gebhart/patrepeval huggingface dataset:
Copper Thiocyanate Inorganic Hole-Transporting Material for High-Efficiency Perovskite Solar Cells (2016)

In this Letter we show that the mixed perovskite in the form of (FAPbI3)0.85(MAPbBr3)0.15 in combination with CuNCS as p-type hole conductor leads to over 16% power conversion efficiency (PCE) under full sun illumination and yields a remarkable monochromatic incident photon-to-electron conversion efficiency of 85%. The devices displayed a short-circuit current density (Jsc) of 21.8 mA/cm2, open-circuit voltage (Voc) of 1100 mV, fill factor (FF) of 0.69, and a PCE of 16.6%. Under similar conditions, the device without CuSCN shows a PCE of 9.5%, with a significant decrease in the Jsc (from 21.8 mA/cm2 to 15.64 mA/cm2) and Voc (from 1100 mV to 900 mV). The high Jsc with CuSCN is mainly due to the effective charge transfer between perovskite and CuSCN, followed by the fast hole transport through CuSCN to the Au. In comparison, the spiro-OMeTAD reference cells showed efficiencies up to 19.65%. Different from most organic hole-transporting materials is the transparency and high hole mobility of CuSCN, which represent a paradigm shift in perovskite solar cells particularly for tandem solar cells.
Automatic semantic locking (2014)

In this paper, we consider concurrent programs in which the shared state consists of instances of linearizable ADTs (abstract data types). We develop a novel automated approach to concurrency control that addresses a common need: the need to atomically execute a code fragment, which may contain multiple ADT operations on multiple ADT instances. In our approach, each ADT implements ADT-specific semantic locking operations that serve to exploit the semantics of ADT operations. We develop a synthesis algorithm that automatically inserts calls to these locking operations in a set of given code fragments (in a client program) to ensure that these code fragments execute atomically without deadlocks, and without rollbacks.
Electromagnetic Penetration Through Apertures in Conducting Surfaces (1978)

In designing hardened systems, one must be able to characterize as well as quantitatively determine the penetration of EMP signals through apertures of general shapes in structures of varying conflgurations. In this paper a tutorial review of a number of methods for analyzing such aperture problems is presented with an emphasis on techniques. The discussion presented herein is reasonably self-contained and is supplemented by references to classical as well as current approaches to the aperture problem. An extensive set of representative numerical results is included.
Stimulation of Early Protein Synthesis as an Assay of Immune Reactivity: Analysis of the Cells Responding to Mitogens and Alloantigens (1974)

Abstract Spleen cells from nonimmune mice were cultured for 24 hr in the presence of phytohemagglutinin (PHA), lipopolysaccharide (LPS), or alloantigens. Data are presented to show that within this time period all three stimuli caused an increase in protein synthesis. The response to PHA and alloantigens was defined as a T cell response by virtue of the effects of anti-θ antibody, adult thymectomy, and velocity cell sedimentation. Similarly, the response to LPS was determined to be a B cell response since it was unaffected by anti-θ antibody or adult thymectomy but was abolished by treatment of responder cells with anti-Ig antiserum and complement. Furthermore, the cells responding to LPS were physically separable from those responding to PHA and alloantigens and sedimented with a velocity characteristic of B lymphocytes.
Phenotype-Based Identification of Host Genes Required for Replication of African Swine Fever Virus (2006)

