gebhart/patrepeval huggingface dataset:
Interaction of visual cues for prominence (2009)

The timing of both eyebrow and head movements of a talking face was varied systematically in a test sentence using an audiovisual speech synthesizer. The audio speech signal was unchanged over all sentences. 33 listeners were given the task of identifying the most prominent word in the test sentence. Results indicate that both eyebrow and head movements are powerful visual cues for prominence and that perceptual sensitivity to timing is on the order of a typical syllable duration of 100-200 ms.
Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis (2006)

Lateral gene transfer is an integral part of genome evolution in most bacteria. Bacteria can readily change the contents of their genomes to increase adaptability to ever-changing surroundings and to generate evolutionary novelty. Here, we report instances of lateral gene transfer in Mycobacterium avium subsp. paratuberculosis, a pathogenic bacteria that causes Johne's disease in cattle. A set of 275 genes are identified that are likely to have been recently acquired by lateral gene transfer. The analysis indicated that 53 of the 275 genes were acquired after the divergence of M. avium subsp. paratuberculosis from M. avium subsp. avium, whereas the remaining 222 genes were possibly acquired by a common ancestor of M. avium subsp. paratuberculosis and M. avium subsp. avium after its divergence from the ancestor of M. tuberculosis complex. Many of the acquired genes were from proteobacteria or soil dwelling actinobacteria. Prominent among the predicted laterally transferred genes is the gene rsbR, a possible regulator of sigma factor, and the genes designated MAP3614 and MAP3757, which are similar to genes in eukaryotes. The results of this study suggest that like most other bacteria, lateral gene transfers seem to be a common feature in M. avium subsp. paratuberculosis and that the proteobacteria contribute most of these genetic exchanges.
Interventions with Potential to Mitigate Injection Site Reactions Following Subcutaneous Elamipretide Administration: A Phase 1, Crossover Study (2023)

Background and Purpose: Elamipretide is a mitochondrial-targeting agent being developed for the treatment of mitochondrial dysfunction-associated diseases. While prior studies have shown that subcutaneous elamipretide is generally safe/well tolerated, injection site reactions (ISRs) were reported in most subjects. We evaluated the efficacy of interventions to mitigate ISRs, identify underlying ISR mechanisms, and evaluate the pharmacokinetic and safety profile of subcutaneous elamipretide. Experimental Approach: Subcutaneous elamipretide 60 mg was administered to healthy subjects (N=10) on six separate occasions with/without potential ISR interventions (mometasone furoate, ice application, tacrolimus ointment, doxepin cream, and oral diphenhydramine). ISR clinical/self-assessments, blood samples, and safety data were collected at predetermined intervals. Preclinical studies investigated mast cell-specific receptor MRGPRX2 mediation of ISRs. Key Results: Mometasone significantly reduced the incidence of induration/swelling and pruritus. Diphenhydramine significantly decreased the incidence of induration; 50% reported somnolence. Ice application significantly reduced the incidence of pain, although it reduced elamipretide’s maximum plasma concentration and area-under-the-curve from time 0-6hrs versus elamipretide alone. Preclinical data suggest that SQ-elamipretide induced ISRs by activating MRGPRX2 in humans and its ortholog Mrgprb2 in mice. Conclusion and Implications: Elamipretide activated MRGPRX2 and Mrgprb2 receptors, resulting in activation of mast cells and inflammation in mouse models, suggesting that targeting mast-cell activation may ameliorate elamipretide ISRs. Topical mometasone prior to subcutaneous elamipretide demonstrated significant reductions in ISR signs and symptoms and did not cause significant changes in elamipretide plasma exposure or additional adverse events. Therefore, mometasone prior to subcutaneous injection of elamipretide warrants further investigation in clinical studies for alleviating ISRs.
Oxidation of copper nanowire based transparent electrodes in ambient conditions and their stabilization by encapsulation: application to transparent film heaters (2018)

Whereas the integration of silver nanowires in functional devices has reached a fair level of maturity, the integration of copper nanowires still remains difficult, mainly due to the intrinsic instability of copper nanowires in ambient conditions. In this paper, copper nanowire based transparent electrodes with good performances (33 Ω sq-1 associated with 88% transparency) were obtained, and their degradation in different conditions was monitored, in particular by electrical measurements, transmission electron microscopy, x-ray photoelectron spectrometry and Auger electron spectroscopy. Several routes to stabilize the random networks of copper nanowires were evaluated. Encapsulation through laminated barrier film with optical clear adhesive and atmospheric pressure spatial atomic layer deposition were found to be efficient and were used for the fabrication of transparent film heaters.
ACTIVE INLET FLOW CONTROL TECHNOLOGY DEMONSTRATION (2000)

