gebhart/patrepeval huggingface dataset:
Adaptive online context-sensitive inlining (2003)

As current trends in software development move toward more complex object-oriented programming, inlining has become a vital optimization that provides substantial performance improvements to C++ and Java programs. Yet, the aggressiveness of the inlining algorithm must be carefully monitored to effectively balance performance and code size. The state-of-the-art is to use profile information (associated with call edges) to guide inlining decisions. In the presence of virtual method calls, profile information for one call edge may not be sufficient for making effectual inlining decisions. Therefore, we explore the use of profiling data with additional levels of context sensitivity. In addition to exploring fixed levels of context sensitivity, we explore several adaptive schemes that attempt to find the ideal degree of context sensitivity for each call site. Our techniques are evaluated on the basis of runtime performance, code size and dynamic compilation time. On average, we found that with minimal impact on performance (+/-1%) context sensitivity can enable 10% reductions in compiled code space and compile time. Performance on individual programs varied from -4.2% to 5.3% while reductions in compile time and code space of up to 33.0% and 56.7% respectively were obtained.
The sensing of bacteria: emerging principles for the detection of signal sequences by formyl peptide receptors (2016)

The ability to detect specific chemical signatures released by bacteria and other microorganisms is a fundamental feature of immune defense against pathogens. There is increasing evidence that chemodetection of such microorganism-associated molecular patterns (MAMPs) occurs at many places in the body including specific sets of chemosensory neurons in the mammalian nose. Formyl peptide receptors (FPRs) are a unique family of G protein-coupled receptors (GPCRs) that can detect the presence of bacteria and function as chemotactic receptors. Here, we highlight the recent discovery of a vast family of natural FPR agonists, the bacterial signal peptides (or signal sequences), thus providing new insight into the molecular mechanisms of bacterial sensing by human and mouse FPRs. Signal peptides in bacteria are formylated, N-terminal protein signatures required for directing the transfer of proteins through the plasma membrane. After their cleavage and release, signal peptides are available for FPR detection and thus provide a previously unrecognized MAMP. With over 170 000 predicted sequences, bacterial signal peptides represent one of the largest families of GPCR ligands and one of the most complex classes of natural activators of the innate immune system. By recognizing a conserved three-dimensional peptide motif, FPRs employ an unusual detection mechanism that combines structural promiscuity with high specificity and sensitivity, thus solving the problem of detecting thousands of distinct sequences yet maintaining selectivity. How signal peptides are released by bacteria and sensed by GPCRs and how these processes shape the responses of other cells and whole organisms represents an important topic for future research.
First Demonstration oftheSimplest Cross-field Ubitron (2006)

Thesimplest cross-field Ubitron isamagnetically waveguide, characterized byinner RCandouter Raradii, pro- insulated coaxial diode withacold cathode comprising anumber ducing high-power microwave oscillations. oflongitudinally oriented single emitters periodically arranged in TheRFM operates asanoscillator duetotheinternal feed- theazimuthal planeofthediode (atransparent cathode). This backoftheinteracting system rotating electron flow - elec- typeofcathode isessentially awiggler withazimuthally periodic magnetic andelectric exciting radially oscillating electrontromagnetic fields andradiates eitherin manyfrequencies as currents within theelectron flowrotating around thecathode in synchronism cansimultaneously occurwithmanypossible crossed magnetic andelectric fields. Thecathode inside the eigenmodes ofthecoaxial waveguide (Fig. 1),orinasingle waveguide isalso aperiodic electro-dynamical system character- frequency excited asaresult ofmodecompetition. izedbyasetofazimuthal eigenmodes capable ofsynchronously interacting withtheexcited radially oscillating currents. Com- N' N puter simulations ofthecross-field Ubitron demonstrate control- ling microwave generation bychanging theexternal magnetic field withefficiency of>10%.Results ofinitial experiments are am presented. 1.DESCRIPTION OFCROSS-FIELD UBITRON b)hN Therippled-field magnetron (RFM), orcross-field freeelec- Fig. 1.(a)Cross-section ofRFMinthecathode plane; (b) Configuration of Therippled-field magnetron (RFM), orcross-field freeelecd -s1de teRFM tronlaser (FEL) proposed byBekefi asahigh-power source of
ChemInform Abstract: BioMOFs: Metal—Organic Frameworks for Biological and Medical Applications (2010)

