gebhart/patrepeval huggingface dataset:
Three‐Dimensional Bioactive and Biodegradable Scaffolds Fabricated by Surface‐Selective Laser Sintering (2004)

Surface-selective laser sintering (SSLS) has been developed for fabrication of three-dimensional polymer composite scaffolds with precise dimensions and intricate structure (see Figure), which are bioactive and biodegradable. SSLS allows sintering of polymer powders by melting only the surface layers of particles, which prevents overheating of internal domains, allowing incorporation of bioactive molecules into the structures.
Diffusion Spectrum Imaging tractography in complex cerebral white matter: an investigation of the centrum semiovale (2004)

Brain fiber tracking is a very challenging issue as we need to solve a difficult inverse problem i.e. retrieve continuous intermixing trajectories from a discretized, low-pass filtered position-orientation space of finite resolution. In particular fiber crossing is a recognized problem for Diffusion Tensor Imaging (DTI) tractography [1] as the diffusion tensor can only identify accurately the fiber orientation when the axonal population in each MRI voxel is unique. Recently, we have described a novel approach to diffusion MRI, Diffusion Spectrum Imaging (DSI) which affords the capacity to accurately image multiple fiber directions at each location (Fig A) [2,3].
Young guns/object orientation (2006)

OOPSLA attendees have traditionally looked to the panel program for red-meat relief from a diet of high-fiber technical track material and abstruse Onward! exotica. However, panels often feature a tired parade of the usual suspects: the same faces hawking the same hackneyed twentieth century ideas over and over again. At the same time, familiar names are a predicable draw. The effect is that it may take many years for new blood to find its way into the panel program.This panel seeks to break this logjam by featuring only panelists at or under the age of 0x20. They will offer their opinions and insights as to what we have been doing wrong for the last twenty years and what they will have to do fix it. Grudging recognition of what has gone right may be offered as well.Mechanisms to guarantee the anonymity of the most brash positions will allow the participants to be provocative as well as precocious.
Temperature Programed Desorption Using an off‐the‐Shelf Hybrid Microwave Oven (2008)

This chapter contains sections titled: Abstract Introduction Hybrid Microwave Concept SRNL Hybrid Microwave Oven Hybrid Microwave Operation Conclusions Acknowledgements References
Physiological modulation of CFTR activity by AMP-activated protein kinase in polarized T84 cells (2003)

The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-activated, ATP-gated Cl(-) channel and cellular conductance regulator, but the detailed mechanisms of CFTR regulation and its regulation of other transport proteins remain obscure. We previously identified the metabolic sensor AMP-activated protein kinase (AMPK) as a novel protein interacting with CFTR and found that AMPK phosphorylated CFTR and inhibited CFTR-dependent whole cell conductances when coexpressed with CFTR in Xenopus oocytes. To address the physiological relevance of the CFTR-AMPK interaction, we have now studied polarized epithelia and have evaluated the localization of endogenous AMPK and CFTR and measured CFTR activity with modulation of AMPK activity. By immunofluorescent imaging, AMPK and CFTR share an overlapping apical distribution in several rat epithelial tissues, including nasopharynx, submandibular gland, pancreas, and ileum. CFTR-dependent short-circuit currents (I(sc)) were measured in polarized T84 cells grown on permeable supports, and several independent methods were used to modulate endogenous AMPK activity. Activation of endogenous AMPK with the cell-permeant adenosine analog 5-amino-4-imidazolecarboxamide-1-beta-d-ribofuranoside (AICAR) inhibited forskolin-stimulated CFTR-dependent I(sc) in nonpermeabilized monolayers and monolayers with nystatin permeabilization of the basolateral membrane. Raising intracellular AMP concentration in monolayers with basolateral membranes permeabilized with alpha-toxin also inhibited CFTR, an effect that was unrelated to adenosine receptors. Finally, overexpression of a kinase-dead mutant AMPK-alpha1 subunit (alpha1-K45R) enhanced forskolin-stimulated I(sc) in polarized T84 monolayers, consistent with a dominant-negative reduction in the inhibition of CFTR by endogenous AMPK. These results indicate that AMPK plays a physiological role in modulating CFTR activity in polarized epithelia and suggest a novel paradigm for the coupling of ion transport to cellular metabolism.
Automatic heart volume measurement from CMR images using ant colony optimization with iterative salient isolated thresholding (2012)

