gebhart/patrepeval huggingface dataset:
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill (2012)

The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.
The fracture toughness of titanium‐fiber‐reinforced bone cement (1992)

Fracture of the poly(methyl methacrylate) bone cement mantle can lead to the loosening and ultimate failure of cemented total joint prostheses. The addition of fibers to the bone cement increases fracture resistance and may reduce, if not eliminate, in vivo fracturing. This study discusses the effect of incorporating titanium (Ti) fibers on fracture toughness. Essential characteristics of the composite bone cement included a homogeneous and uniform fiber distribution, and a minimal increase in apparent viscosity of the polymerizing cement. Ti fiber contents of 1%, 2%, and 5% by volume increased the fracture toughness over non-reinforced bone cement by up to 56%. Bone cements of two different viscosities were used as matrix material, but when reinforced with the same fiber type and content, they showed no difference in fracture toughness. Four different fiber aspect ratios (68, 125, 227, 417) were tested. At 5% fiber content, there was no statistically significant dependence of fracture toughness on fiber aspect ratio. Scanning electron microscopy revealed important toughening mechanisms such as fiber/matrix debonding, local fracture path alteration, and ductile fiber deformation and fracture. Fiber fracture was evidence that the critical fiber length was exceeded. The surfaces of the Ti fibers were rough and irregular, indicating that a high degree of mechanical interlock between matrix and fiber was likely. The energy absorption contribution of plastic deformation and ductile fracture is absent in brittle fibers, like carbon, but is a distinction of the Ti fibers used in this study.
Linearized Third-Derivative Spectroscopy with Depletion-Barrier Modulation (1972)

Low-field (third-derivative) electroreflectance spectra taken on fully depleted space-charge regions are shown to be linear in the modulation potential and free from experimentally induced line-shape distortions due to modulation wave-form, dc bias, or barrier-potential effects. Using a metal-semiconductor (Schottky diode) configuration, accurate threshold energies of the ${{E}_{0}}^{\ensuremath{'}}$ triplet of Ge are obtained. The observed spin-orbit-splitting energy of the valence band confirms that the highest transition also occurs at $\ensuremath{\Gamma}$.
The three‐dimensional structure of Asp189Ser trypsin provides evidence for an inherent structural plasticity of the protease (1999)

Trypsin mutant Asp189Ser, first described by Gráf et al. [Gráf, L., Jancsó, A., Szilágyi, L., Hegyi, G., Pintér, K., Náray-Szabó, G., Hepp, J., Medzihradszky, K. & Rutter, W.J. (1988) Proc. Natl Acad. Sci. USA 85, 4961-4965] has played an important role in recent studies on the structural basis of substrate-specific catalysis by serine proteases. The present work reports the three-dimensional structure of this mutant crystallized in unliganded form: the first unliganded rat trypsin structure reported. The X-ray structure of the Asp189Ser trypsin mutant in complex with bovine pancreatic trypsin inhibitor is already known. The X-ray structure of free Asp189Ser rat trypsin revealed that the single amino acid mutation at the bottom of the substrate binding pocket of trypsin resulted in extensive structural changes around the mutated site and in dimerization of the mutant, in contrast with the complexed enzyme the structure of which is practically the same as that of wild-type trypsin. The structural rearrangement in the mutant was shown to be restricted to the activation domain region providing further evidence for the allosteric property of this structural-functional unit of the enzyme. This study supports our view that the plasticity of the activation domain may play an important role in the mechanism of substrate-specific serine protease action.
Detecting Anomalous Activity on Networks with the Graph Fourier Scan Statistic (2013)

We consider the problem of deciding, based on a single noisy measurement at each vertex of a given graph, whether the underlying unknown signal is constant over the graph or there exists a cluster of vertices with anomalous activation. This problem is relevant to several applications such as surveillance, disease outbreak detection, biomedical imaging, environmental monitoring, etc. Since the activations in these problems often tend to be localized to small groups of vertices in the graphs, we model such activity by a class of signals that are supported over a (possibly disconnected) cluster with low cut size relative to its size. We analyze the corresponding generalized likelihood ratio (GLR) statistics and relate it to the problem of finding a sparsest cut in the graph. We develop a tractable relaxation of the GLR statistic based on the combinatorial Laplacian of the graph, which we call the graph Fourier scan statistic, and analyze its properties. We show how its performance as a testing procedure depends directly on the spectrum of the graph, and use this result to explicitly derive its asymptotic properties on a few significant graph topologies. Finally, we demonstrate theoretically and with simulations that the graph Fourier scan statistic can outperform naive testing procedures based on global averaging and vertex-wise thresholding. We also demonstrate the usefulness of the GFSS by analyzing groundwater Arsenic concentrations from a U.S. Geological Survey dataset.
Synthesis, characterization and ab initio investigation of a panchromatic ullazine–porphyrin photosensitizer for dye-sensitized solar cells (2016)

