gebhart/patrepeval huggingface dataset:
Cross-Linked Peptidoglycan Mediates Lysostaphin Binding to the Cell Wall Envelope of<i>Staphylococcus aureus</i> (2006)

Staphylococcus simulans bv. staphylolyticus secretes lysostaphin, a bacteriocin that cleaves pentaglycine cross bridges in the cell wall of Staphylococcus aureus. The C-terminal cell wall-targeting domain (CWT) of lysostaphin is required for selective binding of this bacteriocin to S. aureus cells; however, the molecular target for this was unknown. We used purified green fluorescent protein fused to CWT (GFP-CWT) to reveal species-specific association of the reporter with staphylococci. GFP-CWT bound S. aureus cells as well as purified peptidoglycan sacculi. The addition of cross-linked murein, disaccharides linked to interconnected wall peptides, blocked GFP-CWT binding to staphylococci, whereas murein monomers or lysostaphin-solubilized cell wall fragments did not. S. aureus strain Newman variants lacking the capacity for synthesizing polysaccharide capsule (capFO), poly-N-acetylglucosamine (icaAC), lipoprotein (lgt), cell wall-anchored proteins (srtA), or the glycolipid anchor of lipoteichoic acid (ypfP) bound GFP-CWT similar to wild-type staphylococci. A tagO mutant strain, defective in the synthesis of polyribitol wall teichoic acid attached to the cell wall envelope, displayed increased GFP-CWT binding. In contrast, a femAB mutation, reducing both the amount and the length of peptidoglycan cross-linking (monoglycine cross bridges), showed a dramatic reduction in GFP-CWT binding. Thus, the CWT domain of lysostaphin directs the bacteriocin to cross-linked peptidoglycan, which also serves as the substrate for its glycyl-glycine endopeptidase domain.
The reduction of vat dyes by indirect electrolysis (1994)

The reduction of vat dyes by an indirect electrolytic process is described. The dyeing procedure and the relevant dyeing parameters for this new reduction technique are discussed. The dyeing results are comparable with those obtained by standard experiments using sodium dithionite. After removal by filtration techniques of the remaining dye from the exhausted dyebath, regeneration of the reducing agent by cathodic reduction is possible. The results demonstrate the applicability of this reduction method for larger‐scale vat dyeing procedures.
Ultrafine microstructure composites prepared by chemical vapor deposition. Annual report, January-December 1988 (1987)

The goal is to develop an analytical model that predicts the experimental conditions that permit the preparation of ultrafine-microstructure ceramic composites by chemical vapor deposition (CVD). The model is to be based on classical thermodynamics, mass transport, kinetic, nucleation, and growth theory. The model will be validated for two dispersed-phase composite systems. One system will be boron nitride plus aluminum nitride; the other hafnium diboride plus silicon carbide. The BN + AlN system is of interest for radomes, windows, and tribological applications while HfB2 + SiC offers potential as a high-temperature oxidation-resistant material including oxidation protective coatings for carbon-carbon composites. Thermodynamic analyses of the BN + AlN and the HfB/sub 2/ + SiC systems were completed. These computerized studies indicate that both composite systems can be prepared by codeposition using commercially available, conventional reagents.
The Immuno-Inflammatory Mechanism for Tissue Injury in Inflammatory Bowel Disease and <i>Helicobacter pylori</i>-Infected Chronic Active Gastritis (2001)

The gastrointestinal mucosa is exposed to myriads of infectious and food antigens, and a unique barrier mechanism handles them on the mucosal surface, and specific immune responses to these antigens call on the mucosal immune system in the mucosal tissues to maintain homeostasis of gastrointestinal functions and structure. Abrogation of these mucosal defense mechanisms may lead to alter immunologic homeostasis in the gastrointestinal tract and to induce pathological features of inflammatory bowel disease (IBD) and Helicobacter pylori-infected chronic active gastritis, including chronic active inflammation, mucosal atrophy and tissue injuries. Regardless of the initiating cause of these long-standing chronic active mucosal inflammations, characteristic immuno-inflammatory mechanisms are involved in their pathogenesis, that is, similar and/or different specific prolonged impaired and excessive immuno-inflammatory responses following the abrogation of the mucosal barrier system are present in the diseased mucosa with IBD and H. pylori infection, respectively.
Structure and Function of the UvrB Protein (1995)