Manual segmentation of CMR images is inefficient and inconsistent method for measuring ventricular volumes. In this study, a new technique (ACOISIT) is developed and implemented for measuring ventricular volumes. The technique is based on automatic delineation of bloodmyocardium border using ant colony optimization with salient isolated thresholding. The technique was implemented on datasets from eight volunteers and the results were compared to manual segmentation. ACOISIT showed good agreement with the gold standard and was faster and more consistent than manual segmentation.
Nonlinear sinogram filter design for backprojection reconstruction (2002)

This work focuses on a tomographic image reconstruction method which will be referred to as nonlinear backprojection (NBP). Rather than explicitly statistically modeling the forward process and the unknown image, the authors train an optimal nonlinear backprojection operator which can be implemented non-iteratively. Under appropriate assumptions, the method forms its estimate by applying nonlinear filters to sinogram data, followed by conventional backprojection. The nonlinear filters are designed through off-line training. Nonlinear backprojection shows promising results relative to both filtered backprojection and MAP Bayesian methods.
Supplementary Data from Global Phosphoproteomics Reveal CDK Suppression as a Vulnerability to KRas Addiction in Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
AACrobat (2017)

Gaze-based alternative and augmentative communication (AAC) devices provide users with neuromuscular diseases the ability to communicate with other people through only the movement of their eyes. These devices suffer from slow input, causing a host of communication breakdowns to occur during face-to-face conversations. These breakdowns lead to decreased user autonomy, conversation quality, and communication partner engagement. Attempts to improve communication through these devices has mainly focused on throughput and rate enhancement, though this has only attained meager results to date. In this work, we address this issue from the top down by considering AAC devices as a form of groupware and designing interactions around this groupware that facilitate better conversations for all involved communicators. We first present qualitative findings on issues with gaze-based AAC and end-user communication preferences; we identify several design guidelines for improving these systems and then present AACrobat, a system that embodies these guidelines and introduces novel interactions by extending gaze-based AAC devices with a mobile companion app. Finally, we present early feedback on AACrobat through three case studies of users with ALS.
Fractal network model for simulating abdominal and lower extremity blood flow during resting and exercise conditions (2007)

We present a one-dimensional (1D) fluid dynamic model that can predict blood flow and blood pressure during exercise using data collected at rest. To facilitate accurate prediction of blood flow, we developed an impedance boundary condition using morphologically derived structured trees. Our model was validated by computing blood flow through a model of large arteries extending from the thoracic aorta to the profunda arteries. The computed flow was compared against measured flow in the infrarenal (IR) aorta at rest and during exercise. Phase contrast-magnetic resonance imaging (PC-MRI) data was collected from 11 healthy volunteers at rest and during steady exercise. For each subject, an allometrically-scaled geometry of the large vessels was created. This geometry extends from the thoracic aorta to the femoral arteries and includes the celiac, superior mesenteric, renal, inferior mesenteric, internal iliac and profunda arteries. During rest, flow was simulated using measured supraceliac (SC) flow at the inlet and a uniform set of impedance boundary conditions at the 11 outlets. To simulate exercise, boundary conditions were modified. Inflow data collected during steady exercise was specified at the inlet and the outlet boundaries were adjusted as follows. The geometry of the structured trees used to compute impedance was scaled to simulate the effective change in the cross-sectional area of resistance vessels and capillaries due to exercise. The resulting computed flow through the IR aorta was compared to measured flow. This method produces good results with a mean difference between paired data to be 1.1 +/- 7 cm(3) s(- 1) at rest and 4.0 +/- 15 cm(3) s(- 1) at exercise. While future work will improve on these results, this method provides groundwork with which to predict the flow distributions in a network due to physiologic regulation.
Higher Angiotensin II Type 1 Receptor Levels and Activity in the Postmortem Brains of Older Persons with Alzheimer’s Dementia (2021)