A panchromatic ullazine–porphyrin dye was synthesized, characterized and applied as a light harvester in dye-sensitized solar cells.
Effects of Chitosan and Lactic Acid on Enzymatic Activities and Bioactive Compounds during Germination of Black Rice (2004)

The effect of chitosan on enzymatic activities and on bioactive compounds was characterized during germination at 25℃ for 7 days to search for a method to produce a germinated black rice. The germination rate was reduced by the addition of lactate and chitosan. The rotting rate was greatly decreased by chitosan, suggesting that the addition of chitosan into a germination solution might be an effective method for controlling fungal contamination during the germination of cereals. The addition of 100 and 200 ppm chitosan increased α-amylase activity after 7 days by up to 152% and 197%, respectively. The activities of β-amylase and β-glucosidase were lower with 200 ppm chitosan than in distilled water and 100 ppm lactate. The amount of total soluble phenolics and total flavonoids decreased rapidly for four days and thereafter remained constant until the seventh day. The antioxidant activity of germinated black rice, in terms of hydrogen-donating activity, increased slowly and did not correspond to the changes of total soluble phenolics and total flavonoids. The amount of phytic acid was reduced by the addition of 200 ppm chitosan compared to distilled water, indicating that chitosan could be used as an elicitor for the increase of phytase activity during the germination of black rice.
Molecular Analysis of the Capsule Gene Region of Group A <i>Streptococcus</i> : the <i>hasAB</i> Genes Are Sufficient for Capsule Expression (1998)

Enzymes directing the biosynthesis of the group A streptococcal hyaluronic acid capsule are encoded in the hasABC gene cluster. Inactivation of hasC, encoding UDP-glucose pyrophosphorylase in the heavily encapsulated group A streptococcal strain 87-282, had no effect on capsule production, indicating that hasC is not required for hyaluronic acid synthesis and that an alternative source of UDP-glucose is available for capsule production. Nucleotide sequence and deletion mutation analysis of the 5.5 kb of DNA upstream of hasA revealed that this region is not required for capsule expression. Many (10 of 23) group A streptococcal strains were found to contain insertion element IS1239' approximately 50 nucleotides upstream of the -35 site of the hasA promoter. The presence of IS1239' upstream of hasA did not prevent capsule expression. These results elucidate the molecular architecture of the group A streptococcal chromosomal region upstream of the has operon, indicate that hasABC are the sole components of the capsule gene cluster, and demonstrate that hasAB are sufficient to direct capsule synthesis in group A streptococci.
Regiocontrolled C-8 Acylation of Castanospermine (1996)

Abstract A convenient route to previously unknown 8-acylated castanospermines is illustrated by synthesis of the butyryl derivative.
Continuous arterial spin labeling at the human common carotid artery: the influence of transit times (2004)

Abstract In evaluating the sensitivity of arterial spin labeling (CASL) and for quantification of perfusion, knowledge of the transit time from the labeling plane to the imaging slice is crucial. The purpose of the current study was to obtain estimates of transit times relevant under the specific experimental conditions of CASL in human subjects using a separate local labeling coil at the neck. Specifically, the post‐label delay (PLD), i.e. the time between the end of the labeling period and the image acquisition, was varied either with or without additional application of crusher gradients to suppress intravascular signal contributions. The overall sensitivity change for varying the PLD between 1000 and 1700 ms was low. A tissue transit time from the neck to an axial supraventricular section through Broca's knee was obtained by fitting the PLD dependence to a two‐compartment model. Averaging over subjects yielded 1930 ± 110 ms for the tissue transit time, and 73 ± 5 ml min −1 100 g −1 for the cerebral blood flow. Small areas that exhibited a very high signal change upon labeling were indicative of regional variation in cerebral blood flow related to vascular anatomy. Copyright © 2004 John Wiley & Sons, Ltd.
Activated T cells recruit exosomes secreted by dendritic cells via LFA-1 (2008)