UvrB plays a central role in (A)BC excinuclease. To identify the regions of UvrB which are involved in interacting with UvrA, UvrC, and DNA, deletion mutants, point mutants, and various fusion forms of UvrB were constructed and characterized. We found that the region encompassing amino acid residues 115-250 of UvrB binds to UvrA, while the region encompassing amino acid residues 547-673 binds to both UvrA and UvrC. In addition, the region between these two domains, which contains the helicase motifs II-VI, was found to be involved in binding to DNA. Within this DNA-binding region, two point mutants, E265A and E338A, were found to be unable to bind DNA while two residues, Phe-365 and Phe-496, were identified to interact with DNA. Furthermore, fluorescence quenching studies with mutants F365W and F496W and repair of thymine cyclobutane dimers by photoinduced electron transfer by these mutants suggest that residues Phe-365 and Phe-496 interact with DNA most likely through stacking interactions.
SPECT image analysis using statistical parametric mapping: comparison of technetium-99m-HMPAO and technetium-99m-ECD. (1997)

We present a method of image analysis to semiquantitatively measure rCBF in SPECT images and the changes seen due to differences between the two radiotracers.
A modified path-following algorithm using a known algebraic path (1999)

A new computationally efficient path-following algorithm is presented for source localization that uses a uniform linear sensor array. An algebraic relation is demonstrated between the bearing of a source under a plane wave assumption and the actual source bearing and range. This relation can be used as a path to follow to the peak of the 2-D MUSIC spectrum. As a result, in the case of an array that has m sensors with n sources, this new algorithm can reduce the number of searches to n independent 1-D searches following the known algebraic path.
Alternative algorithms for the optimization of a simulation model of a multimodal container terminal (2006)

Multimodal container terminals (MMCTs) are very complex and consequently require synchronization and balancing of container transfers at each node. The problem being investigated is the minimization of ship delays at the port by considering handling and travelling time of containers from the time the ship arrives at port until all the containers from that ship leave the port. When dealing with export containers, the problem would be that of the handling and travelling time of the containers from when they first arrive at the port until the ship carrying the containers departs from the port. Owing to the dynamic nature of the environment, a large number of timely decisions have been reviewed in accordance with the changing conditions of the MMCTs. The model has been run and tested with a small-size problem using CPLEX. A more realistic model is extremely difficult to solve and is in fact proven to be computationally intractable (NP-hard). Metaheuristics have been developed to deal with the intractability so that near-optimal solutions could be obtained in reasonable time.
Bitcoin Transaction Graph Analysis (2015)

Bitcoins have recently become an increasingly popular cryptocurrency through which users trade electronically and more anonymously than via traditional electronic transfers. Bitcoin's design keeps all transactions in a public ledger. The sender and receiver for each transaction are identified only by cryptographic public-key ids. This leads to a common misconception that it inherently provides anonymous use. While Bitcoin's presumed anonymity offers new avenues for commerce, several recent studies raise user-privacy concerns. We explore the level of anonymity in the Bitcoin system. Our approach is two-fold: (i) We annotate the public transaction graph by linking bitcoin public keys to "real" people - either definitively or statistically. (ii) We run the annotated graph through our graph-analysis framework to find and summarize activity of both known and unknown users.
Development and Analysis of a Pd(0)-Catalyzed Enantioselective 1,1-Diarylation of Acrylates Enabled by Chiral Anion Phase Transfer (2016)

Enantioselective 1,1-diarylation of terminal alkenes enabled by the combination of Pd catalysis with a chiral anion phase transfer (CAPT) strategy is reported herein. The reaction of substituted benzyl acrylates with aryldiazonium salts and arylboronic acids gave the corresponding 3,3-diarylpropanoates in moderate to good yields with high enantioselectivies (up to 98:2 er). Substituents on the benzyl acrylate and CAPT catalyst significantly affect the enantioselectivity, and multidimensional parametrization identified correlations suggesting structural origins for the high stereocontrol.
Dividend Policy and Institutional Holdings: Evidence from Australia (2020)