This paper presents results from a joint Lockheed Martin/NASA Glenn effort to design and verify an ultra-compact, highly-survivable engine inlet subsonic duct based on the emerging technology of Active Inlet Flow Control (AIFC). In the AIFC concept, microscale actuation (~mm in size) is used in an approach denoted ‘secondary flow control’ to intelligently alter a serpentine duct’s inherent secondary flow characteristics with the goal of simultaneously improving the critical systemlevel performance metrics of total pressure recovery, spatial distortion, and RMS turbulence. In this approach, separation control is a secondary benefit, not a design requirement. The baseline concept for this study was a 4:1 aspect ratio ultra-compact (L/D=2.5) serpentine duct that fully obscured line-of-sight view of the engine face. At relevant flow conditions, this type of duct exhibits excessive pressure loss and distortion because of extreme wall curvature. Two sets of flow control effectors were designed with the intent of establishing high performance levels to the baseline duct. The first set used two arrays of 36 co-rotating microvane vortex generators (VGs); the second set used two arrays of 36 micro air-jet (microjet) VGs, which were designed to produce the same ‘vorticity signature’ as the microvanes. Optimization of the microvane array was accomplished using a Design of Experiments (DOE) methodology to guide selection of parameters used in multiple Computational Fluid Dynamics (CFD) flow solutions. A verification test conducted in the NASA Glenn W1B test facility indicated low pressure recovery and high distortion for the baseline duct without flow control. With microvane flow control, at a throat Mach number of 0.60, pressure recovery was increased 5%, and both spatial distortion and turbulence were decreased approximately 50%. Microjet effectors also provided significantly improved performance over the baseline configuration. Nomenclature
A Breath of Fresh Air (2010)

According to the Collaborative on Health and the Environment, asthma is estimated to affect 300 million people worldwide. Asthma is the leading cause of hospitalization in children. G‐protein coupled receptors (GPCR) are a large family of transmembrane proteins that cells use to communicate with the environment. Beta‐2‐adrenergic receptor (B2AR) is a member of this family and binds to the small hormone adrenaline. The G‐protein relays the message to relax the muscles in the lungs and to open airways. In the case of a person with asthma, this interaction causes the lungs to constrict and airways to close. Our hypothesis will model the interaction of B2AR and GalphaS. These components move inward surrounding the ligand binding site, forming a "toggle switch" for receptor activation. By getting a better understanding of the structural changes following G protein binding, improved therapeutics can be developed to target the active receptor. People afflicted with respiratory diseases will be able to take a breath of fresh air. The El Capitan High School SMART (Students Modeling a Research Topic) Team is a partnership between a researcher and a group of students who used current data to create a physical model of B2AR interacting with GalphaS using 3D printing technology. Supported by a grant from the HHMI Pre‐College Program.
Swarm: robust and fast clustering method for amplicon-based studies (2014)

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units, improving the amount of meaningful biological information that can be extracted from amplicon-based studies.
Palladium oxide-decorated mesoporous silica on graphene oxide nanosheets as a heterogeneous catalyst for the synthesis of β-substituted indole derivatives (2021)

In this work, an efficient and facile strategy has been adopted for the stepwise synthesis of the RGO-MSiO2/PdO hybrid nanomaterial (HY-NM). Herein, a hybrid nanostructure of mesoporous silica over graphene oxide (GO) sheets has been developed followed by immobilizing palladium oxide nanoparticles (PdO NPs), and then it has been utilized for catalyzing a multicomponent reaction (MCR). To authenticate the successful synthesis of the HY-NM and successive immobilization of PdO NPs, various physicochemical characterization techniques were utilized such as SEM, EDAX, HR-TEM, HR-XRD, TGA, BET, FT-IR, and XPS analysis. The activity of the HY-NM has been determined by performing the catalyst-mediated synthesis of β-substituted indole derivatives (yield 90-98%). The excellent catalytic activity of the prepared HY-NM could be observed due to its high surface area and large porosity, which facilitates the penetration and interaction of reactant molecules with the catalytic active species. This protocol eliminates the requirement of further purification after the isolation of the product from the reaction mixture. The ease of handling, recyclability of the catalyst, and simple work-up procedure are the main features of this protocol. The synthesized HY-NM could be recycled for multiple catalytic cycles making it a very effective heterogeneous catalyst.
Analyzing the Human Serum Antibody Responses to a Live Attenuated Tetravalent Dengue Vaccine Candidate (2020)

