gebhart/patrepeval huggingface dataset:
Efficient phage display of intracellularly folded proteins mediated by the TAT pathway (2011)

Phage display with filamentous phages is widely applied and well developed, yet proteins requiring a cytoplasmic environment for correct folding still defy attempts at functional display. To extend applicability of phage display, we employed the twin-arginine translocation (TAT) pathway to incorporate proteins fused to the C-terminal domain of the geneIII protein into phage particles. We investigated functionality and display level of fluorescent proteins depending on the translocation pathway, which was the TAT, general secretory (SEC) or signal recognition particle (SRP) pathway mediated by the TorA, PelB or DsbA signal sequences, respectively. Importantly, for green fluorescent protein, yellow fluorescent protein and cyan fluorescent protein, only TAT, but not SEC or SRP, translocation led to fluorescence of purified phage particles, although all three proteins could be displayed regardless of the translocation pathway. In contrast, the monomeric red fluorescent protein mCherry was functionally displayed regardless of the translocation pathway. Hence, correct folding and fluorophor formation of mCherry is not limited to the cytosol. Furthermore, we successfully displayed firefly luciferase as well as an 83 kDa argonaute protein, both containing free cysteines. This demonstrates broad applicability of the TAT-mediated phagemid system for the display of proteins requiring cytoplasmic factors for correct folding and should prove useful for the display of proteins requiring incorporation of co-factors or oligomerization to gain function.
Outcome-Guided Counterfactuals for Reinforcement Learning Agents from a Jointly Trained Generative Latent Space (2022)

We present a novel generative method for producing unseen and plausible counterfactual examples for reinforcement learning (RL) agents based upon outcome variables that characterize agent behavior. Our approach uses a variational autoencoder to train a latent space that jointly encodes information about the observations and outcome variables pertaining to an agent's behavior. Counterfactuals are generated using traversals in this latent space, via gradient-driven updates as well as latent interpolations against cases drawn from a pool of examples. These include updates to raise the likelihood of generated examples, which improves the plausibility of generated counterfactuals. From experiments in three RL environments, we show that these methods produce counterfactuals that are more plausible and proximal to their queries compared to purely outcome-driven or case-based baselines. Finally, we show that a latent jointly trained to reconstruct both the input observations and behavioral outcome variables produces higher-quality counterfactuals over latents trained solely to reconstruct the observation inputs.
Surface recombination of O and H2 on meteoric dust as a source of mesospheric water vapor (1999)

One of the most provocative recent developments in mesospheric science is the discovery of a narrow layer of water vapor located near 70 km altitude where the H 2 O mixing ratio reaches the highest values observed in the middle atmosphere [ Summers et al. , 1997a]. This layer can only be explained by a local source of H 2 O, which is contrary to conventional gas phase chemistry that predicts net H 2 O destruction in that part of the mesosphere. Although suggestions have been made that this layer is produced by an influx of small comets releasing water in the upper atmosphere, we propose that the reaction O + H 2 → H 2 O on the surface of meteoric dust can account for the observed H 2 O layer. Using a chemical‐transport model we find that the inclusion of this reaction with a reaction probability of ∼0.01 yields a model H 2 O layer with the observed characteristics. We suggest that the key to understanding the origin of the H 2 O layer lies in coincident observations of mesospheric H 2 and H 2 O.
Functional Outcome After Blunt and Penetrating Carotid Artery Injuries: Analysis of the National Trauma Data Bank (2005)

Blunt CAI is associated with more severe functional disability at discharge than penetrating CAI. Even when compared with a similarly injured control group, blunt CAI results in significant additional severe functional disabilities in feeding, expression, and locomotion.
Distal radius nonunion after volar locking plate fixation of a distal radius fracture: a case report. (2017)