This paper investigates the relationship between dividend payout and institutional ownership for all Australian listed firms in the period between 2001 and 2015. In our univariate tests, we find that institutional investors, in general, prefer dividend-paying firms more than non-paying firms, and for the dividend-paying firms in our sample, institutional investors hold more shares in the firms who pay higher dividends. We further explore the causality between dividend payout and institutional ownership in our multivariate tests with our panel data. The results show an insignificant effect of institutional ownership (dividend payout) on the future dividend payout (institutional ownership) while controlling for firms’ fundamentals, that a higher dividend yield does not attract more institutional investors and that there is no catering to Australian institutional investors.
Evaluation of a Two-Phase scid Mouse Model Preconditioned with Anti-Interferon-  Monoclonal Antibody for Drug Testing against Cryptosporidium parvum (1995)

One 1-mg injection of anti-interferon-gamma monoclonal antibody (anti-IFN-gamma MAb) into newly weaned scid mice 2 h before challenge with Cryptosporidium parvum oocysts markedly exacerbated the course of the infection for > or = 47 days, compared with challenged mice that received an equivalent dose of irrelevant MAb. Oocyst excretion in feces started 4-6 days after challenge and continued at high levels for > or = 47 days. Loss of body weight was also apparent. The extent and distribution of mucosal infection were profound, involving the stomach and several segments of the small and large intestines. The acute phase, which involved infection of the gut, was during the first 25 days after challenge. The following chronic phase consistently involved, in addition, infection of the hepatobiliary tract. The acute phase is a useful model in which to test luminally active drugs, while the chronic phase may be used in the future to test drugs that are active against hepatobiliary tract infections as well.
Using local optimality criteria for efficient information retrieval with redundant information filters (1996)

We consider information retrieval when the data—for instance, multimedia—is computationally expensive to fetch. Our approach uses “information filters” to considerably narrow the universe of possibilities before retrieval. We are especially interested in redundant information filters that save time over more general but more costly filters. Efficient retrieval requires that decisions must be made about the necessity, order, and concurrent processing of proposed filters (an “execution plan”). We develop simple polynomial-time local criteria for optimal execution plans and show that most forms of concurrency are suboptimal with information filters. Although the general problem of finding an optimal execution plan is likely to be exponential in the number of filters, we show experimentally that our local optimality criteria, used in a polynomial-time algorithm, nearly always find the global optimum with 15 filters or less, a sufficient number of filters for most applications. Our methods require no special hardware and avoid the high processor idleness that is characteristic of massive-parallelism solutions to this problem. We apply our ideas to an important application, information retrieval of captioned data using natural-language understanding, a problem for which the natural-language processing can be the bottleneck if not implemented well.
High-resolution transmission electron microscopy of mesoporous MCM-41 type materials (1994)

High-resolution transmission electron microscopy of MCM-41 shows for the first time clearly the hexagonal shape of the pores, and allows direct observation of the transition from a lamellar to the hexagonal phase.
Stable semiconductor black phosphorus (BP)@titanium dioxide (TiO2) hybrid photocatalysts (2015)

Over the past few decades, two-dimensional (2D) and layered materials have emerged as new fields. Due to the zero-band-gap nature of graphene and the low photocatalytic performance of MoS2, more advanced semiconducting 2D materials have been prompted. As a result, semiconductor black phosphorus (BP) is a derived cutting-edge post-graphene contender for nanoelectrical application, because of its direct-band-gap nature. For the first time, we report on robust BP@TiO2 hybrid photocatalysts offering enhanced photocatalytic performance under light irradiation in environmental and biomedical fields, with negligible affected on temperature and pH conditions, as compared with MoS2@TiO2 prepared by the identical synthesis method. Remarkably, in contrast to pure few layered BP, which, due to its intrinsic sensitivity to oxygen and humidity was readily dissolved after just several uses, the BP@TiO2 hybrid photocatalysts showed a ~92% photocatalytic activity after 15 runs. Thus, metal-oxide-stabilized BP photocatalysts can be practically applied as a promising alternative to graphene and MoS2.
A pH‐ and ionic strength‐responsive polypeptide hydrogel: Synthesis, characterization, and preliminary protein release studies (1999)

