gebhart/patrepeval huggingface dataset:
Temperature-Sensitive Mutants of Influenza Virus. XIII. Evaluation of Influenza A/Hong Kong/68 and A/Udom/72 ts and Wild-Type Viruses in Tracheal Organ Culture at Permissive and Restrictive Temperatures (1977)

Local thermal sensation modelling gained importance due to developments in personalized and locally applied heating and cooling systems in office environments. The accuracy of these models depends on skin temperature prediction by thermophysiological models, which in turn rely on accurate environmental and personal input data. Environmental parameters are measured or prescribed, but personal factors such as clothing properties and metabolic rates have to be estimated. Data for estimating the overall values of clothing properties and metabolic rates are available in several papers and standards. However, local values are more difficult to retrieve. For local clothing, this paper revealed that full and consistent data sets are not available in the published literature for typical office clothing sets. Furthermore, the values for local heat production were not verified for characteristic office activities, but were adapted empirically. Further analyses showed that variations in input parameters can lead to local skin temperature differences (∆Tskin,loc=0.4 – 4.4ºC). These differences can affect the local sensation output, where ∆Tskin,loc=1ºC is approximately one step on a 9-point thermal sensation scale. In conclusion, future research should include a systematic study of local clothing properties and the development of feasible methods for measuring and validating local heat production. Local thermal sensation modelling gained importance due to developments in personalized and locally applied heating and cooling systems in office environments. The accuracy of these models depends on skin temperature prediction by thermophysiological models, which in turn rely on accurate environmental and personal input data. Environmental parameters are measured or prescribed, but personal factors such as clothing properties and metabolic rates have to be estimated. Data for estimating the overall values of clothing properties and metabolic rates are available in several papers and standards. However, local values are more difficult to retrieve. For local clothing, this paper revealed that full and consistent data sets are not available in the published literature for typical office clothing sets. Furthermore, the values for local heat production were not verified for characteristic office activities, but were adapted empirically. Further analyses showed that variations in input parameters can lead to local skin temperature differences (∆Tskin,loc=0.4 – 4.4ºC). These differences can affect the local sensation output, where ∆Tskin,loc=1ºC is approximately one step on a 9-point thermal sensation scale. In conclusion, future research should include a systematic study of local clothing properties and the development of feasible methods for measuring and validating local heat production.
Control Design and Digital Implementation of a Fast 2-Degree-of-Freedom Translational Optical Image Stabilizer for Image Sensors in Mobile Camera Phones (2017)

This study presents design, digital implementation and performance validation of a lead-lag controller for a 2-degree-of-freedom (DOF) translational optical image stabilizer (OIS) installed with a digital image sensor in mobile camera phones. Nowadays, OIS is an important feature of modern commercial mobile camera phones, which aims to mechanically reduce the image blur caused by hand shaking while shooting photos. The OIS developed in this study is able to move the imaging lens by actuating its voice coil motors (VCMs) at the required speed to the position that significantly compensates for imaging blurs by hand shaking. The compensation proposed is made possible by first establishing the exact, nonlinear equations of motion (EOMs) for the OIS, which is followed by designing a simple lead-lag controller based on established nonlinear EOMs for simple digital computation via a field-programmable gate array (FPGA) board in order to achieve fast response. Finally, experimental validation is conducted to show the favorable performance of the designed OIS; i.e., it is able to stabilize the lens holder to the desired position within 0.02 s, which is much less than previously reported times of around 0.1 s. Also, the resulting residual vibration is less than 2.2-2.5 μm, which is commensurate to the very small pixel size found in most of commercial image sensors; thus, significantly minimizing image blur caused by hand shaking.
Ultra-thin film metasurface (Conference Presentation) (2017)