Aging is a key risk factor in Alzheimer's dementia (AD) development and progression. The primary dementia-protective benefits of angiotensin II subtype 1 receptor (AT1R) blockers are believed to arise from systemic effects on blood pressure. However, a brain-specific renin-angiotensin system (b-RAS) exists, which can be altered by AT1R blockers. Brain RAS acts mainly through 3 angiotensin receptors: AT1R, AT2R, and AT4R. Changes in these brain angiotensin receptors may accelerate the progression of AD. Using postmortem frontal cortex brain samples of age- and sex-matched cognitively normal individuals (n = 30) and AD patients (n = 30), we sought to dissect the b-RAS changes associated with AD and assess how these changes correlate with brain markers of oxidative stress, inflammation, and mitochondrial dysfunction as well as amyloid-β and paired helical filament tau pathologies. Our results show higher protein levels of the pro-inflammatory AT1R and phospho-ERK (pERK) in the brains of AD participants. Brain AT1R levels and pERK correlated with higher oxidative stress, lower cognitive performance, and higher tangle and amyloid-β scores. This study identifies molecular changes in b-RAS and offers insight into the role of b-RAS in AD-related brain pathology.
Improved method for the synthesis of phosphatidylcholines. (1984)

An improved method for the synthesis of phosphatidylcholines from phosphatidic acid and choline is described. The technique utilizes the tetraphenylborate salt of choline together with the condensing agent 2,4,6-triisopropylbenzenesulfonyl chloride. The yields in the reaction are consistently in the range 70-75%.
Microfluidic chamber arrays for whole-organism high-throughput combinatorial chemical screening based on behavioral responses (2010)

Microorganisms are used in genetic research and drug screening because of their low complexity, ease of maintenance, and similar genetics to humans; however, their size makes it difficult for researchers to physically manipulate these microorganisms. This limits the scale on which experiments can be run. We have developed microfluidic technologies to enable high-throughput drug screening. The easy-to-use device allows rapid loading and housing C. elegans in a circular chamber array during drug screening. In addition, chemicals can be precisely delivered to the worms. Our device increases the parallel experimentation number of separate, identifiable microorganisms by ten folds.
All‐Solution‐Processed Red and Orange‐Red Organic Light‐Emitting Diodes with High‐Efficiencies: The Effect of Mixed‐Host Emissive Layers and Thermal Annealing Treatment (2019)

The instability of the organic light-emitting diodes (OLEDs) during operation can be attributed to the existence of point defects on the organic layers. In this work, the effect of mixed-host emissive layer and the thermal annealing treatment were investigated to eliminate defects and to boost the device performance. The mixed-host system includes 4,4',4''-tri (9-carbazoyl) triphenylamine (TCTA) and 2,7-bis(diphenylphosphoryl)-9, 9'-spirobi[fluorene] (SPPO13). The mixed-host emissive layer with thermal annealing treatment showed low roughness and few pinholes, and the devices fabricated from this emissive layer exhibited high efficiencies, high stabilities, and long lifetimes. The red and orange-red OLEDs exhibited efficiencies of 13.9 cd/A and 24.35 cd/A, respectively. The longest half-lifetime (L<sub>0</sub> =500 cd/m<sup>2</sup> ) of the red and orange-red OLEDs were 158 h and 180 h, respectively. Efforts were made to solve problems in large-area coating and to reduce the number of defects on in organic layer. Large-active-area (active area=3 cm×4 cm) red phosphorescent OLEDs (PhOLEDs) devices were realized with very high current efficiency up to 9 cd/A.
Estimation of high frequency scattered microwave electric field using the extended Born approximation [microwave imaging applications] (2004)

In this paper, we investigate and evaluate the performance of the extended Born approximation in a high frequency band, up to 18 GHz. We reformulate the EBA in terms of the dielectric constant. The scattered electric fields using the EBA are compared with the exact model. We demonstrate a guideline for choosing the grid size and discuss the dependence of the accuracy of EBA on size and permittivity of the anomaly. In addition, the EBA model is applied to the two anomalies case. In our work, the dielectric perturbation instead of conductivity perturbation is emphasized.
Access control caching strategies (2010)