A novel polypeptide hydrogel has been synthesized by crosslinking poly(L-glutamic acid) (PLG) with poly(ethylene glycol) (PEG). The PLG-PEG hydrogel was shown to be highly hydrophilic, and the extent of swelling varied with pH, increasing at higher ionization of the PLG. Aside from electrostatic effects, such as ion–ion repulsion and internal ion osmotic pressure, circular dichroism studies showed that swelling response to pH also is affected by secondary structural attributes associated with the polypeptide backbone. Modification of the polypeptide by changing its hydrophobicity and degree of ionization was an effective method for altering the overall extent of pH-responsive swelling. Rapid de-swelling (contraction) was observed when the PLG-PEG hydrogel was transferred from high to low pH buffer solution, and this swelling/de-swelling behavior was reversible over repeated cycles. Drug release from swollen hydrogels was examined using the model protein lysozyme. Rapid de-swelling of the hydrogel was found to be an effective means of facilitating lysozyme release. The crosslinking of synthetic polypeptides with PEG appears to be a highly versatile approach to the preparation of pH-responsive biodegradable hydrogels. © 1999 John Wiley & Sons, Inc. J Biomed Mater Res, 47, 595–602, 1999.
Human Factors and the Systems Development Process (2003)

Internet systems have the potential to reach a huge and unknown audience. How easy a system is to use will usually determine its success or failure and consequently the business and yet the human factors elements of systems are rarely considered. Usability describes the ease with which people can use a system to complete a task. It is often the case however that development teams focus more on the technology and less on the users when designing systems resulting in software that is not useable and therefore does not satisfy users’ need. This chapter presents recent research, which examines one approach to developing a web-based information system and demonstrates how the composition of the development team through the inclusion of people with an understanding of user needs is important to the quality of the final product and ultimately the success of the system.
Analysis of 2-TFTs AMOLED pixel circuit based on an on-current model of poly-Si TFTs (2014)

In this study, we present an analysis on the typical 2T1C pixel circuit for active-matrix organic light-emitting diode (AMOLED) displays based on an analytical on-current model for polycrystalline Si (poly-Si) thin film transistors (TFTs). We focus on the charging time for the storage capacitor and driving current for the OLED. The voltage variation caused by the charge injection and clock feedthrough effects is estimated. The analysis based on the analytical poly-Si models is more accurate than the conventional one based on the MOSFET model, and more explicit and flexible than by using a circuit simulator.
cAMP-PKA-CaMKII signaling pathway is involved in aggravated cardiotoxicity during Fuzi and Beimu Combination Treatment of Experimental Pulmonary Hypertension (2016)

Aconiti Lateralis Radix Praeparata (Fuzi) and Fritillariae Thunbergii bulbus (Beimu) have been widely used clinically to treat cardiopulmonary related diseases in China. However, according to the classic rules of traditional Chinese medicine, Fuzi and Beimu should be prohibited to use as a combination for their incompatibility. Therefore, it is critical to elucidate the paradox on the use of Fuzi and Beimu combination therapy. Monocrotaline-induced pulmonary hypertension rats were treated with either Fuzi, Beimu, or their combination at different stages of PH. We demonstrated that at the early stage of PH, Fuzi and Beimu combination significantly improved lung function and reduced pulmonary histopathology. However, as the disease progressed, when Fuzi and Beimu combination were used at the late stage of PH, right ventricular chamber dilation was histologically apparent and myocardial apoptosis was significantly increased compared with each drug alone. Western-blotting results indicated that the main chemical ingredient of Beimu could down-regulate the protein phosphorylation levels of Akt and PDE4D, whereas the combination of Fuzi and Beimu could up-regulate PKA and CaMKII signaling pathways. Therefore, we concluded that Fuzi and Beimu combination potentially aggravated the heart injury due to the inhibition of PDK1/Akt/PDE4D axis and subsequent synergistic activation of βAR-Gs-PKA/CaMKII signaling pathway.
Performance of the GPRS RLC/MAC protocols with VoIP traffic (2003)

