gebhart/patrepeval huggingface dataset:
Assessment of cytogenetic damage by quantitation of micronuclei in human peripheral blood erythrocytes. (1986)

The incidence of micronuclei (Howell-Jolly bodies) in peripheral blood erythrocytes of splenectomized and nonsplenectomized humans was evaluated as an index of genotoxic exposure. Subjects with intact spleens had very low frequencies of micronucleated cells among circulating erythrocytes, even when these individuals were exposed to known clastogenic agents used in cancer therapy (no micronuclei were seen in 100,000 cells). After splenectomy, the frequency of micronuclei among erythrocytes of untreated subjects rose slowly and after 4 mo established a steady-state level of approximately 2.0/1000, a value similar to that reported for human bone marrow (Goetz et al. Relationship between experimental results in mammals and man: cytogenetic analysis of bone marrow injury induced by a single dose of cyclophosphamine. Mutat. Res., 31: 247-254, 1985; and Hogstedt et al. Micronuclei and chromosome aberrations in bone marrow cells and lymphocytes of humans exposed mainly to petroleum vapors. Hereditas, 94: 179-187, 1981. Chemotherapy increased these levels, with individual samples from patients on daily treatment often having values greater than 5 times higher than control levels. The frequency of micronucleated erythrocytes rose as the duration of clastogenic exposure increased and returned to near base-line levels approximately 4 mo after treatment was discontinued. These findings suggest that it will be possible to use analyses of circulating erythrocytes to assess genotoxic exposures among splenectomized human populations. The ease of sample preparation and scoring should make it possible to monitor individuals with greater statistical power than is feasible with conventional cytogenetic techniques.
Containment and mitigation of transgene flow from crops. (2003)

Two general approaches are used to deal with transgene flow: containment of the transgenes within the transgenic crop; or transgenic mitigation of the effects of the primary transgenic trait should it escape. Most containment mechanisms severely restrict gene flow only in one direction. Gene flow (leakage) is inevitable even in that direction, allowing spread through the population of undesired species, unless mitigated. Limitations to containing transgene flow Several molecular mechanisms have been proposed to contain transgenes by preventing introgression to relatives via pollen. These containment strategies can either suppress gene outflow from the crop, or protect the crop from inflow from wild or weedy relatives.1 The proposals to integrate the transgene in the plastid or mitochondrial genomes do not preclude the relative from pollinating the crop and then acting as the recurrent pollen parent. Claims of no paternal inheritance of plastome-encoded traits have been not substantiated, indeed maternal inheritance is leaky. Tobacco and other species typically transmit transplastomic traits via pollen at a frequency of 10–3–10–4 in laboratory experiments. A large-scale field experiment utilized a Setaria italica (foxtail millet) with chloroplast-inherited atrazine resistance (bearing a nuclear dominant red leaf base marker) crossed with five different male sterile yellow- or
Intact Free Prostate-Specific Antigen and Free and Total Human Glandular Kallikrein 2. Elimination of Assay Interference by Enzymatic Digestion of Antibodies to F(ab‘)2 Fragments (2006)

Various blood constituents can interfere with immunoassays, usually by binding the Fc portion of antibodies. Our previously developed assays for intact free prostate-specific antigen (PSA), free human kallikrein 2 (hK2), and total hK2 frequently yielded falsely high results despite including an excess of scavenger antibodies. We investigated whether this interference could be eliminated by replacing monoclonal capture or tracer antibodies with F(ab')2 or recombinant Fab fragments. Female heparin plasma samples (n = 1092), which should have negligible PSA and hK2, and male samples (n = 957) were analyzed to identify samples manifesting interference, which then were used to optimize protocols for the immunoassays. We compared original assays (monoclonal antibodies) versus optimized assays (F(ab')2 fragments: denatured mouse IgG added as scavenger) using another set of EDTA plasma (n = 113), heparin plasma (n = 160), and serum samples (n = 171). With the original assays, the frequency of falsely elevated hK2 and intact free PSA was 15 and 13%, respectively. The optimized assays eliminated 70-85% of these falsely elevated results and importantly reduced the magnitude in the remainder. F(ab')2 fragmentation was the most important factor in reducing interference. The optimized intact free PSA, free hK2, and total hK2 assays manifested high accuracy close to the lower limit of detection.
Complement: Classical and Lectin Pathways (2015)

