gebhart/patrepeval huggingface dataset:
Why do strategies to strengthen primary health care succeed in some places and fail in others? Exploring local variation in the effectiveness of a community health worker managed digital health intervention in rural India (2021)

Local contextual factors were significant influences on the effectiveness of this DHI-enabled PHC service strategy intervention. Local adaptions need to be planned for, monitored and responded to over time. By identifying plausible explanations for variation in outcomes between clusters, we identify potential strategies to strengthen such interventions.
Noradrenaline dose levels predicts futility of liver transplantation in patients with paracetamol-overdose related acute liver failure (ALF) (2015)

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Retrieval of atmospheric properties from hyper and multispectral imagery with the FLAASH atmospheric correction algorithm (2005)

Atmospheric Correction Algorithms (ACAs) are used in applications of remotely sensed Hyperspectral and Multispectral Imagery (HSI/MSI) to correct for atmospheric effects on measurements acquired by air and space-borne systems. The Fast Line-of-sight Atmospheric Analysis of Spectral Hypercubes (FLAASH) algorithm is a forward-model based ACA created for HSI and MSI instruments which operate in the visible through shortwave infrared (Vis-SWIR) spectral regime. Designed as a general-purpose, physics-based code for inverting at-sensor radiance measurements into surface reflectance, FLAASH provides a collection of spectral analysis and atmospheric retrieval methods including: a per-pixel vertical water vapor column estimate, determination of aerosol optical depth, estimation of scattering for compensation of adjacency effects, detection/characterization of clouds, and smoothing of spectral structure resulting from an imperfect atmospheric correction. To further improve the accuracy of the atmospheric correction process, FLAASH will also detect and compensate for sensor-introduced artifacts such as optical smile and wavelength mis-calibration. FLAASH relies on the MODTRAN TM radiative transfer (RT) code as the physical basis behind its mathematical formulation, and has been developed in parallel with upgrades to MODTRAN in order to take advantage of the latest improvements in speed and accuracy. For example, the rapid, high fidelity multiple scattering (MS) option available in MODTRAN4 can greatly improve the accuracy of atmospheric retrievals over the 2-stream approximation. In this paper, advanced features available in FLAASH are described, including the principles and methods used to derive atmospheric parameters from HSI and MSI data. Results are presented from processing of Hyperion, AVIRIS, and LANDSAT data.
Comprehensive splice-site analysis using comparative genomics (2006)

We have collected over half a million splice sites from five species-Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana-and classified them into four subtypes: U2-type GT-AG and GC-AG and U12-type GT-AG and AT-AC. We have also found new examples of rare splice-site categories, such as U12-type introns without canonical borders, and U2-dependent AT-AC introns. The splice-site sequences and several tools to explore them are available on a public website (SpliceRack). For the U12-type introns, we find several features conserved across species, as well as a clustering of these introns on genes. Using the information content of the splice-site motifs, and the phylogenetic distance between them, we identify: (i) a higher degree of conservation in the exonic portion of the U2-type splice sites in more complex organisms; (ii) conservation of exonic nucleotides for U12-type splice sites; (iii) divergent evolution of C.elegans 3' splice sites (3'ss) and (iv) distinct evolutionary histories of 5' and 3'ss. Our study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.
Three‐dimensional simulation of bubble column flows with bubble coalescence and breakup (2005)

Abstract Three‐dimensional (3‐D) Euler/Euler simulations of two‐phase (gas/liquid) transient flow were performed using a multiphase flow algorithm based on the finite‐volume method. These numerical simulations cover laboratory‐scale bubble columns of different diameters, operated over a range of superficial gas velocities in the churn‐turbulent regime (8 to 30 cm/s) and at different operating pressures (up to 1 MPa). The bubble population balance equation (BPBE) is implemented in the two‐fluid model (TFM) and algebraic slip mixture model (ASMM). Simulated time‐averaged axial liquid velocity, turbulence stress, and gas holdup are compared with experimental data of Chen et al., Ong, and Shaikh et al. Moreover, to ensure the experimentally observed lack of dependency of holdup radial profiles on column height in the fully developed region, coalescence rates in the computations had to be enhanced consistently compared to model‐predicted values. Quantitative agreement is then obtained between the experimental data and simulations for the time‐averaged gas holdup and axial liquid velocity profiles. However, the simulations significantly underestimate the turbulent stress because the velocity field cannot be fully resolved. Simulated bubble size distributions indicate that the volume fraction of small bubbles is uniform in a cross section, whereas that of the large bubbles peaks in the center of the column. The simulation correctly captures the high‐pressure effect, which at fixed gas superficial velocity pushes the bubble column flow toward bubbly flow. The simulation also predicts that, although the small bubble volume fraction may not change with superficial gas velocity in the churn‐turbulent flow regime, the bubble size distribution still remains single modal but is wider and contains larger bubble sizes when superficial gas velocity is increased. © 2005 American Institute of Chemical Engineers AIChE J, 51: 696–712, 2005
Cloning and Characterization of the Major Promoter of the Human Protein Kinase C 6 Gene (1992)