We describe a 59-year-old man who had nonunion of a right distal radius fracture after volar locking plate fixation. He underwent open reduction and internal fixation with a volar locking plate system for a dorsally displaced, unstable distal radius fracture at a previous hospital 5 months ago. Radiographs of the injured wrist showed nonunion of the distal radius with 1.5-mm ulnar minus variance. Radiographs of the unaffected wrist showed 3.5-mm ulnar plus variance. Intraoperative findings of surgical revision showed an unstable nonunion; thus, debridement of the nonunion, autogenous inlay bone grafting, and internal fixation using another type of volar locking plate system were performed. Healing of the re-operative site was confirmed radiographically 3 months postoperatively. We considered that volar locking plate fixation with excessive distraction of the fracture may lead to nonunion.
Balance and knee extensibility evaluation of hemiplegic gait using an inertial body sensor network (2013)

It was concluded that the wearable bio-motion acquisition platform provided a practical approach that was effective in discriminating gait symptoms between hemiplegic and asymptomatic subjects. The extensibility of hemiplegic patients' lower limbs was significantly lower than that of normal subjects, and the hemiplegic gait had worse balance level compared with normal gait. The effect of rehabilitation training of hemiplegic gait could be quantitatively analyzed.
Death and Dying in Hospitalized Pediatric Patients: A Prospective Multicenter, Multinational Study (2021)

<b><i>Background:</i></b> For hospitalized children admitted outside of a critical care unit, the location, mode of death, "do-not-resuscitate" order (DNR) use, and involvement of palliative care teams have not been described across high-income countries. <b><i>Objective:</i></b> To describe location of death, patient and terminal care plan characteristics of pediatric inpatient deaths inside and outside the pediatric intensive care unit (PICU). <b><i>Design:</i></b> Secondary analysis of inpatient deaths in the Evaluating Processes of Care and Outcomes of Children in Hospital (EPOCH) randomized controlled trial. <b><i>Setting/Subjects:</i></b> Twenty-one centers from Canada, Belgium, the United Kingdom, Ireland, Italy, the Netherlands, and New Zealand. <b><i>Measurement:</i></b> Descriptive statistics were used to compare patient and terminal care plan characteristics. A multivariable generalized estimating equation examined if palliative care consult during hospital admission was associated with location of death. <b><i>Results:</i></b> A total of 365 of 144,539 patients enrolled in EPOCH died; 219 (60%) died in PICU and 143 (40%) died on another inpatient unit. Compared with other inpatient wards, patients who died in PICU were less likely to be expected to die, have a DNR or palliative care consult. Hospital palliative care consultation was more common in older children and independently associated with a lower adjusted odds (95% confidence interval) of dying in PICU [0.59 (0.52-0.68)]. <b><i>Conclusion:</i></b> Most pediatric inpatient deaths occur in PICU where patients were less likely to have a DNR or palliative care consult. Palliative care consultation could be better integrated into end-of-life care for younger children and those dying in PICU.
Strong and Coherent Coupling of a Plasmonic Nanoparticle to a Subwavelength Fabry–Pérot Resonator (2015)

A major aim in experimental nano- and quantum optics is observing and controlling the interaction between light and matter on a microscopic scale. Coupling molecules or atoms to optical microresonators is a prominent method to alter their optical properties such as luminescence spectra or lifetimes. Until today strong coupling of optical resonators to such objects has only been observed with atom-like systems in high quality resonators. We demonstrate first experiments revealing strong coupling between individual plasmonic gold nanorods (GNR) and a tunable low quality resonator by observing cavity-length-dependent nonlinear dephasing and spectral shifts indicating spectral anticrossing of the luminescent coupled system. These phenomena and experimental results can be described by a model of two coupled oscillators representing the plasmon resonance of the GNR and the optical fields of the resonator. The presented reproducible and accurately tunable resonator allows us to precisely control the optical properties of individual particles.
Stable algorithms for link analysis (2001)

The Kleinberg HITS and the Google PageRank algorithms are eigenvector methods for identifying ``authoritative'' or ``influential'' articles, given hyperlink or citation information. That such algorithms should give reliable or consistent answers is surely a desideratum, and in~\cite{ijcaiPaper}, we analyzed when they can be expected to give stable rankings under small perturbations to the linkage patterns. In this paper, we extend the analysis and show how it gives insight into ways of designing stable link analysis methods. This in turn motivates two new algorithms, whose performance we study empirically using citation data and web hyperlink data.
Caractérisation de composés chimiques agissant sur le phénomène d'épissage alternatif du gène LMNA responsable du vieillissement précoce : applications dans l'obésité (2013)

