gebhart/patrepeval huggingface dataset:
Two‐Dimensional<sup>1</sup>H‐NMR and CD Structural Analysis in a Micellar Medium of a Bovine α<sub>s1</sub>‐Casein Fragment having Benzodiazepine‐Like Properties (1997)

The conformation of the benzodiazepine-like decapeptide, YLGYLEQLLR, corresponding to residues 91-100 of bovine alphaS1-casein, has been examined in SDS micelles using CD, two-dimensional 1H-NMR and restrained molecular-dynamics simulation. Evidence is presented that the decapeptide adopts a rigid structure in water/SDS micellar medium, but not in water or dimethylsulfoxide. The three-dimensional structure, consistent with the proton-proton distances obtained from the quantitative analysis of the two-dimensional NOEs, was generated by restrained energy minimization and molecular-dynamics simulation. In water/SDS micellar medium, YLGYLEQLLR adopts an amphipathic helicoid structure with distinct hydrophobic and hydrophilic faces. The relative disposition of the tyrosine aromatic rings was compared with that of the aromatic rings in the benzodiazepines.
Organolithium route to poly(arylsilane)s (1991)

Abstract Various poly(arylsilane)s magnified image The poly(carbosilane)s prepared in this way are of higher molecular weight than when prepared by the Wurtz‐type condensation route previously reported. TG shows 40–50% overll weight loss attained at 500–600°C.
Chemotaxonomic Analysis of Bacterial Populations Colonizing the Rectal Mucosa in Patients with Ulcerative Colitis (2004)

The etiology of ulcerative colitis (UC) is unknown, but evidence links it to bacteria belonging to the normal colonic microbiota. The aims of this study were to characterize bacteria colonizing the rectal epithelium, and to investigate whether significant differences existed in UC. Rectal biopsy specimens were obtained via endoscopy from 9 patients with active colitis and 10 patients without inflammatory bowel disease. Complex bacterial communities colonized the rectal mucosa in all subjects. Overall, 72 bacterial taxa (18 genera) were detected. Twenty species were common to both groups, but only differences in bifidobacteria were statistically significant (P=.005). Peptostreptococci were only detected in patients with UC. Microscopy showed that bacteria in mucosal biofilms often occurred in microcolonies. Interindividual variations in mucosal biofilms made it difficult to assign a role for specific bacteria in UC etiology. However, differences in bifidobacteria and peptostreptococci may implicate these organisms in this disease.
Polarization of Nuclei in Metals (1953)

A new method for polarizing nuclei, applicable only to metals, is proposed. It is shown that if the electron spin resonance of the conduction electrons is saturated, the nuclei will be polarized to the same degree they would be if their gyromagnetic ratio were that of the electron spin. This action results from the paramagnetic relaxation processes that occur by means of the hyperfine structure interaction between electron and nuclear spins. A shift of the electron spin resonance due to the same interaction will occur for large amounts of polarization and should provide a direct indication of the degree of polarization.
Transformation of a type 4 encapsulated strain of Streptococcus pneumoniae (1999)

Streptococcus pneumoniae strain JNR.7/87 is a highly virulent, type 4 encapsulated Gram-positive bacterium whose transformability has not been tested previously, and whose genome is currently being sequenced. The strain was transformed at very low efficiency by addition of exogenous competence-stimulating peptide: However, the efficiency was too low and irreproducible to be useful in many genetic studies. Therefore, the effects on transformation efficiency of changing different components of competence-stimulating peptide-induced transformation have been examined. Screening of growth media was followed by optimization of pre-induction culture acidification, glycine concentration, and induction time. An optimized protocol was developed whereby S. pneumoniae strain JNR.7/87 was transformed reproducibly with a streptomycin resistance (SmR) marker at an efficiency of ~105 colony forming units per 108 cells.
Efficient storage and retrieval of very large document databases (1986)

