gebhart/patrepeval huggingface dataset:
DNA "fingerprints" and segregation analysis of multiple markers in human pedigrees. (1986)

Tandem-repetitive DNA hybridization probes based on a putative human recombination signal detect multiple polymorphic minisatellite fragments in human DNA. The genetic complexity of the resulting individual-specific DNA "fingerprints" was investigated by studying a large sibship affected by neurofibromatosis and a more extensive pedigree segregating for two different hemoglobinopathies. The segregation of up to 41 different heterozygous DNA fragments from each parent could be analyzed in a single sibship, using two different repeat probes. Most of these variable DNA fragments could not be paired as alleles, to an extent which suggests that the DNA fingerprints are together derived from approximately 60 heterozygous loci (approximately 120 variable fragments), only a proportion of which can be scored in a given individual. Two or three of the DNA fragments detected by one probe showed tight linkage and may be derived from long minisatellite(s) that are cleaved to produce more than one polymorphic DNA fragment. Excluding allelic and linked DNA fragments, almost all remaining scorable fragments segregated independently, allowing up to 34 unlinked loci to be examined simultaneously. These loci are scattered over most or all of the human autosomes. Minisatellite probes are therefore suitable for rapid marker generation and can be applied to linkage analysis in human pedigrees.
PulseNet: The Molecular Subtyping Network for Foodborne Bacterial Disease Surveillance, United States (2001)

PulseNet, the national molecular subtyping network for foodborne disease surveillance, was established by the Centers for Disease Control and Prevention and several state health department laboratories to facilitate subtyping bacterial foodborne pathogens for epidemiologic purposes. PulseNet, which began in 1996 with 10 laboratories typing a single pathogen (Escherichia coli O157:H7), now includes 46 state and 2 local public health laboratories and the food safety laboratories of the U.S. Food and Drug Administration and the U.S. Department of Agriculture. Four foodborne pathogens (E. coli O157:H7; nontyphoidal Salmonella serotypes, Listeria monocytogenes and Shigella) are being subtyped, and other bacterial, viral, and parasitic organisms will be added soon.
Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions (2013)

Methane is an important greenhouse gas and microbes in the environment play major roles in both global methane emissions and terrestrial sinks. However, a full mechanistic understanding of the response of the methane cycle to global change is lacking. Recent studies suggest that a number of biological and environmental processes can influence the net flux of methane from soils to the atmosphere but the magnitude and direction of their impact are still debated. Here, we synthesize recent knowledge on soil microbial and biogeochemical process and the impacts of climate change factors on the soil methane cycle. We focus on (i) identification of the source and magnitude of methane flux and the global factors that may change the flux rate and magnitude in the future, (ii) the microbial communities responsible for methane production and terrestrial sinks, and (iii) how they will respond to future climatic scenarios and the consequences for feedback responses at a global scale. We also identify the research gaps in each of the topics identified above, provide evidence which can be used to demonstrate microbial regulation of methane cycle and suggest that incorporation of microbial data from emerging -omic technologies could be harnessed to increase the predictive power of simulation models.
THE EFFECT OF PROTEOLYTIC ENZYME SERRATIOPEPTIDASE IN THE TREATMENT OF EXPERIMENTAL IMPLANT-RELATED INFECTION (2006)

Background: Infection around an implanted orthopaedic device is a devastating complication, and the treatment of infections involving slime-forming bacteria is especially difficult. The purpose of the present study was to evaluate the effectiveness of a proteolytic enzyme, serratiopeptidase, in the eradication of a periprosthetic infection in an in vivo animal model. Methods: In sixty Sprague-Dawley rats, the medullary canal of the right femur was drilled through the intercondylar notch and was inoculated with a Staphylococcus epidermidis strain (ATCC 35984) with a high slime-producing capacity. The cavity was filled with polymethylmethacrylate cement, and a Kirschner wire that had contact with the knee joint was inserted. None of the animals received any treatment for two weeks. Twenty rats were killed at two weeks after the inoculation in order to determine if the infection had become established. The remaining forty rats were randomized into two groups. One group received serratiopeptidase enzyme injections into the knee joint in addition to antibiotic therapy for four weeks, and the other group received intra-articular saline solution injections together with the same antibiotic therapy. The animals from both groups were killed two weeks after the end of therapy (on Day 56). The knee specimens were evaluated bacteriologically and histologically to determine the prevalence of persistent infection and the effects of the enzyme on local tissue. Results: At two weeks, inoculated bacteria grew on culture of specimens from twelve (63.2%) of nineteen animals in the no-treatment group. Microbiological testing suggested that infection persisted in only one (5.6%) of eighteen animals in the serratiopeptidase-and-antibiotic group, whereas it was present in six (37.5%) of sixteen animals in the antibiotic-only group (p = 0.001). Histological evaluation showed similar results (kappa = 0.92). Conclusions: Serratiopeptidase was effective for eradicating infection caused by biofilm-forming bacteria in this experimental animal model. The antibiofilm property of the enzyme may enhance antibiotic efficacy in the treatment of staphylococcal infections.
Group motion graphs (2005)

