gebhart/patrepeval huggingface dataset:
Replication Data for: Evolution of Metastable Structures at Bimetallic Surfaces from Microscopy and Machine-Learning Molecular Dynamics (2021)

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.
Fully Automatic MRI-Based Hippocampus Volumetry Using FSL-FIRST: Intra-Scanner Test-Retest Stability, Inter-Field Strength Variability, and Performance as Enrichment Biomarker for Clinical Trials Using Prodromal Target Populations at Risk for Alzheimer’s Disease (2017)

The impact of intra-scanner test-retest and inter-field strength variability of FIRST-HV on clinical tasks is negligible. In addition, FIRST-HV is useful for enrichment in clinical MCI trials.
The art and science of achieving zero COVID-19 transmissions in staff at a large community care facility in Singapore using implementation science: a retrospective analysis (2021)

<ns4:p> <ns4:bold>Background:</ns4:bold> The Singapore COVID-19 multi-ministry taskforce commissioned community care facilities (CCFs) as a hospital-sparing strategy amidst rising coronavirus disease 2019 (COVID-19) cases. An exhibition centre was repurposed within ten days as an ad-hoc 3200-bed medical facility (CCF@EXPO) to isolate and treat infected patients amidst concerns of potential COVID-19 transmissions to healthcare staff. This paper deconstructs the implementation of the CCF@EXPO infection prevention and control (IPC) innovation and elicits critical factors which enabled zero transmission of COVID-19 to staff during 100 days of operation using an implementation science framework. </ns4:p> <ns4:p> <ns4:bold>Methods:</ns4:bold> This study employed retrospective analysis using the integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) framework. The CCF@EXPO IPC innovation comprised five key elements: (a) physical environment, (b) work practices, (c) tools and technology, (d) staff training, and (e) audits. Contextual assessment was conducted for baseline and 100 <ns4:sup>th</ns4:sup> day of CCF@EXPO operations. Actions taken to improve scores between these timepoints were mapped against the Expert Recommendations for Implementing Change (ERIC) tool to surface key implementation strategies. </ns4:p> <ns4:p> <ns4:bold>Results:</ns4:bold> Positive shifts were observed in all constructs of the i-PARIHS framework, between baseline and 100 <ns4:sup>th</ns4:sup> day. The largest shifts were in work practices, tools and technology, and staff training. Key implementation strategies used included: rapid Plan-Do-Study-Act (PDSA) cycles, identifying champions, team building, creating a culture of collaborative learning, multi-disciplinary teamwork, transparency in communications and decision-making, and skillful facilitation. </ns4:p> <ns4:p> <ns4:bold>Conclusions:</ns4:bold> Rapid PDSA cycles anchored by principles to ensure staff safety, was the key approach used in implementation of the CCF@EXPO IPC innovation. Retrospective analysis using the i-PARIHS framework is useful to elicit success factors and to inform preparedness planning of future pandemics. </ns4:p>
A parametric analysis of microbolometer pixel designs (2011)

As microbolometer pixel dimensions for infrared imagers continue to decrease, the need for full-wave analysis in the design process is enhanced. Using reflectance as the validation point, an electromagnetic model of a dual-layer microbolometer pixel design was created for a 25 &mu;m pixel design, and an in-depth study of the design was performed. With this model validated, further explorations were completed with a reduced size pixel. While simulating multiple variations of specific parameters, such as bridge thickness, upper and lower cavity heights, and different absorber configurations, a new evaluation metric of dissipated power in the structure was studied. This metric, provided by finite element analysis, provides great insight into absorption properties within the microbolometer structure, properties that cannot be directly measured but that are critical to the functionality of the pixel design. In this paper parametric analysis of microbolometer pixel designs are presented via both reflectance and dissipated power full-wave analysis.
Asymmetric Synthesis of Highly Substituted Azapolycyclic Compounds via 2-Alkenyl Sulfoximines:  Potential Scaffolds for Peptide Mimetics (2006)