The authors have developed an information retrieval system named AIR (Augmented Information Retrieval system), which might be one of the most efficient systems for very large document databases. AIR can store the document data compactly and retrieve them quickly. The techniques bringing AIR to the high efficiency, the data compression, the quick keyword index, and the automatic keyword selection, are discussed. These techniques, which are based on the statistical properties of word occurrence, are fairly simple, so that the information retrieval systems employing them can be implemented with ease. The data compression technique reduces English text by a factor of 4. The quick keyword index decreases the average number of disk accesses to retrieve a keyword to about 0.3. The automatic keyword selection technique roughly halves both the number of different keywords and the size of the inverted file with only 2% loss of retrieval power.
Photochemistry of metalloporphyrin complexes. Ligand photoisomerization via intramolecular energy transfer (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of metalloporphyrin complexes. Ligand photoisomerization via intramolecular energy transferDavid G. Whitten, Peter D. Wildes, and Carol A. DeRosierCite this: J. Am. Chem. Soc. 1972, 94, 22, 7811–7823Publication Date (Print):November 1, 1972Publication History Published online1 May 2002Published inissue 1 November 1972https://pubs.acs.org/doi/10.1021/ja00777a025https://doi.org/10.1021/ja00777a025research-articleACS PublicationsRequest reuse permissionsArticle Views335Altmetric-Citations50LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
High Throughput Microfluidic Electrical Impedance Flow Cytometry for Assay of Micro Particles (2010)

Recent advances in microfluidics and microfabrication techniques have led to a variety of portable and inexpensive lab-on-a-chip devices to make quantitative assays of microscale and nanoscale bioparticles. Among them, electrical impedance flow cytometers have become an indispensable tool in clinical and research laboratories for analysis of micro/ nano bio-objects. Because of their simplicity and capability of single cell analysis, electrical impedance flow cytometers have been used widely to detect and characterize latex beads, pollen, biological cells, bacteria, viruses and DNA. One long standing drawback of the electrical impedance flow cytometers is their low throughput, namely they can only process a small amount of analyte at one time. To enable rapid analysis and real time detection of micro and nano objects, high throughput microfluidic electrical impedance flow cytometers have been developed to analyze a large volume of sample in a reasonable time. These devices are especially useful for rapid detection of bio-objects present in ultra low concentrations without a need for tedious preconcentration. In this article, we will review the state-of-the-art high throughput microfluidic electric impedance sensors for rapid analysis of micro bioparticles, including 1) multi-channel Coulter counters, 2) multiplexed resistive pulse sensors, 3) electrical impedance spectroscopy sensors and 4) radio frequency high bandwidth particle counters. Advantages and limitations of each type of impedance sensors are discussed.
Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase (1991)

The overproduction, purification, and determination of the active-site catalytic nucleophile of the DNA (cytosine-5)-methyltransferase (DCMtase) enzyme M.HaeIII are reported. Incubation of purified M.HaeIII with an oligodeoxynucleotide specifically modified with the mechanism-based inhibitor 5-fluoro-2'-deoxycytidine [Osterman, D. G., et al. (1988) Biochemistry 27, 5204-5210], in the presence of the cofactor S-adenosyl-L-methionine (AdoMet), resulted in the formation of a covalent DNA-M.HaeIII complex, which was purified to homogeneity. Characterization of the intact complex showed it to consist of one molecule of the FdC-containing duplex oligonucleotide, one molecule of M.HaeIII, and one methyl group derived from AdoMet. Exhaustive proteolysis, reduction, and alkylation of the DNA-M.HaeIII complex led to the isolation of two DNA-bound peptides--one each from treatment with Pronase or trypsin--which were subjected to peptide sequencing in order to identify the DNA attachment site. Both peptides were derived from the region of M.HaeIII containing a Pro-Cys sequence that is conserved in all known DCMtases. At the position of this conserved Cys residue (Cys71), in the sequence of each peptide, was found an unidentified amino acid residue; all other amino acid residues were in accord with the known sequence. It is thus concluded that Cys71 of M.HaeIII forms a covalent bond to DNA during catalytic methyl transfer. This finding represents a direct experimental verification for the hypothesis that the conserved Cys residue of DCMtases is the catalytic nucleophile [Wu, J. C., & Santi, D. V. (1987) J. Biol. Chem. 262, 4778-4786].(ABSTRACT TRUNCATED AT 250 WORDS)
Polysilicon TFTs with low gate line resistance and low off-state current suitable for large area and high resolution LCDs (2003)