Metasurfaces, the two-dimensional (2D) sub-wavelength artificial structures, where light is not required to have a deep penetration, have shown the ability to tailor the amplitude, phase and polarization of light. The functionalities of various optical components can be realized by metasurface-based design, such as beam splitters, filters, waveplates, deflector, lens and holograms. Here, we propose a new type of metasurface based on the concept of ultra-thin film interference and experimentally demonstrate its feasibilities in beam deflector, light focusing and broadband meta-hologram in visible spectrum. Considering an ultra-thin thin film interference system, a sandwich structure, composed of air, a lossy material layer and a metallic mirror, the reflection of this system can be regarded as the linear superposition of the partial reflections from first interface and from the cavity after several roundtrips. First, we calculate the phases and reflections of various thicknesses of amorphous silicon (a-Si) on top of aluminum layer under normal illumination of an unpolarized light in the wavelength region from 400 to 850nm. 2 π phase coverage can be achieved by changing the film thickness of a-Si within 50 nanometers. We select two thicknesses (2-level phase modulation) for the demonstration of meta-devices. The ultra-flat grating metasurface for beam steering are designed. The reflection angles of grating metasurface can be modulated by changing its period, while the specular reflection is inhibited. We further demonstrate computer-generated holograms (CGH) based on ultra-thin interference metasurface. The holographic images are reconstructed by the combinations of phase- and amplitude- modulation. These devices show the great potential and CMOS-compatibility in the application of optics, display, security printing, and metasurface-based optical storage system.
Ventricular Remodeling In Ischemic Cardiomyopathy (2006)

Heart failure in the setting of reduced systolic pump function, if left untreated, is characterized by progressive ventricular dilation and dysfunction. Many of the major advances in pharmacologic treatments for heart failure achieved over the last two decades came with the recognition that this process, referred to as ventricular remodeling, results from abnormal mechanical stress on the myocardium (increased preload and afterload) and chronic neurohormonal activation (Figure 1). In the acute setting, loss of myocytes (as during infarction) or a defect of myocardial contraction (e.g., idiopathic cardiomyopathies) reduces overall ventricular pump function. This leads to reduced blood pressure and cardiac output, which activates autonomic reflexes that leads to increased circulating levels of neurohormones. It is believed, on a teleological basis, that these reflexes evolved in order to allow animals to cope with periods of increased energy demand (fight or flight) and to deal with acute blood loss. In parallel with autonomic reflex activation, decreased systemic blood pressure and flow lead to renal hypoperfusion, which increases aldosterone, renin and angiotensin, I (which leads to angiotensin II) production. In the short term, these factors attempt to restore cardiac output and blood pressure via mechanisms that are considered adaptive. However, if sustained, neurohormonal activation and increased mechanical stresses conspire in a maladaptive process to drive cellular hypertrophy and elongation, global recapitulation of a fetal gene program, myocardial fibrosis, ventricular enlargement and dysfunction, apoptosis1 and sets up a milieu for dyscoordinated myocardial contraction (e.g., conduction defects) and ventricular arrhythmias. A systemic inflammatory response also has been documented with increases of a multitude of cytokines which are also believed to contribute importantly to myocyte loss and disease progression.2,3
Detection and Analysis of Threats to the Energy Sector: DATES (2010)

This report summarizes Detection and Analysis of Threats to the Energy Sector (DATES), a project sponsored by the United States Department of Energy and performed by a team led by SRI International, with collaboration from Sandia National Laboratories, ArcSight, Inc., and Invensys Process Systems. DATES sought to advance the state of the practice in intrusion detection and situational awareness with respect to cyber attacks in energy systems. This was achieved through adaptation of detection algorithms for process systems as well as development of novel anomaly detection techniques suited for such systems into a detection suite. These detection components, together with third-party commercial security systems, were interfaced with the commercial Security Information Event Management (SIEM) solution from ArcSight. The efficacy of the integrated solution was demonstrated on two testbeds, one based on a Distributed Control System (DCS) from Invensys, and the other based on the Virtual Control System Environment (VCSE) from Sandia. These achievements advance the DOE Cybersecurity Roadmap [DOE2006] goals in the area of security monitoring. The project ran from October 2007 until March 2010, with the final six months focused on experimentation. In the validation phase, team members from SRI and Sandia coupled the two test environments and carried out a number of distributed and cross-site attacks against various points in one or both testbeds. Alert messages from the distributed, heterogeneous detection components were correlated using the ArcSight SIEM platform, providing within-site and cross-site views of the attacks. In particular, the team demonstrated detection and visualization of network zone traversal and denial-of-service attacks. These capabilities were presented to the DistribuTech Conference and Exhibition in March 2010. The project was hampered by interruption of funding due to continuing resolution issues and agreement on cost share for four months in 2008. This resulted in delays in finalizing agreements with commercial partners, and in particular the Invensys testbed was not installed until December 2008 (as opposed to the March 2008 plan). The project resulted in a number of conference presentations and publications, and was well received when presented at industry forums. In spite of some interest on the part of the utility sector, we were unfortunately not able to engage a utility for a full-scale pilot deployment.
Modulation of Intestinal Microbiome Prevents Intestinal Ischemic Injury (2017)