African swine fever virus (ASFV) produces a fatal acute hemorrhagic fever in domesticated pigs that potentially is a worldwide economic threat. Using an expressed sequence tag (EST) library-based antisense method of random gene inactivation and a phenotypic screen for limitation of ASFV replication in cultured human cells, we identified six host genes whose cellular functions are required by ASFV. These included three loci, BAT3 (HLA-B-associated transcript 3), C1qTNF (C1q and tumor necrosis factor-related protein 6), and TOM40 (translocase of outer mitochondrial membrane 40), for which antisense expression from a tetracycline-regulated promoter resulted in reversible inhibition of ASFV production by >99%. The effects of antisense transcription of the BAT3 EST and also of expression in the sense orientation of this EST, which encodes amino acid residues 450 to 518 of the mature BAT3 protein, were investigated more extensively. Sense expression of the BAT3 peptide, which appears to reversibly interfere with BAT3 function by a dominant negative mechanism, resulted in decreased synthesis of viral DNA and proteins early after ASFV infection, altered transcription of apoptosis-related genes as determined by cDNA microarray analysis, and increased cellular sensitivity to staurosporine-induced apoptosis. Antisense transcription of BAT3 reduced ASFV production without affecting abundance of the virus macromolecules we assayed. Our results, which demonstrate the utility of EST-based functional screens for the detection of host genes exploited by pathogenic viruses, reveal a novel collection of cellular genes previously not known to be required for ASFV infection.
Spectroscopy and Chemometrics for Cultural Heritage and Forensics: Conservation of Magnetic Tape by Identifying Degraded Polymer Signatures; and Characterizing the Chemiluminescent Reaction of Luminol with Blood (2015)

The first half of this manuscript focuses on the identification of degraded magnetic tape using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and multivariate statistics. For several decades before the digital era, magnetic tape was the dominant audio and visual recording medium. A majority of magnetic tapes contain polyester urethane (PEU) binders, which are known to degrade via hydrolysis, making the retrieval of recorded data difficult and at times impossible. Degraded tapes are currently identified through visual inspection followed by playback on vintage equipment. However, if degraded tapes are played, they are likely to stick and shed onto player guides and heads, resulting in irreversible data-loss. A total of 133 quarter-inch audio tapes were analyzed by ATR-FTIR. Classification of IR spectra in regards to tape playability was accomplished using principal component analysis (PCA) followed by quadratic discriminant analysis (QDA) and K-means cluster analysis. The first principal component suggests intensities at the following wavenumbers to be representative of non-playable tapes: 1730 cm−1, 1700 cm−1, 1255 cm−1, and 1140 cm−1. QDA and cluster analysis both successfully identified 93.78% of non-playable tapes in the calibration set and 92.31% of non-playable tapes in the test set. This application of IR spectra assessed with multivariate statistical analysis offers a path to greatly improve efficiency of audio tape preservation. The second half of this manuscript addresses the wide range of reported detection limits of the forensic luminol test for bloodstains. Luminol (3-aminophthalhydrazide) has been used for blood-stain detection by forensic investigators for over 60 years. When a luminol solution is sprayed onto areas suspected of containing blood, it reacts with the heme moiety of hemoglobin to give a faint bluish-white chemiluminescense. Absolute and relative sensitivities of different luminol formulations have been studied for decades. The range of published luminol detection limits for bloodstains spans nearly five orders of magnitude from 100× to more than 5,000,000× dilute bloodstains. We identify several factors that could affect the response of luminol to dried bloodstains and control them. We obtain a luminol detection limit of ~200,000× diluted blood as an estimate of the best case detection limit. The outcome of this work is a standardized method for measuring the chemiluminescent intensity emitted from the reaction of bloodstains with luminol.
Novel V-groove Structures On Silicon (1985)

We report the fabrication of novel V-groove structures by etching silicon twice in an anisotropic etch solution. This technique is capable of yielding micron size patterns from large patterns. For example, we have been able to reduce a 7 &mu;m pattern down to 1 &mu;m. This technique finds useful application in novel diffracting grating structures.
Radiofungicidal Effects of External Gamma Radiation and Antibody-Targeted Beta and Alpha Radiation on Cryptococcus neoformans (2008)

We evaluated the clonogenic survival, membrane permeability, metabolic activity (XTT reduction), and apoptosis (FLICA binding) of Cryptococcus neoformans cells subjected to gamma rays from an external source, and beta and alpha particles delivered to fungal cells by capsule-specific antibody. We found that gamma, beta, and alpha radiation affected cells through different pathways.
A magnetic and electrical study of archaeological structures at Loma Alta, Michoacan, Mexico (1997)