The application of metalated, enantiomerically pure acyclic and cyclic 2-alkenyl sulfoximines for the synthesis of highly substituted aza(poly)cyclic ring systems is described. The method relies on a one-pot combination of a reagent-controlled allyl transfer reaction to alpha- or beta-amino aldehydes, followed by a Michael-type cyclization of the intermediate vinyl sulfoximines generated in the first step. The sulfur-free target compounds are preferentially obtained by samarium iodide treatment of the sulfonimidoyl substituted heterocycles. In addition to this methodological work, initial results on the biological activity of selected examples are reported. Furthermore, a concept for the transformation of peptidic lead structures into non-peptide mimetics is described, and the relevance of the new approach to highly substituted azaheterocycles in this context is discussed.
Dual-responsive nanoparticles release cargo upon exposure to matrix metalloproteinase and reactive oxygen species (2015)

Micellar nanoparticles were designed to be responsive to matrix metalloproteinases (MMPs) and reactive oxygen species (ROS), each of which is upregulated in the pathology of inflammatory diseases. The amphiphilic polymer-based nanoparticle system consists of a hydrophilic shell responsible for particle morphology change and aggregation, together with a hydrophobic block designed to release cargo in the presence of ROS.
Fabrication and characteristics of Al/sub x/Ga/sub 1-x/As heterojunction phototransistors with wide-gap window (1991)

The fabrication process and device characteristics of Al/sub 0.7/Ga/sub 0.3/As/Al/sub 0.2/Ga/sub 0.8/As heterojunction phototransistors are described. The interface between the emitter and base layers becomes rough with the increase in the Al content of the emitter layer, and it causes a decrease in the optical conversion gain of the heterojunction phototransistors. A spacer layer with the same Al content as that in the emitter layer is inserted between the emitter and base layers. Both the interface morphology and the optical conversion gain are improved. Enhanced by the avalanche multiplication in the base-collector junction, an optical conversion gain of 1500 is achieved in spite of the shorter diffusion length in the Al/sub 0.2/Ga/sub 0.8/As base layer. The device exhibits a photoresponse in the range of 520-780 nm, i.e., from green to red light.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Double Salt Ionic Liquids Containing the Trihexyl(tetradecyl)phosphonium Cation: The Ability to Tune the Solubility of Aromatics, Ethers, and Lipophilic Compounds (2016)

The chemical and physical properties of an ionic liquid (IL) can be tuned with the addition of a second IL, forming a Double Salt Ionic Liquid (DSIL). Here, the solubilities of lipophilic solutes with long alkyl chains ( e.g. , heptane, methyl palmitate) were tuned in the DSIL [C 4 mim] x [P 66614 ] (1-x) [NTf 2 ] ([C 4 mim] + = 1-butyl-3-methylimidazolium, [P 66614 ] + = trihexyl(tetradecyl)phosphonium, [NTf 2 ] - = bis(trifluoromethylsulfonyl)imide) by increasing the [P 66614 ] + concentration. Additionally, density and viscosity of the DSILs were also modified with the [P 66614 ] + concentration. The solubility of solvents totally miscible with [P 66614 ][NTf 2 ], such as benzene and toluene, could only be tuned in the DSILs when [P 66614 ] + /[NTf 2 ] - ≤ 0.33, since at higher ratios these solutes were totally miscible with the DSILs. The interactions between the ions account for the different solvent behaviors in the DSILs. Using 1 H NMR, 19 F NMR, and FT-IR spectroscopy, a preferential interaction was observed between the [NTf 2 ] - anion with [C 4 mim] + compared to that with [P 66614 ] + . Also, interactions between [C 4 mim] + and [P 66614 ] + through alkyl chain aggregations were demonstrated.
Low-Rate Image Retrieval with Tree Histogram Coding (2009)

To perform image retrieval using a mobile device equipped with a camera, the mobile captures an image, transmits data wirelessly to a server, and the server replies with the associated database image information. Query data compression is crucial for low-latency retrieval over a wireless network. Fo
Growth factors can enhance lymphocyte survival without committing the cell to undergo cell division. (1995)