Polysilicon TFTs (thin-film transistors) with a self-aligned platinum silicide (PtSi) gate line are studied. The PtSi was formed by reacting Pt with gate polysilicon films, and the minimum sheet resistance, 2 Omega / Square Operator , was obtained. A delay time calculation indicated that the resistance was low enough to drive a 14-in diagonal LCD (liquid-crystal display) with 780 gate lines. Boron-doped TFTs in channel polysilicon films were fabricated and compared with nondoped TFTs. Off-state current was reduced by optimizing the dose or using XeCl-lasers annealing in hydrogen-passivated TFTs. Simulations of device characteristics were carried out to understand the boron dose dependence. The effect of boron dose was seen to be strongly affected by trap state density in polysilicon films.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An important step towards a prevascularized islet microencapsulation device: in vivo prevascularization by combination of mesenchymal stem cells on micropatterned membranes (2018)

Extrahepatic transplantation of islets of Langerhans could aid in better survival of islets after transplantation. When islets are transfused into the liver 60-70% of them are lost immediately after transplantation. An important factor for a successful extrahepatic transplantation is a well-vascularized tissue surrounding the implant. There are many strategies known for enhancing vessel formation such as adding cells with endothelial potential, the combination with angiogenic factors and / or applying surface topography at the exposed surface of the device. Previously we developed porous, micropatterned membranes which can be applied as a lid for an islet encapsulation device and we showed that the surface topography induces human umbilical vein endothelial cell (HUVEC) alignment and interconnection. This was achieved without the addition of hydrogels, often used in angiogenesis assays. In this work, we went one step further towards clinical implementation of the device by combining this micropatterned lid with Mesenchymal Stem Cells (MSCs) to facilitate prevascularization in vivo. As for HUVECs, the micropatterned membranes induced MSC alignment and organization in vitro, an important contributor to vessel formation, whereas in vivo (subcutaneous rat model) they contributed to improved implant prevascularization. In fact, the combination of MSCs seeded on the micropatterned membrane induced the highest vessel formation score in 80% of the sections.
Innovation in Drying (1996)

ABSTRACT Drying is one of the oldest unit operations and yet it is one of the least understmd and most complex. Several drying technologics have reached maturity viz. furher R&D resources are unlikely to yield appreciable returns on investment. innovative approaches are needed to meet the challenges of global competitiveness. efficient energy utilization, environmental impact and product quality. New products and new processes often demand new drying techniques. Some of the innovations are a result of “technology push” as opposed to “market-pull“. In view of the large time scale of drying technologies most innovations art evolutionary rather than revolutionary. This paper attempts to characterize the process of innovation, identify features common to new drying tcchnologies and survey some innovative dryen.
In vitro susceptibility of Bacillus spp. to selected antimicrobial agents (1988)

Although often dismissed as contaminants when isolated from blood cultures, Bacillus spp. are increasingly recognized as capable of causing serious systemic infections. As part of a clinical-microbiological study, 89 strains of Bacillus spp. isolated from clinical blood cultures between 1981 and 1985 had their species determined and were tested for antimicrobial agent susceptibility to 18 antibiotics. Species of isolates were determined by the API 50CH and API 20E systems. Bacillus cereus (54 strains) was the most common species isolated, followed by B. megaterium (13 strains), B. polymyxa (5 strains), B. pumilus (4 strains), B. subtilis (4 strains), B. circulans (3 strains), B. amyloliquefaciens (2 strains), B. licheniformis (1 strain), and Bacillus spp. (3 strains). Microdilution MIC susceptibility tests revealed all B. cereus strains to be susceptible to imipenem, vancomycin, chloramphenicol, gentamicin, and ciprofloxacin. Non-B. cereus strains were most susceptible to imipenem, vancomycin, LY146032, and ciprofloxacin. Disk susceptibility testing suggested that B. cereus was rarely susceptible to penicillins, semisynthetic penicillins, or cephalosporins with the exception of mezlocillin. In contrast, many non-B. cereus strains were susceptible to penicillins, semisynthetic penicillins, and cephalosporins, but marked variability was noted among species.
Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda (2012)