This paper describes the results of high spatial resolution magnetic and resistivity surveys of the Loma Alta site in Michoacan, Mexico. This site is the largest of a series of man-made earthen islands built up within an ancient freshwater basin. Occupied during three main phases from 100 BC to AD 850, the site now shows no surface detail of the underlying structural complexity. Test pits and trenches excavated during several field seasons revealed a fraction of the large ceremonial complex and provided isolated archaeological data difficult to interpret. Geophysical prospection aimed to investigate the so far unknown settlement pattern and detect architectural remains. Magnetic prospecting of the stone architecture turned out to be excellent due to the high contrast between the volcanic rock and the sedimentary fill. A fluxgate gradiometer survey of the entire mound surface defined a large number of small aligned positive and negative magnetic anomalies. Electrical surveys complemented and verified the magnetic results. A series of verification excavations exposed structural elements predicted by the prospecting and aided a further interpretation of the data. The major results of the study are discussed, as they provide a clear image of the orthogonal layout of the highly structured ceremonial site. © 1997 John Wiley & Sons, Ltd.
Codetta: predicting the genetic code from nucleotide sequence (2022)

Supplementary data are available at Bioinformatics online.
Investigation of optimal display size for viewing T1‐weighted MR images of the brain using a digital contrast‐detail phantom (2016)

We clarified the relationship between the display size of MRI images and observer performance using a digital contrast-detail (d-CD) phantom. The d-CD phantom was developed using Microsoft Visual Basic 2010 Express. It had a 512 × 512 matrix in size and a total of 100 holes, whose diameter increased stepwise from 4 to 40 pixels with a 4-pixel interval in the vertical direction; the contrast varied stepwise in the horizontal direction. The digital driving level (DDL) of the back-ground, the width of the DDL, and the contrast were adjustable. These parameters were determined on the basis of the actual T1-weighted magnetic resonance (MR) images of the brain. In this study, the DDL, width, and contrast were set to 85, 20, and 1, respectively. The observer performance study was performed for three different display sizes (30 cm × 30 cm as the enlarged size, 16 cm × 16 cm as the original size, and 10 cm × 10 cm as the reduced size) using a 2-megapixel color liquid crystal display monitor, and it was analyzed using Friedman and Wilcoxon statistical tests. The observer performances for the original display (p < 0.01) and the reduced display sizes (p < 0.01) were superior to that observed for the enlarged size, whereas there was no significant difference between the original display and reduced display sizes (p = 0.31). Evaluation with the digital phantom simulating MR imaging also revealed that the original and reduced display sizes were superior to the enlarged display size in observer performance. The d-CD phantom enables a short-term evaluation of observer performance and is useful in analyzing relation-ship between display size and observer performance.
Safety evaluation of food contact paper and board using chemical tests and in vitro bioassays: role of known and unknown substances (2010)

In vitro toxicological tests have been proposed as an approach to complement the chemical safety assessment of food contact materials, particularly those with a complex or unknown chemical composition such as paper and board. Among the concerns raised regarding the applicability of in vitro tests are the effects of interference of the extractables on the outcome of the cytotoxicity and genotoxicity tests applied and the role of known compounds present in chemically complex materials, such as paper and board, either as constituents or contaminants. To answer these questions, a series of experiments were performed to assess the role of natural substances (wood extracts, resin acids), some additives (diisopropylnaphthalene, phthalates, acrylamide, fluorescent whitening agents) and contaminants (2,4-diaminotoluene, benzo[a]pyrene) in the toxicological profile of paper and board. These substances were individually tested or used to spike actual paper and board extracts. The toxic concentrations of diisopropylnaphthalenes and phthalates were compared with those actually detected in paper and board extracts showing conspicuous toxicity. According to the results of the spiking experiments, the extracts did not affect the toxicity of tested chemicals nor was there any significant metabolic interference in the cases where two compounds were used in tests involving xenobiotic metabolism by the target cells. While the identified substances apparently have a role in the cytotoxicity of some of the project samples, their presence does not explain the total toxicological profile of the extracts. In conclusion, in vitro toxicological testing can have a role in the safety assessment of chemically complex materials in detecting potentially harmful activities not predictable by chemical analysis alone.
Microcapsules as drug delivery devices. (1982)