Modern enterprise systems comprise a ne-grained enforcement of complex access control policies. Consequently, the ecient evaluation of security policies is a signicant factor for the overall system performance. Moreover, modern enterprise systems are inherently based on process and workow models. These models enable new approaches for improving the performance of security evaluations. Caching is widely used for improving the performance and the reliability of systems. The dynamic nature of today’s workow systems, both in terms of changing workows and in terms of dynamic security policies impose particular challenges on the caching of access control decisions. We present a caching strategy that exploits business process models for avoiding cache misses. Moreover, we provide a detailed performance analysis of dierent caching strategies for static and dynamic aspects of access control policies, providing the required metrics for informed design decisions.
CMUT with mechanically coupled plate actuators for low frequencies (2019)

Abstract In this paper we present a structural analytical model for a capacitive micromachined ultrasonic transducer (CMUT), based on a sacrificial release fabrication process and comprised of electro-mechanical plate actuators transferring their motion to a coupling roof structure on top. The structure features a larger average displacement compared to conventional designs at lower operational frequencies. Low operational frequencies in the range of – are beneficial for airborne applications due to their frequency-dependent strong wave attenuation in air, limiting the signal-to-noise ratio. The eigenfrequency dependence on the roof mass is calculated analytically and lumped elements, which can be used in equivalent circuits, are extracted. In addition, finite element analyses utilizing a shell-beam model are conducted. Experimental results, based on digital holographic microscopy, reveal the usability of the deduced model within an uncertainty of 8%. The developed dimensionless form of the analytical model can be used for future design purposes.
A Virtual Plant for Integrated Continuous Manufacturing of a Carfilzomib Drug Substance Intermediate, Part 3: Manganese-Catalyzed Asymmetric Epoxidation, Crystallization, and Filtration (2020)

This article describes the process characterization and development of models to inform a process control strategy to prepare (R,R)-epoxy ketone 2, an intermediate in the manufacture of carfilzomib. Model calibration for relevant unit operations and the development of a dynamic integrated flowsheet-level model in gPROMS FormulatedProducts software enabled investigation of the impact of process disturbances and model uncertainties on the critical quality attributes (CQAs) and identification of critical process disturbances and failure modes to guide a process control strategy. The model development was similar to that described in the previous parts of this series, but with the added complexity of comparing two distinct kinetic formulations for the epoxidation reaction. The main CQAs for this process were (1) the conversion of enone 1 (target ≥99.0 mol % conversion) and (2) the purity target for solids prior to cake wash (target ≥97.5% purity by weight). Conversion of enone was not always achieved with the expected disturbances: whereas 99.5% conversion was expected for normal operating conditions, 97.2% conversion was predicted for the worst-case combination of disturbances. The chiral purity of crystalline (R,R)-epoxy ketone 2 was not always achieved with the expected disturbances: 98.2% purity was expected for normal operating conditions, and 96.7% purity was expected for the worst-case combination of disturbances. These analyses allowed for rank ordering of critical process parameters that impact conversion and suitable manipulated variables to develop a robust process control strategy for the manufacturing scheme.
Endoscopic Healing in Induction and Maintenance with Ustekinumab in the Phase 3 UNITI Crohnʼs Disease Program: 2016 ACG Presidential Poster Award (2016)