Abstract Review: 41 refs.
C-TMLE for continuous tuning (2017)

Robust inference of a low-dimensional parameter in a large semi-parametric model relies on external estimators of infinite-dimensional features of the distribution of the data. Typically, only one of the latter is optimized for the sake of constructing a well behaved estimator of the low-dimensional parameter of interest. Optimizing more than one of them for the sake of achieving a better bias-variance trade-off in the estimation of the parameter of interest is the core idea driving the general template of the collaborative targeted minimum loss-based estimation (C-TMLE) procedure. This chapter discusses an implementation/instantiation of the C-TMLE procedure where the optimization is carried out over a set of continuous tuning parameters, like for instance a regularization parameter in a lasso penalty. Under mild assumptions, the resulting TMLE estimator remains asymptotically linear and Gaussian, allowing the construction of confidence regions of given asymptotic levels.
Spatial alignment of structural images on single-shot and readout-segmented (RESOLVE) diffusion images in the optic nerve for tractography template generation (2023)

Purpose Successful utilization of anatomical templates in the evaluation of diffusion-weighted neuroimaging-studies requires accurate registration of intra-individual datasets. We investigated the feasibility of structural MRI image registration onto single-shot and read-out segmented echo-planar diffusion-weighted imaging variants for use in tractographic samplings of the visual system, in particular the optic nerve. Methods Slab volumes of the optic nerve pathway from thirteen volunteers were acquired and preprocessed. Three neuroradiologists marked landmarks (ROIs, regions of interest) on two diffusion-weighted and one structural dataset. Structural ROIs were respectively registered (6/12 degrees of freedom, DOF) onto single-shot (ss-EPI) and readout-segmented (rs-EPI) volumes. All six ROI/FOD (fibre orientation distribution) combinations underwent a targeted tractography task (MRtrix3: iFOD2). Results Inter-rater reliability for ROI-placement was highest in VIBE images (0.66 to 0.95, mean 0.85) and lower in both ss-EPI (mean 0.77) and rs-EPI (0.46 to 0.84, mean 0.64). Sufficient FOD generation in the optic nerve was successful in 12/26 of all cases for ss-EPI volumes (46.2% of cases) and in 18/26 for rs-EPI volumes (69.2%). Spatial shift of VIBE-drawn ROI-coordinates after 6-DOF registration was highest for ss-EPI-targets (medians: 1.15 to 1.4 mm; rs-EPI 0.82 to 0.93 mm), whereas 12-DOF registration caused less spatial shifts (ss-EPI: 0.64 to 1.03 mm; rs-EPI: 0.58 mm to 0.79 mm). Tractography results revealed no significant differences between ss-EPI and rs-EPI sequences on cases with mutual generation of sufficient FODs (n=10). Conclusion Structurally-placed ROIs (highest inter-rater reliability) with 6-DOF registration onto rs-EPI targets (highest FOD-generation rate) seems most suitable for white matter template generation.
Correction [to “Actinometric measurements and theoretical calculations of j(03), The rate of photolysis of ozone to 0(1D)”] (1980)

recently determined that N20 reduces the sensitivity of the chemiluminescent NO analyzer through enhanced NO2* quenching in the reaction chamber. MuItiplying by 1.55(_+0.1) will correct measured J(03) values for this enhanced quehing.
Reformulating linear programs with transportation constraints—With applications to workforce scheduling (2003)