We introduce Group Motion Graphs, a data-driven animation technique for groups of discrete agents, such as flocks, herds, or small crowds. Group Motion Graphs are conceptually similar to motion graphs constructed from motion-capture data, but have some important differences: we assume simulated motion; transition nodes are found by clustering group configurations from the input simulations: and clips to join transitions are explicitly constructed via constrained simulation. Graphs built this way offer known bounds on the trajectories that they generate, making it easier to search for particular output motions. The resulting animations show realistic motion at significantly reduced computational cost compared to simulation, and improved control.
Oncogenic BRAF and the tumor suppressor IGFBP7 in the genesis of atypical spitzoid nevomelanocytic proliferations (2009)

Rare reports indicate that the frequency of BRAFV600E mutations is high in atypical Spitz nevi. The purpose of this study was to ascertain the utility of the RAF/RAS mutational status as a diagnostic adjunct in lesions with histologic features that deviate from a typical Spitz nevus and, to examine expression of Insulin growth factor binding protein 7 (IGFBP7), a tumor suppressor acting through autocrine/paracrine pathways to inhibit BRAF-MEK-ERK signaling, in the same. Genomic DNA for genotyping was isolated from 6 regular Spitz nevi and 14 atypical spitzoid nevomelanocytic proliferations (including 1 melanoma with spitzoid histomorphology). NRAS1, NRAS2 and KRAS were analyzed, in addition to BRAFV600E. A mutation in BRAFV600E was noted in only one case-that of a regular Spitz nevus. IGFBP7 expression appeared to be maintained in this case, but was absent in 7/17 cases, which included 5 atypical spitzoid nevomelanocytic proliferations. Lack of expression of IGFBP7 in atypical spitzoid nevomelanocytic proliferations with histologically concerning features but BRAF-WT indicates that the evolutionary path in atypical spitzoid nevomelanocytic proliferations is genetically distinct from that of IGFBP7-negative BRAF-positive melanoma. From an oncogenic BRAF perspective, our findings suggest that the majority of 'atypical' spitzoid nevomelanocytic proliferations are probably no different from conventional Spitz nevi.
Synthesis and SAR Investigations for Novel Melanin-Concentrating Hormone 1 Receptor (MCH1) Antagonists Part 1. The Discovery of Arylacetamides as Viable Replacements for the Dihydropyrimidinone Moiety of an HTS Hit (2007)

Melanin-concentrating hormone (MCH) is involved in the regulation of feeding, water balance, energy metabolism, general arousal and attention state, memory, cognitive functions, and psychiatric disorders. Herein, two new chemical series exemplified by N-[5-(1-{3-[2,2-bis-(4-fluoro-phenyl)-acetylamino]-propyl}-piperidin-4-yl)-2,4-difluoro-phenyl]-isobutyramide (SNAP 102739, 5m) and N-[3-(1-{3-[(S)-2-(4-fluoro-phenyl)-propionylamino]-propyl}-piperidin-4-yl)-4-methylphenyl]-isobutyramide ((S)-6b) are reported. These compounds were designed to improve the pharmacokinetic properties of the high-throughput screening lead compound 1 (SNAP 7941). The MCH1 receptor antagonists 5m and (S)-6b show reasonable pharmacokinetic profiles (rat bioavailability = 48 and 81%, respectively). Compounds 5m and (S)-6b demonstrated the inhibition of a centrally administered MCH-evoked drinking effect, and compound 5m exhibited oral in vivo efficacy in the rat social interaction model of anxiety, with a minimum effective dose = 0.3 mg/kg.
Hydroxypyridinone Extraction Agents for Pu(IV) (2004)