Growth factors have been defined by their ability to promote the proliferative expansion of receptor-bearing cells. For example, antigen-activated T cells expressing the alpha beta gamma form of the interleukin 2 (IL-2) receptor will proliferate in response to IL-2. In contrast, resting T cells, which express the IL-2 receptor beta and gamma chains, do not proliferate in response to IL-2. We demonstrate that the survival of resting T cells following gamma irradiation is greatly enhanced by pretreatment with IL-2. The radioprotective effect of IL-2 is dose dependent, does not result from the induction of cell proliferation, and does not require expression of the IL-2 receptor alpha chain. Thus, the beta gamma IL-2 receptor expressed on resting T cells can transduce signals that promote cell survival without committing the T cell to undergo cell division. IL-4 and IL-7, but not IL-1, IL-3, or IL-6, were also found to enhance the survival of quiescent T cells following gamma irradiation. Thus, certain growth factor-receptor interactions can serve to maintain cell viability in a manner that is independent of their ability to initiate or maintain cell proliferation. These data may have important implications for the use of growth factors in patients being treated with radiation and/or chemotherapy.
DNA Cleavage via Superoxide Anion Formed in Photoinduced Electron Transfer from NADH to γ-Cyclodextrin-Bicapped C60 in an Oxygen-Saturated Aqueous Solution (2002)

γ-Cyclodextrin-bicapped C60 (C60/γ-CyD) shows an efficient DNA cleaving-activity in the presence of NADH (β-nicotinamide adenine dinucleotide, reduced form) in an O2-saturated aqueous solution under visible-light irradiation. No DNA cleavage has been observed without NADH under experimental conditions that are otherwise the same, although singlet oxygen (1O2) has been detected by the ESR spin-trapping of the C60/γ-CyD-O2 system. This indicates that neither triplet excited state of C60/γ-CyD (3C60*/γ-CyD) nor 1O2 produced via an energy transfer from 3C60*/γ-CyD to O2 is an actual reactive species, which is responsible for the DNA damage under the present experimental conditions. In the presence of NADH, photoinduced electron transfer from NADH to 3C60*/γ-CyD occurs to yield two equivalents of the radical anion (C60•-/γ-CyD), which exhibits its characteristic NIR band at 1080 nm. The dynamics of the photoinduced electron transfer have been examined by monitoring the decay of triplet−triplet absorption band at 740 nm and concomitant rise of the NIR absorption band at 1080 nm due to C60•-/γ-CyD with use of the laser flash photolysis for the C60/γ-CyD-NADH system. In the presence of O2, C60•-/γ-CyD disappears via the electron transfer to O2 and an electron transfer from NADH to 1O2 to produced O2•-. The formation of O2•- has been confirmed by the spin trap with DEPMPO (5-diethoxyphosphoryl-5-methyl-1-pyrroline-N-oxide), which is an efficient O2•--trapping agent. The reorganization energy for the reduction of O2 to O2•- is evaluated as 43.4 kcal mol-1, which agrees with the literature value determined directly for the self-exchange between 36O2•- and 32O2. This indicates that the electron transfer from C60•-/γ-CyD to O2 proceeds via an outer-sphere pathway. The O2•- thus produced gives H2O2, ultimately yielding hydroxyl radical, which is shown to be an actual DNA-cleaving reagent.
High-performance Generic Neutrino Detection in a LArTPC near the Earth's Surface with the MicroBooNE Detector (2020)

Large Liquid Argon Time Projection Chambers (LArTPCs) are being increasingly adopted in neutrino oscillation experiments because of their superb imaging capabilities through the combination of both tracking and calorimetry in a fully active volume. Active LArTPC neutrino detectors at or near the Earth's surface, such as the MicroBooNE experiment, present a unique analysis challenge because of the large flux of cosmic-ray muons and the slow drift of ionization electrons. We present a novel Wire-Cell-based high-performance generic neutrino-detection technique implemented in MicroBooNE. The cosmic-ray background is reduced by a factor of 1.4$\times10^{5}$ resulting in a 9.7\% cosmic contamination in the selected neutrino candidate events, for visible energies greater than 200~MeV, while the neutrino signal efficiency is retained at 88.4\% for $ν_μ$ charged-current interactions in the fiducial volume in the same energy region. This significantly improved performance compared to existing reconstruction algorithms, marks a major milestone toward reaching the scientific goals of LArTPC neutrino oscillation experiments operating near the Earth's surface.
Multiple Sclerosis Performance Test: Technical Development and Usability (2019)

NCT02664324.
Environmental and occupational respiratory diseases – 1039. Clinical course and side effects of anti-IgE monoclonal antibody in patients with severe persistent asthma (2013)