L'epissage alternatif des ARNs pre-messagers est le mecanisme majeur de diversification de l'information genetique chez les eucaryotes superieurs. Pres de 70% des genes sont concernes par ce mecanisme. Il arrive malgre tout que l'epissage alternatif soit deregule ce qui conduit a des defauts d'epissage qui provoquent des maladies telles que le syndrome progerique de Hutchinson-Gilford (HGPS). Cette maladie se caracterise notamment par une apparition precoce des signes distinctifs de la vieillesse ainsi que de defauts metaboliques majeurs. Mon travail de these a consiste a selectionner et a caracteriser des composes chimiques modulateurs de l'epissage alternatif en se basant sur le mecanisme moleculaire conduisant a la progeria. Par la suite, l'efficacite de ces molecules a ete testee dans des modeles de souris obeses. Parmi une chimiotheque de plus de 700 molecules chimiques, j'ai pu selectionner sur differents criteres une vingtaine de molecules modulatrices de l'epissage de l'exon 11 du gene LMNA. Une seule molecule a ete capable de diminuer la prise de poids de souris mises sous regime hyperlipidique en favorisant la mise a disposition des lipides et en diminuant la differenciation adipocytaire grâce a son action sur les micros ARN.
Precise measurement of the thermal expansion of silicon near 40 °C (1976)

We report absolute measurements of the thermal-expansion coefficient of single-crystal silicon having a precision of ±0.2%. Five thermal-expansion values have been determined using 1.9 °C temperature measurement intervals within the temperature range 34–44 °C. Our value for the thermal expansion of silicon at 35.22±0.08 °C is 2.683±0.005×10−6 cm/cm °C, which agrees with previous measurements by others and represents an almost fivefold increase in accuracy.
Reaction of the ylide complex [(η5-C5H5)Re(NO)(PPh3)(CH2P+Ar3)]PF6–with η-butyl-lithium–tetramethylenediamine; generation and stereospecific alkylation of a transition metal-substituted Wittig reagent (1986)

The title reaction (tetrahydrofuran, –24 °C, 2 h) gives [(η5-C5H5)Re(NO)(PPh3)([graphic omitted]H–P+Ar3)](2; Ar =p-MeC6H4), which upon treatment with MeOSO2CF3 gives (SS,RR)-[(η5-C5H5)Re(NO)(PPh3){CH(Me)P+Ar3}]PF6–[(SS,RR)-(3)] stereospecifically.
Locating zigbee® nodes using the ti®s cc2431 location engine (2008)

In this paper, we analyze and describe the achievable performance of a Wireless Sensor Network (WSN) testbed platform, which has been deployed at the Center of Excellence DEWS (University of L'Aquila, Italy) for positioning applications, and which is implemented using CC2431 sensor nodes developed by Texas Instruments® (TI)/Chipcon. In particular, we will report on an extensive campaign of measurements aiming at analyzing the performance of the CC2431's hardware location-finder engine when localization needs to be performed in a realistic and dynamic indoor propagation environment. Experimental results will show that the need of site-specific parameters for the correct operation of the location engine may severely reduce the localization accuracy of the system in dynamic environments. A simple solution to counteract this problem will also be introduced, and the related improvement will be quantified via experiments.
Phenylbutyrate Therapy for Pyruvate Dehydrogenase Complex Deficiency and Lactic Acidosis (2013)