Dendritic cells (DCs) are known to secrete exosomes that transfer membrane proteins, like major histocompatibility complex class II, to other DCs. Intercellular transfer of membrane proteins is also observed during cognate interactions between DCs and CD4(+) T cells. The acquired proteins are functional and play a role in regulation of immune responses. How membrane protein transfer is achieved and regulated is unclear. Here we show that T cells can recruit major histocompatibility complex class II-containing DC exosomes secreted in the extracellular milieu during cognate DC-T-cell interactions. Recruitment of these exosomes required T-cell activation and was dependent on leukocyte function-associated antigen-1 (LFA-1) rather than on T-cell receptor specificity. Indeed, inducing a high-affinity state of LFA-1 on resting T cells was sufficient to provoke exosome binding. These results imply that DC exosomes secreted in the extracellular milieu during cognate T-cell-DC interactions are targeted to T cells activated in that microenvironment.
Implication of alternative splicing for expression of a variant NAD(P)H:quinone oxidoreductase-1 with a single nucleotide polymorphism at 465C>T (2002)

Three alleles of the human reduced nicotinamide adenine dinucleotide phosphate:quinone oxidoreductase-1 (NQO1) gene are known; wild-type, 609C>T variant, and 465C>T variant; designated as NQO1*1 and NQO1*2, and NQO1*3, respectively. Previously, we found NQO1*3 in one allele of HCT-116 cells, and in both alleles of the mitomycin C-resistant subline, HCT-116R30A. The NQO1 protein content of HCT-116R30A is 5% that of HCT-116. RT-PCR revealed an exon-4-deleted NQO1 mRNA in both cell lines indicating alternative splicing. However, the cause of the lower expression of NQO1 in HCT-116R30A is unknown. Current data show that HCT-116R30A cells are able to express NQO1 protein from transfected cDNA constructs when RNA splicing is omitted. The ratio of full-length to exon-4-deleted mRNA measured by semiquantitative PCR shows that HCT-116 and HCT-116R30A have ratios of 64 : 36 and 34 : 66, respectively. All other cell lines tested have a ratio of 90 : 10, including HT-29, NIH-125 and NCI-H1688 (homozygous NQO1*1); MCF-7 and HL-60 (heterozygous NQO1*1/*2); and MDA-MB231 (homozygous NQO1*2/*2). Alternative splicing of NQO1 at the 5'-splice site of intron-4 increased in cells with NQO1*3. The 465C>T single nucleotide polymorphism (SNP) disrupts the consensus sequence at the 5'-splice site, which is required for binding by U1 small nuclear RNA (U1 snRNA) in spliceosomes. This defective RNA splicing was partially corrected by transfecting HCT-116R30A cells with U1 snRNA constructs, containing base changes to compensate for the 465 SNP. NQO1 protein and enzymatic activity increased with corrected splicing. The 465 SNP was the major cause of increased alternative splicing and decreased expression of NQO1 protein in HCT-116R30A cells.
A Scalable Controlled Set Invariance Framework with Practical Safety Guarantees (2019)

Most existing methods for guaranteeing safety within robotics require time-consuming set-based computations, which greatly limit their applicability to real-world systems. In recent work, the authors have proposed a novel controlled set invariance framework to tackle this limitation. The framework uses a classical barrier function formulation, but replaces the difficult task of computing large control invariant sets with the more tractable tasks of (i) finding a controller that stabilizes the system to a backup set, and (ii) verifying that this backup set is invariant under the stabilizing controller. In this paper, we build upon these results to show that the requirement of proving invariance of the backup set can be relaxed at the expense of providing weaker guarantees on the safety of the system. This trade-off is shown to be favorable in practice, as the theoretically weaker safety guarantees are sufficient in many practical applications. The end result is a framework with a computational complexity that scales quadratically. The effectiveness of the approach is demonstrated in simulation on a Segway.
Photosystem II: The Water-Splitting Enzyme of Photosynthesis (2012)

The oxygen in our atmosphere is derived and maintained by the water-splitting process of photosynthesis. The enzyme that facilitates this reaction and therefore underpins virtually all life on our planet is known as photosystem II (PSII), a multisubunit enzyme embedded in the lipid environment of the thylakoid membranes of plants, algae, and cyanobacteria. During the past 10 years, crystal structures of a 700-kDa cyanobacterial dimeric PSII complex have been reported with ever-increasing improvement in resolution--the latest at 1.9 Å. Thus, the organizational and structural details of its many subunits and cofactors are now well understood. The water-splitting site was revealed as a cluster of four Mn ions and one Ca ion surrounded by amino-acid side chains, of which seven provide ligands to the metals. The metal cluster is organized as a cubane-like structure composed of three Mn ions and the one Ca2+ ion linked by oxo bonds. The fourth Mn is attached to the cubane via one of its bridging oxygens together with another oxo bridge to an Mn ion of the cubane. The overall structure of the catalytic site provides a framework to propose a mechanistic scheme for the water-splitting process and gives a blueprint for the development of catalysts that mimick the reaction in an artificial chemical system as a means to generate solar fuels.
Comment on ‘‘Lateral restoring force on a magnet levitated above a superconductor’’ [J. Appl. Phys. <b>6</b> <b>7</b>, 2631 (1990)] (1990)