This article was originally published online on 23 April 2013 Omalizumab, a recombinant humanized monoclonal antibody to IgE, is recommended as a new option for the treatment of severe persistent allergic asthma. The purpose of this study is to assess the effects omalizumab treatment on life quality and its side effects in the severe persistent asthma patients. In this study, we evaluated 19 severe persistent asthma patients who received therapy with omalizumab for 8 months. Omalizumab was administered every 2 weeks between the doses of 150 to 375 mg. Symptoms and severity of allergic reactions were recorded before and after being on omalizumab. IgE levels, mean platelet volume (MPV), platelet levels, pulmonary function test and asthma control test were evaluated in all patients before and 8 months after the treatment. Local and systemic side effects of omalizumab were evaluated. Stool parasites were examined at 4th and 8th months after initiation of treatment to investigate any parasitosis. The patients had severe persistent asthma for periods ranging from 3 to 8 years, and they were diagnosed with allergic asthma for 7-28 years. Thrombocytopenia developed in a male patient after the 22nd dose of the drug was given. When the platelet count fell down to 55.000, the omalizumab treatment was suspended. During the therapy period, one patient had parasitosis (giardiasis), one patient had severe side effects, one patient had dyspnea two hours after the injection, and one patient had a dyspnea attack 2 hours after the injection. The changes in MPV levels were not statistically significant. There was also significant decrease in IgE levels after the treatment. Our clinical follow-up study suggesting that monitoring the complete blood cell count might be important in the use of omalizumab. Only in one case, a dyspnea attack occurred 2 hours after the injection. The patient was hospitalized and treated appropriately, and discharged after a 24 hours of follow-up period. Thrombocytopenia developed in one patient and the treatment was suspended. Although we did not have any anaphylaxis, we believe that the patients should be monitored at least for 3 hours after the Omalizumab injection.
Biochemical Characterization of Photosystem II Antenna Polypeptides in Grana and Stroma Membranes of Spinach (1992)

The photosystem (PS) II antenna system comprises several biochemically and spectroscopically distinct complexes, including light-harvesting complex II (LHCII), chlorophyll-protein complex (CP) 29, CP26, and CP24. LHCII, the most abundant of these, is both structurally and functionally diverse. The photosynthetic apparatus is laterally segregated within the thylakoid membrane into PSI-rich and PSII-rich domains, and the distribution of antenna complexes between these domains has implications for antenna function. We report a detailed analysis of the differences in the polypeptide composition of LHCII, CP29, and CP26 complexes associated with grana and stroma thylakoid fractions from spinach (Spinacia oleracea L.), making use of a very high-resolution denaturing gel system, coupled with immunoblots using monospecific antibodies to identify specific antenna components. We first show that the polypeptide composition of the PSII antenna system is more complex than previously thought. We resolved at least five type I LHCII apoproteins and two to three type II LHCII apoproteins. We also resolved at least two apoproteins each for CP29 and CP26. In state 1-adapted grana and stroma thylakoid membranes, the spectrum of LHCII apoproteins is surprisingly similar. However, in addition to overall quantitative differences, we saw subtle but reproducible qualitative differences in the spectrum of LHCII apoproteins in grana and stroma membrane domains, including two forms of the major type II apoprotein. The implications of these findings for models of PSII antenna function in spinach are discussed.
Influence of onabotulinumtoxin A on testes of the growing rat (2016)

Onabotulinumtoxin A (onabotA) is gaining wide medical use in children. However, little is known about its potential testicular effects. The present study was planned to investigate the influence of its injection on the maturing testicular structures in rats. Immature rats were injected in the peritesticular area by onabotA with three doses of (10, 20 and 40 U/kg) three times in a two-week interval. The effect of these injections on fertility indices (sperm parameters, semen quality and testosterone levels) was examined. In addition, levels of antisperm antibodies and several apoptosis parameters were investigated. DNA content in form of ploidy was compared to control group via flow cytometric analysis. Histopathological examination was carried out to confirm the findings. OnabotA-injected groups showed decreased sperm count and semen quality, while sperm vitality, morphology and testosterone levels were not significantly affected. Furthermore, DNA flow cytometric analysis confirmed delayed sperm maturation. Apoptosis markers were significantly increased by the injections. In conclusion, onabotA use in growing rats adversely affected sperm count and maturation. However, it had no significant effects on sperm morphology or vitality. OnabotA testicular effects are mediated, at least partly, by apoptosis.
Serum proteome analysis of systemic JIA and related pulmonary alveolar proteinosis identifies distinct inflammatory programs and biomarkers (2021)