The processes responsible for the evolution of key innovations, whereby lineages acquire qualitatively new functions that expand their ecological opportunities, remain poorly understood. We examined how a virus, bacteriophage λ, evolved to infect its host, Escherichia coli, through a novel pathway. Natural selection promoted the fixation of mutations in the virus's host-recognition protein, J, that improved fitness on the original receptor, LamB, and set the stage for other mutations that allowed infection through a new receptor, OmpF. These viral mutations arose after the host evolved reduced expression of LamB, whereas certain other host mutations prevented the phage from evolving the new function. This study shows the complex interplay between genomic processes and ecological conditions that favor the emergence of evolutionary innovations.
Workload execution strategies and parallel speedup on clustered computers (1999)

A model of system performance for parallel processing on clustered multiprocessors is developed which unifies multiprogramming with speedup and scaled-speedup. The model is used to explore processor to process allocation alternatives for executing a workload consisting of multiple processes. Heuristics are developed that relate cluster size to parallel fraction of a program and to process scaling factors. The basic analytical model is made more sophisticated by incorporating considerations that affect the realizable speedup, including explicit process scaling, Degree of Parallelism (DOP) as a discrete function, and communication overhead. New developments incorporate nonuniform workload, interconnection network probability of acceptance of requests, nonuniform memory access, and multithreaded processes.
Mapping the Energy of Superantigen <i>Staphylococcus</i> Enterotoxin C3 Recognition of an α/β T Cell Receptor Using Alanine Scanning Mutagenesis (2000)

Binding of the T cell receptor (TCR) to a bacterial superantigen (SAG) results in stimulation of a large population of T cells and subsequent inflammatory reactions. To define the functional contribution of TCR residues to SAG recognition, binding by 24 single-site alanine substitutions in the TCR Vbeta domain to Staphylococcus aureus enterotoxin (SE) C3 was measured, producing an energy map of the TCR-SAG interaction. The results showed that complementarity determining region 2 (CDR2) of the Vbeta contributed the majority of binding energy, whereas hypervariable region 4 (HV4) and framework region 3 (FR3) contributed a minimal amount of energy. The crystal structure of the Vbeta8.2-SEC3 complex suggests that the CDR2 mutations act by disrupting Vbeta main chain interactions with SEC3, perhaps by affecting the conformation of CDR2. The finding that single Vbeta side chain substitutions had significant effects on binding and that other SEC3-reactive Vbeta are diverse at these same positions indicates that SEC3 binds to other TCRs through compensatory mechanisms. Thus, there appears to be strong selective pressure on SAGs to maintain binding to diverse T cells.
Stable expression and replication of hepatitis B virus genome in an integrated state in a human hepatoma cell line transfected with the cloned viral DNA. (1987)

A human hepatocellular carcinoma cell line (Huh6-c15) was transfected with a recombinant DNA molecule that consists of tandemly arranged hepatitis B virus (HBV) genome and a neomycin-resistant gene. One clone resistant to G-418 produces and releases surface antigen and e antigen into medium at a high level and accumulates core particles intracellularly. This clone has a chromosomally integrated set of the original recombinant DNA and produces a 3.5-kilobase transcript corresponding to the pregenome RNA as well as HBV DNAs in an extrachromosomal form. Most of these DNAs were in single-stranded or partially double-stranded form and were packaged in the intracellular core particles. In the medium, particles were detected that contained HBV DNA and were morphologically indistinguishable from Dane particles. These results demonstrate that the HBV genome in an integrated state acted as a template for viral gene expression and replication. The cells were maintained for more than 6 months without losing the ability to produce the extrachromosomal HBV DNA and Dane-like particles. Thus, the cells can be used as a model system for analyses of gene expression and DNA replication of HBV in human hepatocytes.
Advertising based on users' photos (2009)