Abstract Twelve different extraction agents, based on the hydroxypyridinone (HOPO) chelating moieties 3,2‐HOPO, 3,4‐HOPO, and 1,2‐HOPO, have been synthesized and characterized for their ability to remove Pu(IV) from nitric acid solutions. Most of these, in particular those based on 1,2‐HOPO, displayed very rapid extraction kinetics and extracted Pu(IV) with large distribution ratios. They were also highly effective in removing Pu(IV) from solutions containing high concentrations of Fe(III) or ethylenediaminetetraacetic acid (EDTA). Stripping the bound Pu(IV) from the chelate complex proved challenging, as only ∼40% was removed even with concentrated (15.8 M) nitric acid.
申丹《短篇叙事小说的文体与修辞：显性情节后面的隐性进程》序言 (2013)

申丹的《短篇叙事小说的文体与修辞》有力地提出了一套关于叙事进程的新理论，其严谨的论证令人信服，回应了该领域一些亟待解决的问题。本书对仅关注情节发展的传统做法提出质疑，揭示出在显性情节和潜藏在表层文本后面的“隐性进程”之间通常存在着某种反讽性差异，并通过六篇叙事文本的阐释实践加以佐证。本书与新亚里士多德学派的修辞性叙事学一脉相承，但大大拓展了其研究范畴。对隐性进程的发掘还可以使读者认识到，某些小说（如曼斯菲尔德的《苍蝇》）真正的道德寓意可能在很大程度上不同于以往批评家的公认评判。
Toward a quantitative assessment of diffusion anisotropy (1996)

Indices of diffusion anisotropy calculated from diffusion coefficients acquired in two or three perpendicular directions are rotationally variant. In living monkey brain, these indices severely underestimate the degree of diffusion anisotropy. New indices calculated from the entire diffusion tensor are rotationally invariant (RI). They show that anisotropy is highly variable in different white matter regions depending on the degree of coherence of fiber tract directions. In structures with a regular, parallel fiber arrangement, water diffusivity in the direction parallel to the fibers (Dparallel approximately 1400-1800 x 10(-6) mm2/s) is almost 10 times higher than the average diffusivity in directions perpendicular to them (D + D)/2 [corrected] approximately 150-300 x 10(-6) mm2/s), and is almost three times higher than previously reported. In structures where the fiber pattern is less coherent (e.g., where fiber bundles merge), diffusion anisotropy is significantly reduced. However, RI anisotropy indices are still susceptible to noise contamination. Monte Carlo simulations show that these indices are statistically biased, particularly those requiring sorting of the eigenvalues of the diffusion tensor based on their magnitude. A new intervoxel anisotropy index is proposed that locally averages inner products between diffusion tensors in neighboring voxels. This "lattice" RI index has an acceptably low error variance and is less susceptible to bias than any other RI anisotropy index proposed to date.
Generation of monoclonal antibodies to cancer/testis (CT) antigen CT10/MAGE-C2. (2006)

CT10/MAGE-C2 is a recently identified antigen that, typically of cancer/testis (CT) antigens, can be found in various malignant tumors and in normal adult testis. As with many other CT antigens, our knowledge is based mainly on mRNA expression data. In the present study, we describe the generation of mAbs to CT10/MAGE-C2 for the analysis of its protein expression. Newly generated clones were chosen based on their reactivity in ELISA, immunoblotting, and immunohistochemistry (IHC). Emphasis was put on the reactivity of newly generated reagents on formalin-fixed, paraffin-embedded tissue to ensure their applicability to archival material. Eventually we selected two clones, LX-CT10.5 and LX-CT10.9, that showed intense reactivity to CT10/MAGE-C2 protein and CT10/MAGE-C2 mRNA-positive cell lines, but no cross-reactivity with other CT antigens. Both mAbs show superior staining characteristics in IHC and are applicable to frozen and paraffin sections. In testis, CT10/MAGE-C2 displays the typical CT pattern with regard to staining of germ cells, which is intense during the early maturation stages. In tumors, we analyzed a limited number of cases displaying the typical heterogeneous CT expression pattern. Interestingly, immunoreactivity was seen solely in the nucleus: No staining was seen in the cytoplasm of tumor cells.
Therapeutic peptides for cancer therapy. Part I – peptide inhibitors of signal transduction cascades (2009)

