Broadening of the T-Cell Repertoire to HIV-1 Gag p24 by Vaccination of HLA-A2/DR Transgenic Mice with Overlapping Peptides in the CAF05 Adjuvant (2013)

Induction of broad T-cell immune responses is regarded as critical for vaccines against the human immunodeficiency virus type 1 (HIV-1) which exhibit high diversity and, therefore, focus has been on inducing cytotoxic CD8 T-cell responses against the more conserved parts of the virus, such as the Gag protein. Herein, we have used the p24 protein which contains a range of conserved T-cell epitopes. We demonstrate that a vaccine of HIV-1 subtype B consensus group-specific antigen (Gag) p24 protein with the CD8-inducing liposomal cationic adjuvant formulation (CAF) 05, induces both CD4 and CD8 T-cell responses in CB6F1 mice. The adjuvanted vaccine also induced functional antigen-specific cytotoxicity in vivo. Furthermore, we found that when fragmenting the Gag p24 protein into overlapping Gag p24 peptides, a broader T-cell epitope specificity was induced in the humanized human leukocyte antigen (HLA)-A2/DR-transgenic mouse model. Thus, combining overlapping Gag p24 peptides with CAF05 appears to be a promising and simple strategy for inducing broader T-cell responses to multiple conserved epitopes which will be relevant for both prophylactic and therapeutic HIV-1 vaccines.
Reinventing Chemistry (2015)

Chemistry is in a period of change, from an era focused on molecules and reactions, to one in which manipulations of systems of molecules and reactions will be essential parts of controlling larger systems. This Essay traces paths from the past to possible futures.
Phase Structures and Self-assembled Helical Suprastructures via Hydrogen Bonding in a Series of Achiral 4-Biphenyl Carboxylic Acid Compounds (2005)

A series of achiral 4-biphenyl carboxylic acid compounds (BPCA-Cn-PmOH) connected with alkoxyl chains having various carbon numbers (n = 6−10) and terminated by phenyl groups with meta-positioned hydroxyl groups was synthesized. Different phase structures including nematic, smectic A (SmA), smectic C (SmC), and highly ordered smectic liquid-crystalline phases along with crystalline phases were identified based on wide-angle X-ray diffraction and electron diffraction experiments. It was found via infrared spectroscopy that the hydrogen (H)-bonds were formed between the carboxylic acids to construct head-to-head dimers as the building blocks for these ordered structural formations. H-bonds formed via the meta-positioned hydroxyl groups also played an important role in forming ordered layers in these structures. The morphology of this series of BPCA-Cn-PmOH as observed under polarized light microscopy showed an oily streak (cylinder) texture with Myelin-figure in the SmA phase. When temperature cools to enter the SmC phase, these streaks (cylinders) started to twist into helical suprastructures, which were not only by the birefringence changes but also by the three-dimensional helical geometry observed in other microscopic techniques. The dynamic conformational changes of the aromatic and aliphatic parts in this series of BPCA-Cn-PmOH at different temperatures correspond well with the thermal transitions via solid-state carbon-13 nuclear magnetic resonance experiments. Computer simulation indicated that the head-to-head dimers possess a twisted rather than a bent conformation. It was deduced that the twisted conformation of the dimers and the terminal meta-substituted phenyl groups at both ends of the dimers are critically important in forming the helical suprastructures.
Design Considerations for a Multi-Projector Display Rendering Cluster (2001)

High-resolution, multi-projector displays are often built using standard consumer electronics. Before designing a PC-cluster rendering system to drive these displays, a number of issues must be addressed. This paper provides an overview of these issues. The issues addressed include the type of parallel rendering algorithm, load balancing, network latency, and network overhead. The goal of this paper is to provide a general overview of the design space and highlight the major tradeoffs between different designs.
Time Reversal Acoustic focusing with random reverberator (2008)

Time Reversal Acoustic (TRA) focusing system based on an external reverberator can provide good focusing with minimum side lobes even with a few transducers. The focusing ability of such system can be increased using reverberator with rough boundaries or by adding internal random scatterers. The experiments were conducted with a reverberator made of a polyethylene bottle filled with water and a single piezoceramic disk attached externally to its wall. Experiments demonstrated that inserting in the bottle random hard scatterers or altering of the bottle surface significantly decreases the size of the focused spot and the level of side lobes. The new pseudo-impulse method of TRA focusing allowed suppressing piezotransducer resonances and provided formation of short wide band signals. The ability of such TRA focusing system based on random reverberator to form simultaneously multiple focuses and produce focal spots of the complex shape has been demonstrated. The application of binary radiation regime led to several fold increasing of the amplitude of the focal spot while the focal structure practically was not affected. Applications of such random focusing system for medical imaging and HIFU treatment is discussed.
LDPC-coded cooperative relay systems: performance analysis and code design (2008)

We treat the problem of designing low-density parity-check (LDPC) codes to approach the capacity of relay channels. We consider an efficient analysis framework that decouples the factor graph (FG) of a <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">B</i> -block transmission into successive partial FGs, each of which denotes a two-block transmission. We develop design methods to find the optimum code ensemble for the partial FG. In particular, we formulate the relay operations and the destination operations as equivalent virtual MISO and MIMO systems, and employ a binary symmetric channel (BSC) model for the relay node output. For AWGN channels, we further develop a Gaussian approximation for the detector output at the destination node. Jointly treating the relay and the destination, we analyze the performance of the LDPC-coded relay system using the extrinsic mutual information transfer(EXIT) chart technique. Furthermore, differential evolution is employed to search for the optimum code ensemble. Our results show that the optimized codes always outperform the regular LDPC codes with a significant gain; in the AWGN case, when Protocol-II is employed and the relay is close to the source, the optimized code performs within 0.1dB to the capacity bound.
DecoBrush (2014)

Structured decorative patterns are common ornamentations in a variety of media like books, web pages, greeting cards and interior design. Creating such art from scratch using conventional software is time consuming for experts and daunting for novices. We introduce DecoBrush, a data-driven drawing system that generalizes the conventional digital "painting" concept beyond the scope of natural media to allow synthesis of structured decorative patterns following user-sketched paths. The user simply selects an example library and draws the overall shape of a pattern. DecoBrush then synthesizes a shape in the style of the exemplars but roughly matching the overall shape. If the designer wishes to alter the result, DecoBrush also supports user-guided refinement via simple drawing and erasing tools. For a variety of example styles, we demonstrate high-quality user-constrained synthesized patterns that visually resemble the exemplars while exhibiting plausible structural variations.