GSM/GPRS networks have been designed to carry both voice and data traffic. Our aims are to study the behaviour of the GPRS mechanisms (RLC/MAC layer and radio resource scheduler) when the application layer carries packetized voice, and determine if the quality of service provided by the network is suitable for the VoIP service. The paper includes a discussion about the voice source model, an analysis of the effects in capacity of a GPRS carrier when feed with VoIP packets, measurements of statistical parameters of the voice traffic stream and a discussion of the influence in the quality of the service.
Hypouricemia and hyperuricemia in type 2 diabetes: two different phenotypes (2001)

In type 2 diabetes, hyperuricemia seems to be associated with the insulin-resistant syndrome and with early onset or increased progression to overt nephropathy, while hypouricemia is associated with worse metabolic control, hyperfiltration and a late onset or decreased progression to overt nephropathy.
Chromatographic resolution and quantitative assay of CNS tissue sphingoids and sphingolipids (2001)

Quantitative separation of ceramide, sphingoids (dihydrosphingosine, sphingosine, psychosine), and glycosphingolipids as individual fractions was achieved with silicic acid, Dowex column chromatography, and specific solvent mixtures that have not been previously described. Purified ceramide, resolved as a single band, was assayed by thin-layer chromatography (TLC) followed by gas chromatography (GC) and high performance liquid chromatography (HPLC). Sphingoids, purified by Dowex, were assayed by GC and HPLC without mild alkaline hydrolysis, which reduces the yield by interfering with the free amino group of psychosine and dihydrosphingosine. Several less polar (than cerebroside) alkali-/acid-labile glycosphingolipids that elute with galactosylceramide were also identified. Neutral and acidic glycosphingolipids, quantitatively recovered and purified to homogeneity, were resolved by TLC. We used these techniques to determine sphingolipids and sphingoids of vertebrate central nervous system (CNS) tissue, using as little as 30-50 mg (wet weight) of tissue. In addition, phosphatidylcholine and sphingomyelin, relevant to ceramide metabolism, were quantitatively recovered in pure form and resolved by TLC. This method, used to study CNS sphingolipid content, may well be applicable to determine the sphingolipid composition of other tissues and cell culture, but further experiments are necessary to ascertain this.
Miniaturized metasurface unit cell for microwave metalens antennas (2017)

In this paper, a miniaturized metasurface unit cell is proposed for microwave metalens antennas. The antennas are designed operating at 2 GHz and a miniaturized two-layered Jerusalem Cross (JC) shaped unit cell with a period of 0.22λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> is introduced for the metalens which offers a maximum transmission phase variation of 215° within the 3-dB insertion loss. With the proposed miniaturized JC unit cell, a dual-polarized one-dimensional metalens element with 3×12 JC unit cells is designed for gain enhancement with the focal length of 130 mm. By repeating this element along the y-axis, it is flexible to design an array of metalens antenna. As example, a 15-element antenna array loaded with a metalens is proposed and the simulated aperture efficiency reaches 55%.
Creation and detection of optical modes with spatial light modulators (2016)

Modal decomposition of light has been known for a long time, applied mostly to pattern recognition. With the commercialization of liquid-crystal devices, digital holography as an enabling tool has become accessible to all, and with it all-digital tools for the decomposition of light have finally come of age. We review recent advances in unravelling the properties of light, from the modal structure of laser beams to decoding the information stored in orbital angular momentum (OAM)-carrying fields. We show application of these tools to fiber lasers, solid-state lasers, and structured light created in the laboratory by holographic laser beam shaping. We show by experimental implementation how digital holograms may be used to infer the intensity, phase, wavefront, Poynting vector, polarization, and OAM density of some unknown optical field. In particular, we outline how virtually all the previous ISO-standard beam diagnostic techniques may be readily replaced with all-digital equivalents, thus paving the way for unravelling of light in real time. Such tools are highly relevant to the in situ analysis of laser systems, to mode division multiplexing as an emerging tool in optical communication, and for quantum information processing with entangled photons.