Given our current knowledge of protein sequences, structures and interaction interfaces, therapeutic peptides that inhibit interactions of interest are easily designed. These peptides are advantageous because they are highly specific for the interaction of interest, and they are much more easily developed than small molecule inhibitors of the same interactions. The main hurdle to application of peptides for cancer therapy is their poor pharmacokinetic and biodistribution parameters. Therefore, successful development of peptide delivery vectors could potentially make possible the use of this new and very promising class of anticancer agents.
Concordant morphologic and gene expression data show that a vaccine halts HER-2/neu preneoplastic lesions (2004)

While much experimental data shows that vaccination efficiently inhibits a subsequent challenge by a transplantable tumor, its ability to inhibit the progress of autochthonous preneoplastic lesions is virtually unknown. In this article, we show that a combined DNA and cell vaccine persistently inhibits such lesions in a murine HER-2/neu mammary carcinogenesis model. At 10 weeks of age, all of the ten mammary gland samples from HER-2/neu–transgenic mice displayed foci of hyperplasia that progressed to invasive tumors. Vaccination with plasmids coding for the transmembrane and extracellular domain of rat p185(neu) followed by a boost with rp185(neu+) allogeneic cells secreting IFN-γ kept 48% of mice tumor free. At 22 weeks, their mammary glands were indistinguishable from those of 10-week-old untreated mice. Furthermore, the transcription patterns of the two sets of glands coincided. Of the 12,000 genes analyzed, 17 were differentially expressed and related to the antibody response. The use of B cell knockout mice as well as the concordance of morphologic and gene expression data demonstrated that the Ab response is the main mechanism facilitating tumor growth arrest. This finding suggests that a new way can be found to secure the immunologic control of the progression of HER-2/neu preneoplastic lesions.
Transdermal Delivery of Drugs (1988)

Transdermal drug delivery involves the continuous administration of therapeutic molecules through the skin. It has the advantage of maintaining constant drug plasma levels and improving patient compliance. Compared to the oral route, losses in bioavailability due to first-pass liver metabolism are reduced. This paper describes the theory of transdermal drug penetration, the role of the skin, in vitro testing, examination of currently available transdermal delivery systems, and recent developments in iontophoresis, prodrugs, and penetration enhancers.
Advances in three-dimensional integral imaging: sensing, display, and applications [Invited] (2013)

Three-dimensional (3D) sensing and imaging technologies have been extensively researched for many applications in the fields of entertainment, medicine, robotics, manufacturing, industrial inspection, security, surveillance, and defense due to their diverse and significant benefits. Integral imaging is a passive multiperspective imaging technique, which records multiple two-dimensional images of a scene from different perspectives. Unlike holography, it can capture a scene such as outdoor events with incoherent or ambient light. Integral imaging can display a true 3D color image with full parallax and continuous viewing angles by incoherent light; thus it does not suffer from speckle degradation. Because of its unique properties, integral imaging has been revived over the past decade or so as a promising approach for massive 3D commercialization. A series of key articles on this topic have appeared in the OSA journals, including Applied Optics. Thus, it is fitting that this Commemorative Review presents an overview of literature on physical principles and applications of integral imaging. Several data capture configurations, reconstruction, and display methods are overviewed. In addition, applications including 3D underwater imaging, 3D imaging in photon-starved environments, 3D tracking of occluded objects, 3D optical microscopy, and 3D polarimetric imaging are reviewed.
Engineering Enzymes for Bioorganic Synthesis: Peptide Bond Formation (1996)

Abstract This paper describes recent progress in the development of novel enzymatic catalysts for bioprocessing, especially for peptide bond formation. Techniques ranging from chemical modifications and specific and random mutagenesis to phage display and catalytic antibody induction used to create novel and efficient catalysts are described. The advantages and drawbacks of each technique and future prospects in the field are discussed.
Mutational Analysis of Putative SCH 28080 Binding Sites of the Gastric H+,K+-ATPase (1997)