<b>Background:</b> Butyrate protects against ischemic injury to the small intestine by reducing inflammation and maintaining the structure of the intestinal barrier, but is expensive, short-lived, and cannot be administered easily due to its odor. Lactate, both economical and more palatable, can be converted into butyrate by the intestinal microbiome. This study aimed to assess in a rat model whether lactate perfusion can also protect against intestinal ischemia. <b>Materials and Methods:</b> Rat intestinal segments were loaded in an <i>in vitro</i> bowel perfusion device, and water absorption or secretion was assessed based on fluorescence of FITC-inulin, a fluorescent marker bound to a biologically inert sugar. Change in FITC concentration was used as a measure of ischemic injury, given the tendency of ischemic cells to retain water. Hematoxylin and eosin-stained sections at light level microscopy were examined to evaluate intestinal epithelium morphology. Comparisons between the data sets were paired Student <i>t</i>-tests or ANOVA with <i>p</i> < 0.05 performed on GraphPad. <b>Results:</b> Lactate administration resulted in a protective effect against intestinal ischemia of similar magnitude to that observed with butyrate. Both exhibited approximately 1.5 times the secretion exhibited by control sections (<i>p</i> = 0.03). Perfusion with lactate and methoxyacetate, a specific inhibitor of lactate-butyrate conversion, abolished this effect (<i>p</i> = 0.09). Antibiotic treatment also eliminated this effect, rendering lactate-perfused sections similar to control sections (<i>p</i> = 0.72). Perfusion with butyrate and methoxyacetate did not eliminate the observed increased secretion, which indicates that ischemic protection was mediated by microbial conversion of lactate to butyrate (<i>p</i> = 0.71). <b>Conclusions:</b> Lactate's protective effect against intestinal ischemia due to microbial conversion to butyrate suggests possible applications in the transplant setting for reducing ischemic injury and ameliorating intestinal preservation during transport.
Interface state density engineering in Hf1-xZrxO2/SiON/Si gate stack (2015)

This work investigates the interface state density, Dit by conductance method for two different processing conditions: (1) cyclic deposition and slot-plane-antenna (SPA) Ar plasma exposure, DSDS, and (2) cyclic deposition and annealing, DADA, during the deposition of ALD Hf1-xZrxO2 to fabricate the TiN/Hf1-xZrxO2/SiON/Si gate stack. The Zr percentage was varied in the dielectrics from x = 0 to 0.31 and 0.8 for DSDS processing and x = 0 to 0.8 for DADA processing. The control samples were deposited with standard atomic layer deposition (ALD) process (As-Dep) without any cyclic treatment. The addition of ZrO2 and SPA plasma exposure is found to suppress interface state generation. DSDS Hf1-xZrxO2 with x = 0.8 demonstrated superior equivalent oxide thickness downscaling and the lowest Dit. The electron affinity variation of Hf and Zr ion seems to contribute to reduced Dit generation after a constant voltage stress. On the other hand, DADA process increases the midgap Dit when Zr is added to HfO2. In addition, DADA processed dielectrics showed higher degradation when stressed because of increased trap assisted tunneling through charged grain boundaries. Furthermore, DSDS Hf1-xZrxO2 (x = 0.8) with two different interfacial layers: (1) UV nitridation of chemically grown SiO2 and (2) plasma oxynitride grown after removing the chemically grown SiO2 was investigated. The interface characteristics observed for SiON formed by UV nitridation seems to be better as compared to that formed by plasma oxynitride, which is attributed to the more uniform nitrogen incorporation by UV nitridation.
A novel small molecule approach for the treatment of propionic and methylmalonic acidemias (2021)