was cloned from a human leukocyte genomic library in EMBL3 bacteri- ophage. This segment of the gene (greater than 54 kilobases in length) encompassed the coding sequence for the amino-terminal regulatory domain of the en- zyme, the 5”untranslated region, and the B’-flanking region. Initiation of transcription was identified by S 1 nuclease analysis and confirmed by RNase protection analysis at 197 base pairs 5’ of the initiator ATG. Sequence analysis of the 5”flanking region revealed it to be extremely G+C-rich
Early Relapses, Onset of Progression, and Late Outcome in Multiple Sclerosis (2012)

Our results indicate dissociation between early inflammatory attacks and onset of the SP phase and further question the validity of relapse frequency as a surrogate marker for late disability. Among the group with frequent early relapses, we observed a large variability of outcomes, ranging from one extreme to the opposite.
Racial and Ethnic Differences in Breast Cancer Survival: Mediating Effect of Tumor Characteristics and Sociodemographic and Treatment Factors (2015)

Racial disparities in breast cancer survival vary by tumor subtype. Interventions are needed to reduce disparities, particularly in the first 2 years after diagnosis among black women with estrogen receptor-positive tumors.
Tuning properties of long-period gratings by plasma post-processing of their diamond-like carbon nano-overlays (2014)

This work presents an application of reactive ion etching (RIE) for effective tuning of spectral response and the refractive index (RI) sensitivity of diamond-like carbon (DLC) nano-coated long-period gratings (LPGs). When oxygen plasma is applied the technique allows for an efficient and well controlled etching of hard and chemically resistant DLC films deposited on optical fibers. We show that optical properties of DLC, especially its refractive index, strongly depend on thickness of the film when it is thinner than 150 nm. The effect of DLC nano-coating deposition and etching on spectral properties of the LPGs is discussed. We have correlated the DLC properties with the shift of the LPG resonance wavelength and have found that both deposition and etching processes took place less effectively than on the electrode when the LPG sample was held above the electrode in the plasma reactor. An advantage of plasma-based etching is a capability for post-processing of the nano-coated structures with a good precision, as well as cleaning the samples and their re-coating according to requested needs. Moreover, the application of RIE allows for post-fabrication tuning of RI sensitivity of the DLC nano-coated LPGs.
Domain Analysis of the Tetraspanins. Studies of CD9/CD63 Chimeric Molecules on Subcellular Localization and Upregulation Activity for Diphtheria Toxin Binding. (2000)

CD9 and CD63 belong to a tetramembrane-spanning glycoprotein family called tetraspanin, and are involved in a wide variety of cellular processes, but the structure-function relationship of this family of proteins has yet to be clarified. CD9 associates with diphtheria toxin receptor (DTR), which is identical to the membrane-anchored form of heparin-binding EGF-like growth factor (proHB-EGF). CD9 upregulates the diphtheria toxin (DT) binding activity of DTR/proHB-EGF, while CD63 does not upregulate the DT binding activity in spite of the fact that this protein also associates with DTR/proHB-EGF on the cell surface. CD9 molecules localize on the cell surface, while those of CD63 localize predominantly at lysosomes and intracellular compartments. We made CD9/CD63 chimeric molecules and then studied their intracellular localization and upregulation activities. The C-terminal regions of CD63, which includes the lysosome sorting motif, showed a strong inhibitory effect on the expression of the chimeric proteins at the cell surface, while mutants lacking the lysosome sorting motif delivered more efficiently on the cell surface, indicating that the lysosome sorting motif contributes to the inhibitory effect of the C-terminal region. However, the N-terminal half of this family of proteins containing the 1st to 3rd transmembrane domains also seems to influence the cell surface expression. For the upregulation of DT binding activity the large extracellular loop (EC2) of CD9 was essential, while the remaining regions influenced the upregulation activity by changing the efficiency of cell surface expression. From these results we discussed the structure-function relationship of this family of proteins.
Focused Topological Value Iteration (2021)