Lactic acidosis is a buildup of lactic acid in the blood and tissues, which can be due to several inborn errors of metabolism as well as nongenetic conditions. Deficiency of pyruvate dehydrogenase complex (PDHC) is the most common genetic disorder leading to lactic acidosis. Phosphorylation of specific serine residues of the E1α subunit of PDHC by pyruvate dehydrogenase kinase (PDK) inactivates the enzyme, whereas dephosphorylation restores PDHC activity. We found that phenylbutyrate enhances PDHC enzymatic activity in vitro and in vivo by increasing the proportion of unphosphorylated enzyme through inhibition of PDK. Phenylbutyrate given to C57BL/6 wild-type mice results in a significant increase in PDHC enzyme activity and a reduction of phosphorylated E1α in brain, muscle, and liver compared to saline-treated mice. By means of recombinant enzymes, we showed that phenylbutyrate prevents phosphorylation of E1α through binding and inhibition of PDK, providing a molecular explanation for the effect of phenylbutyrate on PDHC activity. Phenylbutyrate increases PDHC activity in fibroblasts from PDHC-deficient patients harboring various molecular defects and corrects the morphological, locomotor, and biochemical abnormalities in the noa(m631) zebrafish model of PDHC deficiency. In mice, phenylbutyrate prevents systemic lactic acidosis induced by partial hepatectomy. Because phenylbutyrate is already approved for human use in other diseases, the findings of this study have the potential to be rapidly translated for treatment of patients with PDHC deficiency and other forms of primary and secondary lactic acidosis.
Symposium: Brown v. Board of Education and Its Legacy: A Tribute to Justice Thurgood Marshall, Learning Together: Justice Marshall's Desegregation Opinions (1992)

In this Article, Professor Marcus examines the influence of Justice Thurgood Marshall on the Supreme Court's current school desegregation agenda. Justice Marshall was part of the majority in desegregation cases during his earlier years on the high Court subsequently, however, his role became one of dissenter. Professor Marcus analyzes the divisive issues facing the Court in desegregation litigation, Marshall's positions on such issues, and his legacy to the Court in this area. Finally, the Article assesses the vitality of this legacy in light of two Supreme Court decisions issued after Justice Marshall's retirement.
Cross-Talk with Fluctuation in Heterogeneous Multicore Fibers (2013)

Prediction of cross-talk is an important facet of multicore fiber (MCF) design. Several approaches for estimating cross-talk in MCF have been proposed but none are faultless, especially when applied to MCF with heterogeneous cores. We propose a new calculation approach that attempts to solve this problem. In our approach, cross-talk in multicore fibers is estimated by coupled power theory. The coefficients in the coupled power equation are theoretically calculated by the central limit theorem and by quantum mechanical time-dependent perturbations. The results from our calculations agree with those of Monte Carlo simulations of heterogeneous MCFs.
Water-Ice and Water-Updraft Relationships near −10°C within Populations of Florida Cumuli (1980)

From an in-cloud microphysical data set collected in Florida convective towers that were penetrated close to their tops near -10°C, evidence is presented to show a sequential development of cloud water, rainwater, graupel and crystalline ice as the cloud ages. Of particular interest is the very rapid onset of graupel that appears on repeat penetrations of some, but not all, towers. A separate data set shows a large scatter in the relationship between maximum value of cloud water and vertical velocity which points to the conclusion that measurements of cloud water, by itself, can be misleading as an indication of growth activity. The sequential pass data showing the evolution of ice and water are consistent with a rime-splintering, secondary ice production hypothesis.
Pathogenicity of IFN-γ+ Th17 cells is independent of T-bet (P4128) (2013)

Abstract It is now established that T helper (Th) cell subsets, particularly Th17 cells, are more dynamic than originally anticipated and can acquire the expression of other lineage effector cytokines. However, the molecular cues that dictate their plasticity are unknown. We show that IL-23 plays a central role in the plasticity of Th17 cells and is essential for the generation and propagation of IFN-γ-producing Th17 (IL-17+ IFN-γ+) cells. During the development of experimental autoimmune encephalomyelitis (EAE) IL-17+ IFN-γ+ T cells are preferentially expanded in the central nervous system (CNS). Using an IL-17A-IFN-γ double reporter mouse and I-Ab/MOG38-49 tetramer, we determined that they displayed characteristics of pathogenic T cells, such as GM-CSF expression, and contained the highest number of MOG-specific T cells. Interestingly, the Th1-associated transcription factors T-bet, STAT1 and STAT4 were not involved in the induction of IFN-γ by Th17 cells in vitro. Moreover, in contrast to previous studies showing a role for T-bet in Th1 and Th17-mediated EAE, we demonstrate that T-bet expression in T cells is not required for the emergence of CNS-infiltrating IL-17+ IFN-γ+ T cells and the development of Th17-driven EAE. Our results suggest the existence of different epigenetic programs that regulate IFN-γ expression in Th1 and Th17 cells.
NASA and Industry Benefits of ACTS High Speed Network Interoperability Experiments (2000)