Propionic Acidemia (PA) and Methylmalonic Acidemia (MMA) are inborn errors of metabolism affecting the catabolism of valine, isoleucine, methionine, threonine and odd-chain fatty acids. These are multi-organ disorders caused by the enzymatic deficiency of propionyl-CoA carboxylase (PCC) or methylmalonyl-CoA mutase (MUT), resulting in the accumulation of propionyl-coenzyme A (P-CoA) and methylmalonyl-CoA (M-CoA in MMA only). Primary metabolites of these CoA esters include 2-methylcitric acid (MCA), propionyl-carnitine (C3), and 3-hydroxypropionic acid, which are detectable in both PA and MMA, and methylmalonic acid, which is detectable in MMA patients only (Chapman et al., 2012). We deployed liver cell-based models that utilized PA and MMA patient-derived primary hepatocytes to validate a small molecule therapy for PA and MMA patients. The small molecule, HST5040, resulted in a dose-dependent reduction in the levels of P-CoA, M-CoA (in MMA) and the disease-relevant biomarkers C3, MCA, and methylmalonic acid (in MMA). A putative working model of how HST5040 reduces the P-CoA and its derived metabolites involves the conversion of HST5040 to HST5040-CoA driving the redistribution of free and conjugated CoA pools, resulting in the differential reduction of the aberrantly high P-CoA and M-CoA. The reduction of P-CoA and M-CoA, either by slowing production (due to increased demands on the free CoA (CoASH) pool) or enhancing clearance (to replenish the CoASH pool), results in a net decrease in the CoA-derived metabolites (C3, MCA and MMA (MMA only)). A Phase 2 study in PA and MMA patients will be initiated in the United States.
Computation of Shock Cell Structure of Dual-Stream Jets for Noise Prediction (2008)

Broadband shock cell noise is an important component of aircraft interior noise during cruise. At cruise, the secondary jet of most modern day jet engines is supersonic. As a result, a shock cell structure develops in the jet plume. The interaction of large turbulence structures of the jet flow and the periodic components of the shock cells results in the emission of highly directional broadband shock cell noise. The primary objective of this investigation is to develop a computational method to calculate the shock cell structures ofdual-stream jets issued from separate flow nozzles. Computation of the Fourier modes of such shock cell structures is also considered. Based on the dominant wave numbers computed by the method developed, the frequencies at the peaks of broadband shock cell noise spectra at various radiation directions are calculated. Good agreements are found with experimental measurements over a wide range of primary and secondary jet Mach numbers. The good agreements provide a validation of the accuracy of the computation method.
Transcriptomic variation in proanthocyanidin biosynthesis pathway genes in soybean (Glycine spp.) (2017)

We detected major differences in the transcriptional levels of genes involved in the biosynthesis of proanthocyanidin and anthocyanin among genotypes beginning at the early stage of seed development. The results of the present study provide insights into the underlying genetic variation in proanthocyanidin biosynthesis among soybean genotypes. © 2017 Society of Chemical Industry.
Long-Term Follow-Up of Patients Treated by Gene Therapy for X-Linked Chronic Granulomatous Disease. (2005)