Abstract The classical and lectin pathways of complement are major recognition systems of innate immunity that are found in mammals and other animal species. By means of several multimolecular proteases, each comprising a recognition protein and a protease component, pathogens and other targets are detected and thereby trigger proteolytic reactions. The classical pathway is initiated by C1, a complex of the recognition molecule C1q and two associated enzymes, C1r and C1s, whereas the lectin pathway is initiated by carbohydrate recognition molecules (mannan‐binding lectin (MBL) or one of the three ficolins or collectin‐LK) in complex with another set of enzymes, MBL‐associated serine proteases (MASPs). Both pathways converge to the formation of C3 convertase, a complex protease that cleaves C3, the central component of the complement system. Proteolytic cleavage of C3 generates a series of fragments and elicits various effector mechanisms, including inflammation and phagocytosis. These mechanisms contribute to the elimination of pathogenic microorganisms and altered host cells from blood and tissues and modulate the adaptive immune response. Key Concepts C1q, MBL, CL‐LK and ficolins are pattern‐recognition molecules able to sense motifs on pathogens and altered self‐cells. C1q is a major sensor of apoptotic cells and regulator of immune tolerance. Proteolytic cleavage of C3 is pivotal for amplification of the complement response and labelling of the target particles. Target recognition, proteolysis and complex formation generate conformational changes that underlie complement functioning. Complement activation and activity are tightly regulated to avoid noxious side‐effects on normal host cells and tissues.
Fluorocarbon-Modified Organic Semiconductors:  Molecular Architecture, Electronic, and Crystal Structure Tuning of Arene- versus Fluoroarene-Thiophene Oligomer Thin-Film Properties (2006)

We present here the systematic synthesis and comparative physicochemical characterization of a series of regiochemically varied and core size extension-modulated arene(perfluoroarene)-thiophene oligomers. The molecules investigated are: 5,5''-diphenyl-2,2':5',2'':5'',2'''-quaterthiophene (1), 5,5'-bis[1-[4-(thien-2-yl)phenyl]]-2,2'-dithiophene (2), 4,4'-bis[5-(2,2'-dithiophenyl)]-biphenyl (3), 5,5''-diperfluorophenyl-2,2':5',2'':5'',2'''-quaterthiophene (4), 5,5'-bis[1-[4-(thien-2-yl)perfluorophenyl]]-2,2'-dithiophene (5), 4,4'-bis[5-(2,2'-dithiophenyl)]-perfluorobiphenyl (6), 5,5''-diperfluorophenyl-2,2':5',2''-tertthiophene (7), 5,5'-diperfluorophenyl-2,2'-dihiophene (8), and 5,5-diperfluorophenylthiophene (9). Trends in optical absorption and emission parameters, molecular structures as defined by single-crystal X-ray diffraction, as well as electrochemical redox processes are described. The morphologies and microstructures of the vapor-deposited films grown over a range of growth temperatures have also been characterized. Field-effect transistor (FET) measurements demonstrate that all of these materials are FET-active and, depending on the molecular architecture, exhibit comparably good p- or n-type mobility when optimum film microstructural order is achieved. A very large n-channel mobility of approximately 0.5 cm2/Vs with I(on)/I(off) ratios > 10(8) is achieved for films of 4.
In vitro co-stimulation of anti-tumor activity by soluble B7 molecules. (2006)

In order to investigate the anti-tumor activity of a soluble B7-1/immunoglobulin G fusion protein and explore an effective method to eliminate immune escape of tumor cells, a recombinant vector encoding this fusion protein was constructed and constitutively expressed in Chinese hamster ovary cells. After purification with protein G affinity chromatography, the soluble fusion protein was tested for bioactivity. Results showed that the fusion protein could significantly increase the density of B7-1 molecules on WEHI-3 cells, a mouse leukemia cell line. Through allogeneic mixed lymphocyte tumor cultures, it was demonstrated that, with the presence of the first signal, it could also significantly enhance T cell activation and killing activity against WEHI-3 cells and interleukin-2 secretion by activated mouse T lymphocytes. The conclusion can be drawn that the soluble B7-IgG fusion protein has a potent capacity to generate or enhance anti-tumor immune response in vitro, and its clinical value deserves further investigation.
Imino Acids and Collagen Triple Helix Stability:  Characterization of Collagen-like Polypeptides Containing Hyp-Hyp-Gly Sequence Repeats (2004)