This paper provides synopses of the design. implementation, and results of key high data rate communications experiments utilizing the technologies of NASA's Advanced Communications Technology Satellite (ACTS). Specifically, the network protocol and interoperability performance aspects will be highlighted. The objectives of these key experiments will be discussed in their relevant context to NASA missions, as well as, to the comprehensive communications industry. Discussion of the experiment implementation will highlight the technical aspects of hybrid network connectivity, a variety of high-speed interoperability architectures, a variety of network node platforms, protocol layers, internet-based applications, and new work focused on distinguishing between link errors and congestion. In addition, this paper describes the impact of leveraging government-industry partnerships to achieve technical progress and forge synergistic relationships. These relationships will be the key to success as NASA seeks to combine commercially available technology with its own internal technology developments to realize more robust and cost effective communications for space operations.
Users' Sentiment Analysis in Social Media Context using Natural Language Processing (2014)

The main goal of this research work is to model a natural language processing toolkit to infer users' sentiment analysis for study of feedback about a product, person or thing using the means of social media interactions. A complete discussion on the mechanism behind the data gathering using social networking channels has been made in this research as well as a small account on the design of natural language processing toolkit has been also given. To demonstrate the validation and applicability of the end application, the proposed methodology will be implemented with input sets obtained from live users' interactions on social media and feeding them to a natural language model for observation. In this research, we will also check the validity of the result obtained comparing the results obtained by polls survey and by natural language model.
Application of Thermogravimetric Analysis for the Proximate Analysis of Livestock Wastes (2010)

Abstract There is worldwide interest in deriving increasing amounts of energy from bio-based agricultural materials including not only lignocellulosic residues but also a significant quantity of available livestock manure. This manure can be used as a feedstock for various thermochemical conversion processes such as pyrolysis and gasification. In order to apply these processes, the manure must be properly characterized for volatile matter (VM) and ash contents. The determination of these components is not mentioned specifically in current ASTM standards for livestock manure. In this study, we employed the use of thermogravimetric analysis (TGA) for the rapid assessment of VM and ash content in swine, dairy, rabbit, and poultry manures using references from the ASTM coal and coke standards. The TGA assessment of VM in the manures were the same as those values found by non-automated means (ASTM D3175-07) ranging from 47 to 78 wt%db. The TGA assessment of the ash was also the same when compared to ash results via non-instrumental means following ASTM D3174-04. Ash values ranged from 4 to 47 wt%db. There was one exception when testing a high ash containing swine lagoon sludge. Under the TGA method, this sludge underwent more complete devolatilization and oxidation. This was primarily attributed to the small sample size leading to uniform internal heating. The modification of the TGA ash method aimed at shortening the run time generated similar results as both the original TGA method and non-automated method. Thus, TGA ash determination in manure should occur above 600°C with preferences for the following method: Zero-grade air at 2–4 furnace volumes/min, heating rate of 11°C⋅min−1, temperature range of 110–950°C, and isothermal hold at 950°C for 10 min. VM determination via TGA should follow ASTM D3175-07.
Reachability-based Decision Making for City Driving (2018)

This paper presents the design of a discrete decision making algorithm for vehicles with advanced driver-assistance and automated features. We model the system as a hybrid automaton, where transitions between discrete modes in the automaton correspond to driving mode decisions, and develop a method to determine the timing of mode transitions based on backward and forward reachable sets. The algorithm can be used either as a stand-alone component or as a method to guide an underlying motion planner to safe reference trajectories. Under certain assumptions, the algorithm guarantees safety and liveness, which are validated through computer simulations on a city driving scenario that requires going through multiple discrete modes and includes several surrounding moving obstacles.