Abstract We study linear programming models that contain transportation constraints in their formulation. Typically, these models have a multistage nature and the transportation constraints together with the associated flow variables are used to achieve consistency between consecutive stages. We describe how to reformulate these models by projecting out the flow variables. The reformulation can be more desirable since it has fewer variables and can be solved faster. We apply these ideas to reformulate two well‐known workforce staffing and scheduling problems: the shift scheduling problem and the tour scheduling problem. We also present computational results. © 2003 Wiley Periodicals, Inc. Naval Research Logistics, 2004.
Computing Urban Traffic Congestions by Incorporating Sparse GPS Probe Data and Social Media Data (2017)

Estimating urban traffic conditions of an arterial network with GPS probe data is a practically important while substantially challenging problem, and has attracted increasing research interests recently. Although GPS probe data is becoming a ubiquitous data source for various traffic related applications currently, they are usually insufficient for fully estimating traffic conditions of a large arterial network due to the low sampling frequency. To explore other data sources for more effectively computing urban traffic conditions, we propose to collect various traffic events such as traffic accident and jam from social media as complementary information. In addition, to further explore other factors that might affect traffic conditions, we also extract rich auxiliary information including social events, road features, Point of Interest (POI), and weather. With the enriched traffic data and auxiliary information collected from different sources, we first study the traffic co-congestion pattern mining problem with the aim of discovering which road segments geographically close to each other are likely to co-occur traffic congestion. A search tree based approach is proposed to efficiently discover the co-congestion patterns. These patterns are then used to help estimate traffic congestions and detect anomalies in a transportation network. To fuse the multisourced data, we finally propose a coupled matrix and tensor factorization model named TCE_R to more accurately complete the sparse traffic congestion matrix by collaboratively factorizing it with other matrices and tensors formed by other data. We evaluate the proposed model on the arterial network of downtown Chicago with 1,257 road segments whose total length is nearly 700 miles. The results demonstrate the superior performance of TCE_R by comprehensive comparison with existing approaches.
Human Polyomavirus 7-Associated Pruritic Rash and Viremia in Transplant Recipients (2014)

Human polyomavirus 7 (HPyV7) is one of 11 HPyVs recently discovered through genomic sequencing technologies. Two lung transplant recipients receiving immunosuppressive therapy developed pruritic, brown plaques on the trunk and extremities showing a distinctive epidermal hyperplasia with virus-laden keratinocytes containing densely packed 36-45-nm icosahedral capsids. Rolling circle amplification and gradient centrifugation testing were positive for encapsidated HPyV7 DNA in skin and peripheral blood specimens from both patients, and HPyV7 early and capsid proteins were abundantly expressed in affected tissues. We describe for the first time that HPyV7 is associated with novel pathogenicity in some immunosuppressed individuals.
Unsupervised estimation of image textures using an autoregressive model (2002)

A method of estimating both the number and type of textures in an image is proposed. An autoregressive (AR) texture model is used since it describes spatial behavior in addition to mean and local variation. Solution criteria are formulated based on the concurrent estimation of the number of textures, the texture parameters, and the class of texture samples. This approach avoids problems with the instability of maximum likelihood estimation and results in an algorithm which is composed of three basic operations. The first two operations alternately reestimate the texture parameters and repartition the data into the clusters corresponding to individual textures. The third operation agglomerates clusters to reduce the number of distinct textures. Each operation attempts to minimize the basic solution criteria.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Imaging of dynamic heterogeneities in multiple-scattering media (1997)