Based on Davis’ model for the lateral restoring force on a magnet levitated above a superconductor [J. Appl. Phys. 67, 2631 (1990)], we calculate the restoring force as a function of lateral displacement for a more realistic magnetic field profile.
A new compression technique for binary text images (2002)

In this paper a new lossless binary text image coding technique based on overlapping partitioning is presented. In this technique, the black regions in the image are first partitioned into a number of fully overlapping and nonoverlapping rectangles. After partitioning, the two opposite vertices of each rectangle are compressed using a simple encoding technique. It has been demonstrated that the compression ratios obtained for different text images are better than the nonoverlapping partitioning.
Automatic stabilization of an electron-probe forming system (1975)

Our electron-probe forming system for pattern generation is based on the concept of projecting a demagnified image of a physical object on a target. A complex, automatic probe stabilization method was developed, which does not interfere with system operation. The stabilization system consists of five closed-loop control circuits, activated during beam-off periods and a dynamic, correction-function generator to compensate for deflection astigmatism and field curvature. Probe current is stabilized within 5%; resolution is well within the depth-of-focus range over the lifetime of a cathode. The stabilization can be continuously operated automatically over many cathode life spans by supplementing the circuitry and by adding control software.
A Survey of the Development of Jet Injection in Parenteral Therapy* (1952)

United States Public Health Service and Professor of Anesthesia, Western Reserve University, Cleveland, Ohio (Hingson) Professor of Anatomy, University of Maryland School of Medicine, Baltimore, Maryland (Figge) *Presented before the Twenty-Sixth Annual Congress of Anaesthetists, London, England, September 3–8, 1951, by Dr. W. Royce Hodges, Cumberland, Md. *This study was made possible by grants to the obstetric anesthesia research program of the Johns Hopkins University and Hospital, and the Sinai Hospital, from Abbott Laboratories, Astra Pharmaceutical Company, Ciba Pharmaceutical Products, Eli Lilly Company, Parke, Davis Company, Squibb Institute for Medical Research, Winthrop-Stearns, Inc., and Becton, Dickinson Company.
Cellular Data Services Architecture and Signaling (1994)

0th land and cellular teleDhone networks were originally designed to provide voice communication. However, among land networks in the United States, the demand for data is growing at a rapid annual rate of 20 percent, while demand for voice has slowed to less than 5 percent. Currently, the demand for voice is fueling the expansion to digital techniques in cellular. Since even conservative estimates indicate several million portable computers and fax units will be in use within the next few years, demand for mobile data is certain to grow. Once again, we are faced with the challenge of incorporating data into networks designed for voice. Analog cellular solutions cater to data - but only within the constraints of channels established for voice communication. Digital cellular systems, however, are planned to exist as integrated services networks, and data must be given adequate consideration in the early definition of these networks. This requirement will have a significant impact on the architecture and signaling in digital cellular systems across the globe.
Electrocardiographic and clinical predictors separating atherosclerotic sudden cardiac death from incident coronary heart disease (2011)

SCD and CHD have many risk factors in common. Hypertension, race/ethnicity, BMI, heart rate, QTc, abnormally inverted T wave in any ECG lead group and level of ST elevation in V2 have the potential to separate between the risks of SCD and CHD. These results need to be validated in another cohort.
Context aware Mobile Cloud Computing: Review (2015)

Mobile Cloud Computing has been worldwide accepted as a concept that can significantly improve the user experience when accessing mobile services. Mobile applications have become more popular all across the world. By removing the limitations of mobile devices with respect to storage and computing capabilities and providing new integrated levels of security by centralized maintenance of security-critical software, e.g., mobile payment applications, it is expected that it will find broad acceptance on the business as well as consumer side. Studies indicate that Mobile Cloud Computing (MCC) will additionally help to make visions of context-aware services as real world applications. However, Mobile Cloud Computing concepts rely on an always-on connectivity and will need to provide a scalable and when requested high-quality mobile access. A review study has been done on Mobile Cloud Computing. It exploits the specific information available by the “Mobile Cloud Controller”, i.e., the users' location, context, and requested services, and significantly evolves the Heterogeneous Access Management schemes developed for the traditional heterogeneous access scenarios. In order to evaluate the performance of these intelligent radio access management concepts in the framework of Mobile Cloud Computing, a specialized radio network simulator will be introduced. It will be revealed that a Mobile Cloud Controller establishing Context Management Architecture (CMA) can provide the requested availability and quality of mobile connectivity. In this paper a comprehensive review has been carried out in the context of Mobile Cloud Computing.