Topological value iteration (TVI) is an effective algorithm for solving Markov decision processes (MDPs) optimally, which 1) divides an MDP into strongly-connected components, and 2) solves these components sequentially. Yet, TVI’s usefulness tends to degrade if an MDP has large components, because the cost of the division process isn’t offset by gains during solution. This paper presents a new algorithm to solve MDPs optimally, focused topological value iteration (FTVI). FTVI addresses TVI’s limitations by restricting its attention to connected components that are relevant for solving the MDP. Specifically, FTVI uses a small amount of heuristic search to eliminate provably sub-optimal actions; this pruning allows FTVI to find smaller connected components, thus running faster. We demonstrate that our new algorithm outperforms TVI by an order of magnitude, averaged across several domains. Surprisingly, FTVI also significantly outperforms popular ‘heuristically-informed’ MDP algorithms such as LAO*, LRTDP, and BRTDP in many domains, sometimes by as much as two orders of magnitude. Finally, we characterize the type of domains where FTVI excels — suggesting a way to an informed choice of solver.
Analysis of the adult and embryonic chicken globin genes in chromosomal DNA. (1978)

Globin-specific mRNA has been purified from the red blood cells of anemic adult hens and from those of 5-day and 7-day chick embryos. These RNA preparations were used to synthesize labeled cDNA for solution and filter hybridization (Southern blotting) experiments. Hybridization of cDNAs prepared with separated adult alpha- and beta-mRNAs and of rabbit globin-specific probes to restriction enzyme-digested, filter-bound chicken chromosomal DNA has shown that the adult globin genes of the chicken exist within EcoRI-cleaved chromosomal DNA fragments which are 4.3, 6.0, and 12.5 kilobase pairs (kbp) in size. These fragments contain the majority or entirety of the adult alpha D, beta, and alpha A genes, respectively. Furthermore, we present evidence that the predominant chicken embryonic globins are contained within EcoRI fragments 9.4 and 15 kbp in size. Evidence is also presented that the same globin organization exists in several different breeds of chickens and in several chicken culture cell types. Finally, it is demonstrated that the pattern of globin-specific hybridization to reticulocyte chromosomal DNA digested with several restriction enzymes is unchanged during erythropoietic development.
ChemInform Abstract: Anisotropically Branched Metal Nanostructures (2015)

Abstract Review: syntheses, properties and applications; 50 refs.
Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro‐aerobic conditions (2013)

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD.
A simple method for producing bio-based anode materials for lithium-ion batteries (2020)

Renewable biomaterials are catalytically converted to graphite for use in lithium-ion anodes using a simple and scalable process.
Hierarchical Cascading Algorithm for 2-D FEM Simulation of Finite SAW Devices (2018)

Application of the finite-element method (FEM) for the simulation of surface acoustic wave (SAW) devices has been constrained by the large number of degrees of freedom required, resulting in large memory usage and long computation times. We propose a new 2-D algorithm that takes advantage of the periodic structure typical of SAW devices. The device is partitioned into small, repeatedly occurring building blocks. Only unique building blocks are simulated with FEM. The device geometry is presented as a hierarchical tree of cascading operations, where smaller blocks are combined into larger blocks. This is equivalent to the full FEM simulation of the device, implying the drastic reduction of memory consumption and simulation time for structures with a high degree of periodicity. The method is verified against FEM/BEM-based software. To ensure accurate and efficient simulation, the boundary conditions should be chosen according to the anisotropy of the substrate crystal.
Local antibiotic therapy guided by microbiological diagnosis (2002)

Therapy with tetracycline fibers guided by microbiological diagnosis effectively reduced P. gingivalis and A. actinomycetemcomitans locally, but was unable to completely eradicate the target organisms. Additional systemic antibiotic therapy further reduced P. gingivalis and A. actinomycetemcomitans. The observed persistence patterns suggest that reemergence of A. actinomycetemcomitans was due to recolonization, whereas the strikingly reproducible local reemergence of P. gingivalis in some sites indicated failed eradication.
A novel, radiolabel-free pulse chase strategy to study Kir3 channel ontogeny (2013)

Kir3 channels are essential regulators of cellular excitability, maintaining cells at resting membrane potentials. While much research has been dedicated to elucidating the mechanisms regulating Kir3 channel gating, little is known regarding the channel's early associations with signaling partners, its stability at the plasma membrane or mechanisms regulating its internalization and degradation. To address these issues we have established an inducible Kir3.1 cell line that allows monitoring of a discrete "pulse" of channel as it progresses along the biosynthetic pathway. Using this system, we have been able to track Kir3 maturation and the influence of partner subunits on Kir3 lifetime and stability. Of note, we show that Kir3.1, in the absence of trafficking partner subunits, can exit the endoplasmic reticulum (ER) and reach the Golgi (though not the plasma membrane), and that expression of Kir3.3 subunits drastically reduced levels of Kir3.1 in the cell. We also show that interfering with trafficking from the ER to Golgi has a pronounced inhibitory effect on Kir3.1-Kir3.2 interactions, suggesting that this complex is stabilized either en route to the Golgi or in the Golgi itself. Finally, we showed that the Kir3 channel can reach the cell surface as early as 6 h post-induction and that removal of cell surface-localized channel occurs within 48 h. This system can be adapted to study the life cycle of any cellular protein without the confounds associated with radioactive labeling or the complications noted with expressing supraphysiological levels of proteins.
Chiral cyclobutanones as versatile synthons: the first enantioselective total synthesis of (+)-laurene (1993)