A compound, SCH 28080 (2-methyl-8-(phenylmethoxy)imidazo [1,2-a]pyridine-3-acetonitrile), reversibly inhibits gastric and renal ouabain-insensitive H+,K+-ATPase, but not colonic ouabain-sensitive H+,K+-ATPase. By using the functional expression system and site-directed mutagenesis, we analyzed the putative binding sites of SCH 28080 in gastric H+,K+-ATPase alpha-subunit. It was previously reported that the binding site of SCH 28080, which is a K+-site inhibitor specific for gastric H+,K+-ATPase, was in the first extracellular loop between the first and second transmembrane segments of the alpha-subunit; Phe-126 and Asp-138 were putative binding sites. However, we found that all the mutants in the first extracellular loop including Phe-126 and Asp-138 retained H+, K+-ATPase activity and sensitivity to SCH 28080. Therefore, amino acid residues in the first extracellular loop are not directly involved in the SCH 28080 binding nor indispensable for the H+, K+-ATPase activity. Here we propose a candidate residue that is important for the binding with SCH 28080, Glu-822 in the sixth transmembrane segment. Mutations of Glu-822 to Asp and Ala (mutants termed E822D and E822A, respectively) decreased the ATPase activity to about 45% and 35% of the wild-type enzyme, respectively, while the mutations to Gln and Leu abolished the activity. Mutant E822A showed a significantly lower affinity for K+ than the wild-type enzyme, indicating that Glu-822 is involved in determining the affinity for K+. The sensitivity of mutant E822D to SCH 28080 was 8 times lower than that of the wild-type enzyme. The counterpart of Glu-822 in gastric H+,K+-ATPase is Asp in Na+,K+-ATPase and other colonic ouabain-sensitive H+,K+-ATPase, which are insensitive to SCH 28080. These results suggest that Glu-822 is one of important sites that bind with SCH 28080.
Free viewpoint switching in multi-view video streaming using Wyner-Ziv video coding (2006)

The free viewpoint switching is one of the most important features of multi-view video streaming. The key problem lies in how to achieve the best performance when the camera processing capability and the network bandwidth are limited. In this paper, we propose a novel free viewpoint switching scheme for multi-view video scenario, in which the distributed video coding technique is employed. In this scheme, the multi-camera video sources are encoded separately with the traditional hybrid video coding scheme, and meanwhile an alternative bitstream is produced for every frame based on the Wyner-Ziv coding method for the purpose of error correction when the viewpoint switching occurs. When switching happens, the Wyner-Ziv bits corresponding to the actual reference frame at the switching point is transmitted and used to recover the true reference. Instead of completely removing the mismatch, the proposed switching scheme tries to reduce the mismatch to an acceptable level so as to save the bits for the switching frame. A wavelet transform domain Wyner-Ziv coding method is proposed to produce the Wyner-Ziv bits for the switching frame. Conclusively, with the proposed scheme, the inter-camera communication can be avoided and the drifting error can be controlled efficiently when the viewpoint switching occurs.
Solid acid catalyzed biodiesel production by simultaneous esterification and transesterification (2006)

12-Tungstophosphoric acid (TPA) impregnated on four different supports such as hydrous zirconia, silica, alumina and activated carbon was evaluated as solid acid catalysts for the biodiesel production from low quality canola oil containing upto 20 wt% free fatty acids. The hydrous zirconia supported TPA was found to be the most promising catalyst exhibiting the highest ester yield (∼77%). The FTIR, XRD and nitrogen adsorption analysis revealed that the Lewis acid sites generated by the strong interaction of TPA and surface hydroxyl groups of zirconia are responsible for their higher activity. Further, the optimization of reaction parameters was carried out with the most active catalysts i.e. TPA supported hydrous zirconia and it was found that at 200 °C, 1 : 9 oil to alcohol molar ratio and 3 wt% catalysts loading a maximum ester yield of 90 wt% could be obtained. The catalysts were recycled and reused with negligible loss in activity.
The multi-token inter-arrival time (MTIT) access protocol for supporting IP over WDM ring network (2003)

One of the concepts currently pursued to provide the ideal network architecture for supporting the next generation Internet consists of transmitting the Internet protocol (IP) packets directly over the wavelength division multiplexing (WDM) layer of extant optical networks. The challenge of this concept is to make the optical bandwidth directly accessible to IP with the statistical multiplexing necessary to support the bursty nature of IP traffic in a cost effective way. This paper proposes the multi-token inter-arrival time (MTIT) access protocol designed to achieve a bandwidth efficient multiplexing technique in WDM ring networks. The network throughput is maximized without violating the desired access delay requirement by controlling the "token inter-arrival time" as opposed to controlling the "token rotation time" as proposed in existing standards, e.g., FDDI. It is shown that the MTIT protocol efficiency grows with the number of wavelengths-in full agreement with the WDM technology trend-and does not depend on the packet length-a feature ideal for IP implementation. In addition, the protocol provides a unique token control technique that allows to maintain the channel access delay at a node bounded even within the round trip propagation time of a ring.