A new method of visualizing objects with distinct internal dynamics of the constituent scattering particles embedded in a liquid multiple-scattering medium is presented. We report dynamic multiple-light-scattering experiments and a theoretical model, based on diffusing photon-density waves for concentrated colloidal suspensions in Brownian motion, as a background medium into which is inserted a capillary containing (i) the same suspension under flow, or (ii) suspensions of different particle sizes in Brownian motion. These model objects, with purely dynamic but no static scattering contrast, can be visualized by space-resolved measurements of the time autocorrelation function g2(&#x03C4;) of the scattered light intensity at the sample surface. Maximum contrast occurs at a parameter-dependent finite correlation time &#x03C4;. The physical origin of this effect is outlined. Our data are in excellent quantitative agreement with the model, with no adjustable parameter.
The Effects of Incline Level on Optimized Lower-Limb Exoskeleton Assistance: A Case Series (2022)

For exoskeletons to be successful in real-world settings, they will need to be effective across a variety of terrains, including on inclines. While some single-joint exoskeletons have assisted incline walking, recent successes in level-ground assistance suggest that greater improvements may be possible by optimizing assistance of the whole leg. To understand how exoskeleton assistance should change with incline, we used human-in-the-loop optimization to find whole-leg exoskeleton assistance torques that minimized metabolic cost on a range of grades. We optimized assistance for three non-disabled, expert participants on 5 degree, 10 degree, and 15 degree inclines using a hip-knee-ankle exoskeleton emulator. For all assisted conditions, the cost of transport was reduced by at least 50% relative to walking in the device with no assistance, which is a large improvement to walking comparable to the benefits of whole-leg assistance on level-ground (N = 3). Optimized extension torque magnitudes and exoskeleton power increased with incline. Hip extension, knee extension and ankle plantarflexion often grew as large as allowed by comfort-based limits. Applied powers on steep inclines were double the powers applied during level-ground walking, indicating that greater exoskeleton power may be optimal in scenarios where biological powers and costs are higher. Future exoskeleton devices could deliver large improvements in walking performance across a range of inclines if they have sufficient torque and power capabilities.
Reducing Atelectasis Attenuates Bacterial Growth and Translocation in Experimental Pneumonia (2004)

Besides being one of the mechanisms responsible for ventilator-induced lung injury, atelectasis also seems to aggravate the course of experimental pneumonia. In this study, we examined the effect of reducing the degree of atelectasis by natural modified surfactant and/or open lung ventilation on bacterial growth and translocation in a piglet model of Group B streptococcal pneumonia. After creating surfactant deficiency by whole lung lavage, intratracheal instillation of bacteria induced severe pneumonia with bacterial translocation into the blood stream, resulting in a mortality rate of almost 80%. Treatment with 300 mg/kg of exogenous surfactant before instillation of streptococci attenuated both bacterial growth and translocation and prevented clinical deterioration. This goal was also achieved by reversing atelectasis in lavaged animals via open lung ventilation. Combining both exogenous surfactant and open lung ventilation prevented bacterial translocation completely, comparable to Group B streptococci instillation into healthy animals. We conclude that exogenous surfactant and open lung ventilation attenuate bacterial growth and translocation in experimental pneumonia and that this attenuation is at least in part mediated by a reduction in atelectasis. These findings suggest that minimizing alveolar collapse by exogenous surfactant and open lung ventilation may reduce the risk of pneumonia and subsequent sepsis in ventilated patients.
Basic Research Needs for the Hydrogen Economy. Report of the Basic Energy Sciences Workshop on Hydrogen Production, Storage and Use, May 13-15, 2003 (2004)

The coupled challenges of a doubling in the world's energy needs by the year 2050 and the increasing demands for ''clean'' energy sources that do not add more carbon dioxide and other pollutants to the environment have resulted in increased attention worldwide to the possibilities of a ''hydrogen economy'' as a long-term solution for a secure energy future.
195 Improving Benchmarking in Spine Surgery (2012)