In this paper, we tackle the problem of learning a user's interest from his photo collections and suggesting relevant ads. We address two key challenges in this work: 1) understanding a user's photos to detect his interest, and 2) bridging the lexical and semantic gap between the vocabulary of ads and that of general users' photos. We solve the first problem by employing a data-driven image annotation approach to annotate each photo and modeling a group of photos, and tackle the second problem by learning and matching the topics of users' photos and ads. The experiments based on real flicker data showed the effectiveness of the approach.
Scalable quantum computing architecture with mixed species ion chains (2015)

We describe our work on trapping, cooling and detecting mixed ion species for a scalable ion trap quantum information processing architecture. These mixed species chains in linear RF traps may help solve several problems with scaling ion trap quantum computation to large numbers of qubits. Initial temperature measurements of linear Coulomb crystals containing barium and ytterbium ions indicate that the mass difference does not significantly impede sympathetic cooling of normal modes that couple well to the coolant ions (Ba in our case). Average motional occupation numbers are estimated to be 10 to 20 quanta per mode for these well cooled modes for chains with small numbers of ions, consistent with the Doppler limit temperature. For normal modes that do not couple significantly to the coolant atoms, the occupation numbers are significantly higher, of order several thousand. Strategies for better cooling of these modes are discussed. Further, we are working to implement these techniques in microfabricated surface traps in order to exercise greater control over ion chain ordering and positioning.
Hodgkin's disease with a B-cell phenotype often shows a VDJ rearrangement and somatic mutations in the VH genes (1994)

The nature of Hodgkin and Reed-Sternberg (HRS) cells remains in question. Immunophenotypic studies favor a relation to the lymphoid lineage with the existence of B- and T-cell types. However, studies on the detection of antigen (Ag) receptor gene rearrangements provided inconsistent results. They concur in that rearranged Ig and T-cell receptor (TCR) genes are not demonstrable in most Hodgkin's disease (HD) cases. To clarify whether this is because of the insensitivity of the method of detection or a real absence of clonal Ig heavy chain (IgH) rearrangements, a polymerase chain reaction (PCR) method with high sensitivity was applied, allowing the detection of less than 50 cells with clonally rearranged IgH genes in a mixture of 100,000 germline or individually rearranged cells. In 67 cases of HD, most of those (67%) with B-Ag+ HRS cells express clonal VDJ rearrangements of the IgH gene. No cases with T-cell Ag+ HRS cells harbored detectable clonal VDJ rearrangements. Of 10 sequenced rearranged IgH genes, the VH segment of six contained considerable somatic mutations. These results suggest that the demonstrated VDJ rearrangements stem from the HRS cells themselves and that the HRS cells of cases with rearranged IgH genes are B-cell related and correspond in their differentiation stage either to naive pregerminal center B cells or (more commonly) to germinal center/postgerminal center-derived memory B cells.
Synthesis of Cyclopropanes via Pd(II/IV)-Catalyzed Reactions of Enynes (2007)

This report describes a new Pd-catalyzed oxidation reaction for the stereospecific conversion of enynes into cyclopropyl ketones. Unlike related PdII/0, Au, and Pt-catalyzed cyclopropane-forming reactions, these transformations proceed with net inversion of geometry with respect to the starting olefin. This result is consistent with a PdII/IV mechanism in which the key cyclopropane-forming step involves nucleophilic attack of a tethered olefin onto the PdIV−C bond.
Rapid detection of carbapenemase genes by multiplex real-time PCR (2012)

The new assay was able to detect the presence of six different carbapenemase gene types in a single 3 h PCR.