Introduction: To evaluate endoscopic healing in the ustekinumab(UST) induction (UNITI-1&2)& maintenance (IM-UNITI) Phase 3 studies. Methods: Substudy patients (pts) had colonoscopies at baseline (˜UNITI Wk0), then 8 & 52 weeks later (IM-UNITI Wk44). A single central reader blindly scored all video endoscopies for ulcerations & simplifi ed endoscopic activity score for CD (SES-CD). At induction Wk0, pts received a single IV dose (UST 130mg, UST ˜6mg/kg, or PBO). At maintenance Wk0 (i.e. induction Wk8), pts with clinical response [CR] (CDAI decrease ≥100) to IV UST induction were re-randomized to subcutaneous (SC) PBO or UST 90mg (q12w or q8w) [Primary randomized maintenance population]. For the non-randomized maintenance groups: (1)UST induction non-responders received SC UST 90mg, then continued SC UST 90mg q8w if in CR 8wks later; (2)PBO induction nonresponders received UST IV 130mg, then continued SC UST 90mg q12w if in CR after 8wks; (3)PBO induction responders received PBO throughout. Pts with SES-CD ≥3 (i.e. ulceration in ≥1 segment) at induction Wk0 were eligible for analysis. Primary endpoint was change in SES-CD at induction Wk8 (Integrated UST group [induction studies & doses combined] vs PBO). Efficacy at maintenance Wk44 was evaluated in the primary randomized maintenance population & the post-hoc pooled maintenance population (randomized & nonrandomized populations combined).Table 1a: Induction Week 8 (UNITI-1&2)Table 1b: Maintenance Week 44 (IM-MUNITI)Results: UST induced significantly greater reduction in SES-CD at Wk8 vs PBO. Results were similar by induction study & UST dose. Other induction endoscopic endpoints also consistently favored UST vs PBO (Table 1a). In the primary randomized maintenance population at maintenance Wk44, trends for greater efficacy were seen with UST vs. PBO maintenance (especially UST 90mg q8w) but small sample sizes (UST n=46; PBO n=24) precluded definitive conclusions. In the larger post-hoc pooled maintenance population (Table 1b), consistent trends supporting UST maintenance, again especially UST 90mg q8w, were observed across endoscopic endpoints at Wk44. Conclusion: The endoscopy substudy primary endpoint was met; one IV UST dose induced significantly greater reduction in endoscopic disease activity vs PBO, even at a relatively early Wk8 evaluation. Greater proportions of pts receiving UST maintenance, especially UST 90mg q8w, achieved maintenance endoscopic endpoints vs PBO. Together, these data support efficacy of UST in inducing & maintaining endoscopic healing of the mucosa in CD.
Correlation Between Structure of Bcl‐2 and Its Inhibitory Function of JNK and Caspase Activity in Dopaminergic Neuronal Apoptosis (2000)

To examine the correlation between the structure of Bcl-2 and its inhibitory function of c-Jun N-terminal kinase (JNK) and caspase activity, we established a dopaminergic neuronal cell line, MN9D overexpressing Bcl-2 (MN9D/Bcl-2) or its structural mutants. The mutants comprised a point mutation in the BH1 (G145A; MN9D/BH1) or BH2 (W188A; MN9D/BH2) domain and a deletion mutation in the C-terminal (MN9D/C22), BH3 (MN9D/BH3), or BH4 (MN9D/BH4) domain. As determined by the TUNEL (terminal deoxynucleotidyltransferase nick end-labeling) and MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] reduction assay, apoptotic death of MN9D/Neo cells reached 80-90% within 24 h in response to 1 microM staurosporine. Upon staurosporine treatment, JNK activity increased six- to sevenfold over the basal level within 2-4 h. Treatment of MN9D/Neo with both staurosporine and a caspase inhibitor, Z-VAD, attenuated cell death without suppressing JNK activation. Both staurosporine-induced cell death and JNK activation were attenuated in MN9D/Bcl-2. As determined by cleavage of poly(ADP-ribose) polymerase into 85 kDa, Bcl-2 blocked caspase activity as well. When cells overexpressing one of the Bcl-2 mutants were treated with staurosporine, death was attenuated in MN9D/BH1, MN9D/BH2, and MN9D/C22 but not in MN9D/BH3 and MN9D/BH4. Similarly, both JNK and caspase activation were blocked in MN9D/BH1, MN9D/BH2, and MN9D/C22, whereas they were not suppressed in MN9D/BH3 and MN9D/BH4. Taken together, our data indicate that there exists a close structural and functional correlation of Bcl-2 to JNK and caspase activity in staurosporine-induced dopaminergic neuronal cell death.