A novel and convenient route to the thermodynamically unstable ketone 11via the cyclopentanone 8 which was synthesised by palladium-mediated ring expansion of the chiral siloxyvinylcyclobutanes 9 and 10 has been developed. This leads to an enantioselective total synthesis of (+)- laurene 1.
ChemInform Abstract: Synthesis of Marine Natural Products with Antimalarial Activity (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Radioimmunoprecipitation Test for Detection of Mycoplasma pneumoniae Antibody (1973)

A radioimmunoprecipitation (RIP) test for detection of antibody to M. pneumoniae was developed. The test was performed by using microtiter equipment thus combining ease of performance and the need for small amounts of reagents. Divalent cations did not enhance the RIP antibody titer of human sera to M. pneumoniae indicating that complement or complement components were not fixed. Membrane glycolipids appeared to be the major although not the only antigens involved in the RIP reaction. The RIP method was slightly more sensitive than the complement dependent mycoplasmacidal antibody assay and considerably more sensitive than the standard serologic techniques used for measurement of antibody to M. pneumoniae.
Big fast crowds on PS3 (2006)

Crowds and other flock-like group motion are often modeled as interacting particle systems. These multi-agent simulations are computationally expensive because each agent must consider all of the others, if only to identify its neighbors. For large crowds, simple implementations are too slow since computation grows as the square of agent population. Faster approaches often rely on spatial hashing where a partitioning of space is used to accelerate crowd simulation. This same partitioning can form the basis of a scalable multi-processor approach to large, fast crowd simulations, as in [Quinn et al. 2003]. This paper describes an implementation of that approach for PLAYSTATION®3 which supports simulation and display of simple crowds of up to 15,000 individuals at 60 frames per second.
Interaction of Bap31 and MHC Class I Molecules and Their Traffic Out of the Endoplasmic Reticulum (2009)

The endoplasmic reticulum (ER) protein Bap31 associates with nascent class I MHC molecules. It appears to mediate the export of class I MHC molecules from the ER and may also be involved in their quality control. In this study, we use Förster resonance energy transfer and quantitative fluorescence imaging to show that in human, HeLa cells, Bap31 clusters with MHC class I (HLA-A2) molecules in the ER, and traffics via export vesicles to the ER/Golgi intermediate compartment. Förster resonance energy transfer between Bap31 and HLA-A2 and forward traffic increases when MHC class I molecules are loaded with a pulse of peptide. The increased forward traffic is blocked by overexpression of Bap29, a partner protein for Bap31, which localizes to the ER. Thus, in HeLa cells, Bap31 is involved in the exit of peptide-loaded MHC class I from the ER, and its function is regulated by its interaction with its homologue, Bap29.
Using a pilot study to evaluate an assessment strategy for a future Stage III efficacy trial: Example from tuned lighting demonstration (2021)

Abstract Background Poor sleep among residents in nursing homes is common and associated with decreased function and falls. Tunable lighting which mimics both day and night exposure may improve sleep. In this pilot study, we evaluate an assessment strategy to determine the appropriate outcome measure for a future Stage III efficacy trial. Methods This pilot study uses a crossover design, in which three hallways were randomized to tunable LED or static lighting for two months (December 2018-January, 2019) and then switched to the other condition for two months (February-March, 2019). Residents who had been in the nursing home for at least 90 days were eligible. We measured sleep (primary) and agitation (secondary) outcomes using key informant interviews and available administrative data. We measured sleep by interviewing staff using the Sleep Disorders Inventory (SDI) and Minimum Data Set (MDS) resident assessments. We measured agitation by interviewing staff using the Cohen-Mansfield Agitation Inventory (CMAI) and MDS assessments. We used McNemar’s test and Wilcoxon matched-pairs signed-ranks tests to compare within-person changes for all measures. Results 62 residents, 35 of whom had dementia, had complete MDS and SDI data available. The average resident age was 90 and 77% were Asian. The percent of residents with any sleep disturbances was lower in the tuned vs. static lighting conditions based on MDS measure (4.8% tuned, 14.5% static, p &lt; .10); no difference was observed using the SDI (33.9% tuned, 37.1% static). Sleep disturbances were less frequent in the tuned vs. static lighting conditions for both the MDS and SDI measures (p &lt; .10). No significant differences were observed for agitated behaviors. Conclusions Results suggest that the available MDS sleep measure under detects disturbances compared to the gold standard staff interview. Efficacy trials should consider staff interview as primary study outcome. Sensitivity to change in the MDS-based sleep measure could be tested in Stage III trial to determine appropriateness for Stage IV, pragmatic trial.