Abstract Objectives Recent observations in systemic Juvenile Idiopathic Arthritis (sJIA) suggest an increasing incidence of high-mortality interstitial lung disease, characterized by a variant of pulmonary alveolar proteinosis (PAP). Co-occurrence of macrophage activation syndrome (MAS) and PAP in sJIA suggested a shared pathology, but sJIA-PAP patients also commonly experience features of drug reaction such as atypical rashes and eosinophilia. We sought to investigate immunopathology and identify biomarkers in sJIA, MAS, and sJIA-PAP. Methods We used SOMAscan to measure &gt;1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-PAP and other related diseases. We verified selected findings by ELISA and lung immunostaining. Because the proteome of a sample may reflect multiple states (sJIA, MAS, sJIA-PAP), we used regression modeling to identify subsets of altered proteins associated with each state. We tested key findings in a validation cohort. Results Proteome alterations in active sJIA and MAS overlapped substantially, including known sJIA biomarkers like SAA and S100A9, and novel elevations of heat shock proteins and glycolytic enzymes. IL-18 was elevated in all sJIA groups, particularly MAS and sJIA-PAP. We also identified an MAS-independent sJIA-PAP signature notable for elevated ICAM5, MMP7, and allergic/eosinophilic chemokines, which were all previously associated with lung damage. Immunohistochemistry localized ICAM5 and MMP7 in sJIA-PAP lung. ICAM5’s ability to distinguish sJIA-PAP from sJIA/MAS was independently validated. Conclusions Serum proteins support an sJIA-to-MAS continuum, help distinguish sJIA, sJIA/MAS, and sJIA-PAP, and suggest etiologic hypotheses. Select biomarkers, such as ICAM5, could aid in early detection and management of sJIA-PAP.
Forced expression of the homeodomain protein Gax inhibits cardiomyocyte proliferation and perturbs heart morphogenesis (1997)

The development of the tubular heart into a complex four-chambered organ requires precise temporal and region-specific regulation of cell proliferation, migration, death and differentiation. While the regulatory mechanisms in heart morphogenesis are not well understood, increasing attention has focused on the homeodomain proteins, which are generally linked to morphogenetic processes. The homeodomain containing gene Gax has been shown to be expressed in heart and smooth muscle tissues. In this study, the Gax protein was detected in the nuclei of myocardial cells relatively late in chicken heart development, at a time when myocyte proliferation is declining. To test the hypothesis that the Gax protein functions as a negative regulator of cardiomyocyte proliferation, a replication-defective adenovirus was used to force its precocious nuclear expression during chicken heart morphogenesis. In experiments in which Gax- and beta-galactosidase-expressing adenoviruses were co-injected, clonal expansion of myocytes was reduced, consistent with inhibition of myocyte proliferation. This effect on proliferation was corroborated by the finding that the percentage of exogenous Gax-expressing myocytes that were positive for the cell cycle marker PCNA decreased over time and was lower than in control myocytes. The precocious nuclear expression of Gax in tubular hearts resulted in abnormal heart morphology, including small ventricles with rounded apices, a thinned compact zone and coarse trabeculae. These results suggest a role for the Gax protein in heart morphogenesis causing proliferating cardiomyocytes to withdraw from the cell cycle, thus influencing the size and shape that the heart ultimately attains.
Active Pedestrian Protection by Surround Sensor Technologies (2011)

In the strive for a vision of accident free driving, much progress has been made at the BOSCH Group in the area of active and passive safety systems. A variety of crash avoiding or severity mitigating systems have been launched in the market with valuable benefit. In this paper the authors point out the accident avoiding and crash severity mitigating potential of active pedestrian protection systems using surround sensor information by radar and video vision technologies. They also discuss their additional potential to be exploited in the future. On the one hand the technical challenges have to be mastered to improve the benefit of the state of the art safety systems. On the other hand, onward progress of standardization and regulation are considered necessary to set a reliable legal framework for the rollout and market launch of advanced systems providing extended benefit within the unexploited fields of effect in traffic accident statistics.