INTRODUCTION: Unplanned hospital readmissions increase the total cost of care and affect patients' outcomes. The purpose of this study is to assess the appropriateness of how University Health-System Consortium (UHC) classifies readmissions at our institution and to suggest an improved algorithm for the calculation of the readmission rate. METHODS: We performed a retrospective analysis of 5780 consecutive patient encounters by 10 spine surgeons at UCSF between October 2007 and June 2011 with a primary endpoint of readmission within 30 days. This data was abstracted from the UHC dataset using the Clinical Database/Resource Manager. We performed an independent chart review to determine reasons for readmission. Multivariate logistic regression analysis was used to evaluate predictors of readmission. RESULTS: 281 (4.9%) patients were readmitted within 30 days from the previous discharge date according to the UHC database. Based on our manual chart review, we found that 69 cases should not be included in our readmission rate: 39 cases were planned readmissions for staged procedures, 14 cases were cancelled or rescheduled on the index admission due to unpreventable reasons, and 16 cases were unrelated to spine surgery. We calculated our true readmission rate to be 3.7%. The current UHC algorithm overestimated true spine surgery related readmissions by 25%. We reorganized the algorithm to calculate clinically relevant readmissions. CONCLUSION: To improve patient care, a spine program must be able to distinguish pertinent readmissions. Readmissions for reasons unrelated to the index spine surgery obscure the definition of a spine-related episode of care. Our modified algorithm for readmission evaluates not only hospital re-entry, but also incorporates a diagnosis code that indicates a spine-related complication and thus avoids the 25% overestimate by the UHC algorithm. As institutions consider accountable care models it will be important to define episodes of care that accurately portray and benchmark readmission rates.
HyperFlex: An SDN virtualization architecture with flexible hypervisor function allocation (2015)

Network Virtualization (NV) and Software-Defined Networking (SDN) are both expected to increase the flexibility and programmability of today's communication networks. Combining both approaches may even be a further step towards increasing the efficiency of network resource utilization. Multiple solutions for virtualizing SDN networks have already been proposed, however, they are either implemented in software or they require special network hardware. We propose HyperFlex, an SDN hypervisor architecture that relies on the decomposition of the hypervisor into functions that are essential for virtualizing SDN networks. The hypervisor functions can be flexibly executed in software or hosted on SDN network elements. Furthermore, existing hypervisor solutions focus on data-plane virtualization mechanisms and neglect the virtualization of the control-plane of SDN networks. HyperFlex provides control-plane virtualization by adding a control-plane isolation function, either in software or on network elements. The isolation function ensures that the resources of the control-plane are shared correctly between each virtual SDN network while it also protects the hypervisor resources from resource exhaustion.
Urokinase-type plasminogen activator is effective in fibrin clearance in the absence of its receptor or tissue-type plasminogen activator. (1996)

The availability of gene-targeted mice deficient in the urokinase-type plasminogen activator (uPA), urokinase receptor (uPAR), tissue-type plasminogen activator (tPA), and plasminogen permits a critical, genetic-based analysis of the physiological and pathological roles of the two mammalian plasminogen activators. We report a comparative study of animals with individual and combined deficits in uPAR and tPA and show that these proteins are complementary fibrinolytic factors in mice. Sinusoidal fibrin deposits are found within the livers of nearly all adult mice examined with a dual deficiency in uPAR and tPA, whereas fibrin deposits are never found in livers collected from animals lacking uPAR and rarely detected in animals lacking tPA alone. This is the first demonstration that uPAR has a physiological role in fibrinolysis. However, uPAR-/-/tPA-/- mice do not develop the pervasive, multi-organ fibrin deposits, severe tissue damage, reduced fertility, and high morbidity and mortality observed in mice with a combined deficiency in tPA and the uPAR ligand, uPA. Furthermore, uPAR-/-/tPA-/- mice do not exhibit the profound impairment in wound repair seen in uPA-/-/tPA-/- mice when they are challenged with a full-thickness skin incision. These results indicate that plasminogen activation focused at the cell surface by uPAR is important in fibrin surveillance in the liver, but that uPA supplies sufficient fibrinolytic potential to clear fibrin deposits from most tissues and support wound healing without the benefit of either uPAR or tPA.