BACKGROUND: Dengue virus serotypes 1-4 (DENV-1-4) are the most common vector-borne viral pathogens of humans and the etiological agents of dengue fever and dengue hemorrhagic syndrome. A live-attenuated tetravalent dengue vaccine (TDV) developed by Takeda Vaccines has recently progressed to phase 3 safety and efficacy evaluation. METHODS: We analyzed the qualitative features of the neutralizing antibody (nAb) response induced in naive and DENV-immune individuals after TDV administration. Using DENV-specific human monoclonal antibodies (mAbs) and recombinant DENV displaying different serotype-specific Ab epitopes, we mapped the specificity of TDV-induced nAbs against DENV-1-3. RESULTS: Nearly all subjects had high levels of DENV-2-specific nAbs directed to epitopes centered on domain III of the envelope protein. In some individuals, the vaccine induced nAbs that tracked with a DENV-1-specific neutralizing epitope centered on domain I of the envelope protein. The vaccine induced binding Abs directed to a DENV-3 type-specific neutralizing epitope, but findings of mapping of DENV-3 type-specific nAbs were inconclusive. CONCLUSION: Here we provide qualitative measures of the magnitude and epitope specificity of the nAb responses to TDV. This information will be useful for understanding the performance of TDV in clinical trials and for identifying correlates of protective immunity.
Multi-Zone Modeling and Energy Efficient Control of Shopping Center Cooling (2018)

In this paper we consider the problem of constructing a dynamical model for shopping center HVAC systems, suitable for proposing new high-level control designs to minimize energy consumption for the entire shopping center. We also propose a preliminary control design, to increase energy efficiency. The specific system considered in this paper, is a small section of a Danish shopping center, including three shops and their joint cooling system. The current control solution is investigated and described. A dynamical model is constructed as a grey-box RC-equivalent model, a suitable modeling paradigm for control-oriented models that also have to be scalable. Parameters for the model have been identified through a combination of measurement data from several days of live operation and table-lookup, calculating thermal properties based on shop dimensions. The resulting model is used to propose a preliminary control solution, to increase efficiency by utilizing a higher forward temperature. This is achieved through a control design that seeks to drive valve openings closer to fully open, while still allowing headroom for disturbance rejection. One of the main benefits of this design, is the low implementation barrier, as it does not require alterations to shop-local temperature controllers. Simulations show that the proposed control solution works as intended, without degrading the performance of the existing shop temperature control.
Electrosurgery in Colonoscopy (2009)

1Mount Sinai Hospital, New York, New York, USA. Correspondence: Jerome Waye, MD, Gastroenterology, Mount Sinai Medical Center, 650 Park Avenue, New York, New York 10021, USA. E-mail: [email protected]
Bayesian parameter estimation in image reconstruction from subsampled blurred observations (2004)

In this paper we consider the estimation of the unknown hyperparameters for the problem of reconstructing a high-resolution image from multiple undersampled, shifted, blurred and degraded frames with subpixel displacement errors. We derive mathematical expressions for the iterative calculation of the maximum likelihood estimate (mle) of the unknown hyperparameters given the low resolution observed images. Finally, the proposed method is tested on a synthetic image.
Atrial Fibrillation in Patients with Septic Shock: A One-Year Observational Pilot Study (2019)

In patients with septic shock, AF has a high incidence, and it correlated with a worse outcome. Patients with higher SOFA score are at a greater risk of developing arrhythmia.
Selective Cytotoxic Ru(II) Arene Cp* Complex Salts [R-PhRuCp*]+X−for X = BF4−, PF6−, and BPh4− (2008)

A novel series of ionic Ru(II) arene Cp* sandwich complexes has been synthesized and characterized. Screening results for cytotoxicity against a range of human tumor cell lines and normal human cells indicate that the complexes show promising anticancer activity, which varies with changes in the arene ligand and the anionic counterion.
Self‐Regulative Direct Ink Writing of Frontally Polymerizing Thermoset Polymers (2022)

Abstract The ability to manufacture highly intricate designs is one of the key advantages of 3D printing. Achieving high dimensional accuracy requires precise, often time‐consuming calibration of the process parameters. Computerized feedback control systems for 3D printing enable sensing and real‐time adaptation and optimization of these parameters at every stage of the print, but multiple challenges remain with sensor embedment and measurement accuracy. In contrast to these active control approaches, here, the authors harness frontal polymerization (FP) to rapidly cure extruded filament in tandem with the printing process. A temperature gradient present along the filament, which is dependent on the printing parameters, can impose control over this exothermic reaction. Experiments and theory reveal a self‐regulative mechanism between filament temperature and cure kinetics that allows the frontal cure speed to autonomously match the print speed. This self‐regulative printing process rapidly adapts to changes in print speed and environmental conditions to produce complex, high‐fidelity structures and freestanding architectures spanning up to 100 mm, greatly expanding the capabilities of direct ink writing (DIW).
Quantum-dot mode-locked lasers for microwave-signal generation and 160 Gb/s optical communication (2015)

40 GHz quantum-dot mode-locked lasers providing low-jitter optical and electrical microwave signals are investigated. 160 Gb/s data transmission based on differential quadrature phase-shift keying and optical time-division multiplexing is demonstrated using a packaged module.
Laser patterning and welding of transparent polymers for microfluidic device fabrication (2006)