Abstract Chronic granulomatous disease (CGD) is a primary immunodeficiency in which phagocytic cells of affected patients have impaired antimicrobial activity due to a defect in the production of reactive oxygen species (ROS). CGD is caused by mutations in any one of four genes encoding for the subunits of the NADPH oxidase complex. Although curable by HSC transplantation, this strategy is usually limited only to patients with HLA-matched sibling or unrelated donors, as mismatched transplantation is associated with high morbidity and mortality due to graft failure and slow immune reconstitution. A therapeutic alternative for CGD patients is the genetic modification of autologous HSC. In January 2004 we initiated a Phase I/II clinical trial for X-CGD patients including conditioning with busulfan (8 mg/kg/total dose) prior to infusion of genetically modified HSC. G-CSF mobilized CD34+ cells from 2 adult patients (25 and 26 years) were transduced ex-vivo with a monocistronic gp91phox retroviral vector. Therapeutically significant gene marking levels were detected in neutrophils of both patients with up to 60% functionally corrected phagocytes 14 months after gene therapy. This high correction resulted from an unexpected but temporarily restricted expansion of gene transduced myeloid cells in vivo. In contrast gene marking levels in B-cells has remained constant at a level of 20%, while gene marking in T-cells is below 5%. Gene marking in bone marrow was detected at levels between 30% and 40% one year after transplantation of gene modified cells. Killing assays in vitro have demonstrated antibacterial and antifungal activity in gene transduced phagocytes and both patients recovered of Staph. aureus and Aspergillus fumigatus infections after gene therapy. Our results suggest that gene therapy in combination with bone marrow conditioning is a therapeutic option for inherited diseases affecting the myeloid compartment and can be successfully used to treat CGD.
Neutrophil transendothelial migration hotspots – mechanisms and implications (2021)

During inflammation, leukocytes circulating in the blood stream exit the vasculature in a process called leukocyte transendothelial migration (TEM). The current paradigm of this process comprises several well-established steps, including rolling, adhesion, crawling, diapedesis and sub-endothelial crawling. Nowadays, the role of the endothelium in transmigration is increasingly appreciated. It has been established that leukocyte exit sites on the endothelium and in the pericyte layer are in fact not random but instead may be specifically recognized by migrating leukocytes. Here, we review the concept of transmigration hotspots, specific sites in the endothelial and pericyte layer where most transmigration events take place. Chemokine cues, adhesion molecules and membrane protrusions as well as physical factors, such as endothelial junction stability, substrate stiffness, the presence of pericytes and basement membrane composition, may all contribute to local hotspot formation to facilitate leukocytes exiting the vasculature. In this Review, we discuss the biological relevance of such hotspots and put forward multiple mechanisms and factors that determine a functional TEM hotspot.
New Directions in Carbohydrate Engineering: A Metabolic Substrate-Based Approach to Modify the Cell Surface Display of Sialic Acids (2001)

This review discusses new directions in the emerging field of carbohydrate engineering. Specifically, it describes substrate-based methodologies that are complementary to the recombinant DNA techniques that now dominate metabolic and cellular engineering endeavors. A substrate-based approach consists of intercepting a biosynthetic pathway with an unnatural analog of a metabolic intermediate. The unnatural compound competes with the endogenous substrate for biosynthetic incorporation into a cellular component by action of the natural enzymes of the cell. The incorporation of the unnatural compound into the cellular architecture can directly modulate cellular properties and biological processes. Alternatively, a molecular handle can be included in the design of the unnatural substrate that allows further elaboration upon reaction with an externally delivered reagent. The sialic acid biosynthetic pathway is presented as a model system to illustrate both the practical aspects and theoretical considerations of a substrate-based cellular engineering approach. Specific applications of carbohydrate-based cell surface engineering include chemical construction of new glycosylation patterns on cells, new approaches to targeting tumor cell with either diagnostic or therapeutic agents, and installation of novel receptors on cells for facilitating viral-mediated gene delivery.
Measurement of inclusive two-particle angular correlations in pp collisions with the ATLAS detector at the LHC (2012)

A bstract We present a measurement of two-particle angular correlations in proton- proton collisions at $ \sqrt {s} = 900 $ GeV and 7 TeV. The collision events were collected during 2009 and 2010 with the ATLAS detector at the Large Hadron Collider using a single-arm minimum bias trigger. Correlations are measured for charged particles produced in the kinematic range of transverse momentum p T &gt; 100 MeV and pseudorapidity | η | &lt; 2.5. A complex structure in pseudorapidity and azimuth is observed at both collision energies. Results are compared to pythia 8 and herwig++ as well as to the AMBT2B, DW and Perugia 2011 tunes of pythia 6. The data are not satisfactorily described by any of these models.