This review will deal with techniques for producing drug-filled microcapsules, current applications of such microcapsules, and projected applications of microcapsules as drug delivery devices. Specific encapsulation techniques to be evaluated include coacervation, solvent evaporation, interfacial polymerization, emulsion, and hot melt processes. Selection of capsule coating materials will be another factor considered. Differences in specific design requirements of capsules to be administered i.v., i.m. (or s.c./i.p.), and orally will be discussed at length. Specific examples of current capsules administered by each of the routes will be given.
Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers (2016)

The tumor microenvironment is emerging as a key regulator of cancer growth and progression, however the exact mechanisms of interaction with the tumor are poorly understood. Whilst the majority of genomic profiling efforts thus far have focused on the tumor, here we investigate RNA-Seq as a hypothesis-free tool to generate independent tumor and stromal biomarkers, and explore tumor-stroma interactions by exploiting the human-murine compartment specificity of patient-derived xenografts (PDX).Across a pan-cancer cohort of 79 PDX models, we determine that mouse stroma can be separated into distinct clusters, each corresponding to a specific stromal cell type. This implies heterogeneous recruitment of mouse stroma to the xenograft independent of tumor type. We then generate cross-species expression networks to recapitulate a known association between tumor epithelial cells and fibroblast activation, and propose a potentially novel relationship between two hypoxia-associated genes, human MIF and mouse Ddx6. Assessment of disease subtype also reveals MMP12 as a putative stromal marker of triple-negative breast cancer. Finally, we establish that our ability to dissect recruited stroma from trans-differentiated tumor cells is crucial to identifying stem-like poor-prognosis signatures in the tumor compartment.In conclusion, RNA-Seq is a powerful, cost-effective solution to global analysis of human tumor and mouse stroma simultaneously, providing new insights into mouse stromal heterogeneity and compartment-specific disease markers that are otherwise overlooked by alternative technologies. The study represents the first comprehensive analysis of its kind across multiple PDX models, and supports adoption of the approach in pre-clinical drug efficacy studies, and compartment-specific biomarker discovery.
Peripheral quantitative computed tomography (pQCT) for the assessment of bone strength in most of bone affecting conditions in developmental age: a review (2016)

Peripheral quantitative computed tomography provides an automatical scan analysis of trabecular and cortical bone compartments, calculating not only their bone mineral density (BMD), but also bone geometrical parameters, such as marrow and cortical Cross-Sectional Area (CSA), Cortical Thickness (CoTh), both periosteal and endosteal circumference, as well as biomechanical parameters like Cross-Sectional Moment of Inertia (CSMI), a measure of bending, polar moment of inertia, indicating bone strength in torsion, and Strength Strain Index (SSI). Also CSA of muscle and fat can be extracted. Muscles, which are thought to stimulate bones to adapt their geometry and mineral content, are determinant to preserve or increase bone strength; thus, pQCT provides an evaluation of the functional 'muscle-bone unit', defined as BMC/muscle CSA ratio. This functional approach to bone densitometry can establish if bone strength is normally adapted to the muscle force, and if muscle force is adequate for body size, providing more detailed insights to targeted strategies for the prevention and treatment of bone fragility. The present paper offers an extensive review of technical features of pQCT and its possible clinical application in the diagnostic of bone status as well as in the monitoring of the skeleton's health follow-up.
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences (2006)

Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A search of 302 complete bacterial genomes predicted 403 putative prophage regions, accounting for 2.7% of the total bacterial DNA. Analysis of the 285 putative attachment sites revealed tRNAs are targets for integration slightly more frequently (33%) than intergenic (31%) or intragenic (28%) regions, while tmRNAs were targeted in 8% of the regions. The most popular tRNA targets were Arg, Leu, Ser and Thr. Mapping of the insertion point on a consensus tRNA molecule revealed novel insertion points on the 5' side of the D loop, the 3' side of the anticodon loop and the anticodon. A novel method of constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of the phage/prophage proteomes. This method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes.
Inotersen Improves Norfolk Quality of Life-Diabetic Neuropathy Measures in Patients With Hereditary Transthyretin Amyloidosis with Polyneuropathy in the Phase 3 Study NEURO-TTR (S5.006) (2018)

To evaluate the impact of inotersen, an antisense oligonucleotide inhibitor of transthyretin (TTR) protein production, on quality of life (QOL) in patients with hereditary TTR amyloidosis (hATTR) in the phase 3 study NEURO-TTR (NCT01737398).
Is abdominal CT useful for the management of patients with severe acute colitis complicating inflammatory bowel disease? A study in 54 consecutive patients (2017)

Admission CT is not helpful in surgical decision making in SAC.
RETINA: REal-TIme Network Analyzer (2005)

In this paper, we present an analytical tool called RETINA for analyzing real-time constraints in complex networks with stochastic traffic. RETINA is based on a statistical method called real-time queueing theory and can predict the fraction of late tasks in networks of queues given traffic conditions and queue protocol specifications. Upon submitting a profile of the network structure and data flow descriptions, the user is able to query certain performance metrics. Currently RETINA supports two types of real-time scheduling algorithms (EDF and FIFO) and three types of performance queries: the deadline miss rate of a designated flow, the minimum feasible deadline for a particular flow, and whether all QoS requirements of all flows met when a new flow is added. Simulation results show excellent agreement with the results predicted by our tool. RETINA has made it possible to analyze larger and more realistic networks and can be used to address network design tradeoffs. This use of RETINA to identify and quantify network bottlenecks is presented in the paper.
A comparison of the crystal packing in benzene with the geometry seen in crystalline cyclophane-benzene complexes: guidelines for rational receptor design (1993)

Abstract Self-recognition in crystalline benzene is compared with the recognition of benzene in inclusion complexes of three cyclophane receptors. It is shown that the structural organization of aromatic rings, which determines the packing in the molecular crystal and the binding geometry in the preorganized cavity of the cyclophane host molecules, follows the same principles. It is concluded that the examination of the spatial requirements of the aromatic-aromatic interaction motifs found in crystals should allow one to design host bonding skeletons with high binding selectivity and affinity for a specific aromatic guest.
Effect of Surface Polarity on the Conversion of Threading Dislocations in Solution Growth (2013)

We investigated the dislocation behaviors during the solution growth on Si-face and C-face off-axis 4H-SiC seed crystals by using synchrotron X-ray topography. On Si-face, almost all threading screw dislocations (TSDs) and threading edge dislocations (TEDs) are converted into Frank-type defects and basal plane dislocations (BPDs), respectively. On the other hand, on C-face, TSDs were hardly converted. Some of TEDs were converted to BPDs and BPD-TED reconversion was often occurred. Therefore, to reduce density of threading dislocations in the grown crystal, it is better to use Si-face off-axis seed crystal.
An Information-theoretic Approach for Argument Interpretation (2003)

We describe an information-theoretic argument-interpretation mechanism embedded in an interactive system. Our mechanism receives as input an argument entered through a web interface. It generates candidate interpretations in terms of its underlying knowledge representation -- a Bayesian network, and applies the Minimum Message Length principle to select the best candidate. The results of our preliminary evaluations are encouraging, with the system generally producing plausible interpretations of users&amp;apos; arguments.