CO2-laser-assisted micro-patterning of polymethylmethacrylate (PMMA) or cyclo-olefin copolymer (COC) has a great 
potential for the rapid manufacturing of polymeric devices including cutting and structuring. Channel widths of about 
50 μm as well as large area patterning of reservoir structures or drilling of vias are established. For this purpose a high 
quality laser beam is necessary as well as an appropriate beam forming system. In combination with laser transmission 
welding a fast fabrication of two- and three-dimensional micro-fluidic devices was possible. Welding as well as 
multilayer welding of transparent polymers was investigated for different polymers such as PMMA, polyvinylidene 
fluoride (PVDF), COC, and polystyrene (PS). The laser transmission welding process is performed with a high-power 
diode laser (wavelength 940 nm). An absorption layer with a thickness of several nanometers is deposited onto the 
polymer surfaces. The welding process has been established for the welding of polymeric parts containing microchannels, 
if the width of the channels is equal or larger than 100μm. For smaller feature sizes the absorption layer is 
structured by UV-laser radiation in order to get a highly localized welding seam, e.g., for the limitation of thermal 
penetration and thermal damaging of functional features such as channels, thin walls or temperature-sensitive substances 
often contained in micro-fluidic devices. This process strategy was investigated for the welding of capillary 
electrophoresis chips and capillary blood separation chips, including channel widths of 100 μm and 30 μm. Analysis of 
the thickness of the absorption layer was carried out with optical transmission spectroscopy.
Methods to Register Models and Input/Output Parameters for Integrated Modeling (2010)

Significant resources can be required when constructing integrated modeling systems. In a typical application, components (e.g., models and databases) created by different developers are assimilated, requiring the framework’s functionality to bridge the gap between the user’s knowledge of the components being linked. The framework, therefore, needs the capability to assimilate a wide range of model-specific input/output requirements as well as their associated assumptions and constraints. The process of assimilating such disparate components into an integrated modeling framework varies in complexity and difficulty. Several factors influence the relative ease of assimilating components, including, but not limited to, familiarity with the components being assimilated, familiarity with the framework and its tools that support the assimilation process, level of documentation associated with the components and the framework, and design structure of the components and framework. This initial effort reviews different approaches for assimilating models and their model-specific input/output requirements by considering four case study examples: 1) modifying component models to directly communicate with the framework (i.e., through an Application Programming Interface), 2) developing model-specific external wrappers such that no component model modifications are required, 3) using parsing tools to visually map pre-existing input/output files, and 4) describing and linking models as dynamic link libraries. Most of these examples are derived from assimilation efforts for the widely distributed modeling system called Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES). The review concludes that each has its strengths and weakness, the factors that determine which approaches work best in a given application.
Health-Related Quality of Life in Patients With Progressive Midgut Neuroendocrine Tumors Treated With 177Lu-Dotatate in the Phase III NETTER-1 Trial (2018)

Purpose Neuroendocrine tumor (NET) progression is associated with deterioration in quality of life (QoL). We assessed the impact of <sup>177</sup>Lu-Dotatate treatment on time to deterioration in health-related QoL. Methods The NETTER-1 trial is an international phase III study in patients with midgut NETs. Patients were randomly assigned to treatment with <sup>177</sup>Lu-Dotatate versus high-dose octreotide. European Organisation for Research and Treatment of Cancer quality-of-life questionnaires QLQ C-30 and G.I.NET-21 were assessed during the trial to determine the impact of treatment on health-related QoL. Patients completed the questionnaires at baseline and every 12 weeks until tumor progression. QoL scores were converted to a 100-point scale according to European Organisation for Research and Treatment of Cancer instructions, and individual changes from baseline scores were assessed. Time to QoL deterioration (TTD) was defined as the time from random assignment to the first QoL deterioration ≥ 10 points for each patient in the corresponding domain scale. All analyses were conducted on the intention-to-treat population. Patients with no deterioration were censored at the last QoL assessment date. Results TTD was significantly longer in the <sup>177</sup>Lu-Dotatate arm (n = 117) versus the control arm (n = 114) for the following domains: global health status (hazard ratio [HR], 0.406), physical functioning (HR, 0.518), role functioning (HR, 0.580), fatigue (HR, 0.621), pain (HR, 0.566), diarrhea (HR, 0.473), disease-related worries (HR, 0.572), and body image (HR, 0.425). Differences in median TTD were clinically significant in several domains: 28.8 months versus 6.1 months for global health status, and 25.2 months versus 11.5 months for physical functioning. Conclusion This analysis from the NETTER-1 phase III study demonstrates that, in addition to improving progression-free survival, <sup>177</sup>Lu-Dotatate provides a significant QoL benefit for patients with progressive midgut NETs compared with high-dose octreotide.