The analysis of factors contributing to the stability of proteins is a subject of intense debate. Particularly challenging is the study of structural proteins, since their function is their structure. Among these is collagen, the key structural component of bones, skin, cartilage, tendons, and other connecting tissues. It is well established that the collagen triple helix is characterized by the presence of hydroxyproline, whose content modulates triple helix thermal stability according to the requirement of the host organism. Because of the complexity and the fibrous nature of collagen, data on the stability and structure of this protein have been mainly obtained by the use of collagen-like polypeptides. On the basis of CD characterization of collagen-like polypeptides we here show that the presence of Hyp at the X position of repeating triplets Hyp-Hyp-Gly stabilizes the triple helix significantly. This extra-stabilization has been ascribed, by using molecular modeling, to the formation of a hydrogen bond between Hyp residues belonging to the X and the Y positions of adjacent chains. This communication also provides a comprehensive interpretation of the ensemble of available data on polypeptides containing proline derivatives.
Fabrication of Melt Spun Polypropylene Nanofibers by Forcespinning (2013)

Melt spinning of polypropylene nonwoven nanofiber mats is demonstrated using Forcespinning. The effects of rotational speed and melt flow rate of polymer on fiber diameter were studied. It was observed that melt flow rate of the polymer plays a major role in nanofiber formation and uniformity. Differential scanning calorimetry and X-Ray Diffraction analysis indicate that the crystallinity of nanofibers was decreased when compared to bulk polypropylene and the appearance of an oriented meso-phase (β phase) became evident with nanofiber development. Thermogravimetric analysis demonstrated that melt spinning of polypropylene using the Forcespinning method did not cause molecular degradation of the polymer.
Conformational study of N?-(carboxymethyl)lysine adducts of recombinant a-crystallins (1999)

Although CML adducts of alphaA- and alphaB-crystallins, the major AGE structures formed in vitro, changed protein conformation, no subunit degradation and HMW aggregation were observed. Moreover, the CML adducts increased chaperone-like activity of both alphaA- and alphaB-crystallins. The results suggest that CML formation alone may not play a major role in protein aggregation and lens opacity.
Manejo de hijos y ápices de cultivares de Musa spp. para iniciar la micropropagación y comportamiento durante seis subcultivos in vitro (2002)

Two forms of handling of the tillers were evaluated to extract the apexes that will be established in vitro . One was the method of the planting the rhizomes which below to the small tiller in the concrete beds, to cause the sprout again of the apical bud and its development on a disinfected ground, favored the survival in vitro , remarkably reduced to the number of contaminated apexes and the time required for his establishment with respect to the implantation directly with field material. When complete apexes were implanted was being where greater number of these (78%) were establish, simultaneously that reached the best development and green coloration. You will cultivate them more stable in the multiplication during the beginning of the process of the micropropagation were the hybrid of banana ‘FHIA 01’ and the hybrid of plantain ‘FHIA 20’, nevertheless, this last one presented the smaller coefficient of multiplication between all you will cultivate them, thus produced the smaller amount of accumulated buds in six subcultures. The greater coefficient of multiplication was reached with the hybrid banana ‘FHIA 23’, which produced greater numbers of new buds that appear accumulated, nevertheless, 39.9% presented a remarkable variability coefficient (VC) between subcultures. The banana cultivars did not present differences to each other, and its coefficient of multiplication was greater than the plantain cultivars, excepting the plantain hybrid ‘FHIA 04’. Key words: plantain, hybrids, in vitro management, phenolization, coefficient
RAFT Polymerization – Then and Now (2015)

RAFT Polymerization is currently one of the most versatile and most used methods for implementing reversible deactivation radical polymerization (RDRP) otherwise known as controlled or living radical polymerization. This paper will briefly trace the historical development of RAFT with reference to the kinetics and mechanism of the process. It will also highlight the most recent developments in our laboratories at CSIRO during the period 2011-2014 specifically covering such areas as kinetics and mechanism, RAFT agent development, end-group transformation, RAFT crosslinking polymerization, monomer sequence control and multi-block copolymer synthesis, and high throughput RAFT polymerization.
Interaction of the peroxisome-proliferator-activated receptor and retinoid X receptor. (1993)

The rat peroxisome-proliferator-activated receptor (PPAR) was expressed in insect cells and was shown to bind to a cognate PPAR response element (PPRE) from the acyl-CoA oxidase gene. Upon purification, PPAR was no longer able to bind DNA, although binding could be restored by addition of insect cell extracts. We investigated whether the retinoid X receptor (RXR) could supplement for this accessory activity. The rat RXR alpha cDNA was cloned and it was found that addition of in vitro-translated RXR alpha to purified PPAR facilitated binding of PPAR to a PPRE. Furthermore, an additional activity, which appeared to be distinct from rRXR alpha, was found in COS cell nuclear extracts that enabled binding of PPAR to a PPRE. Transient expression of RXR alpha in CHO cells was found to be essential for the response of a chloramphenicol acetyltransferase reporter construct containing PPREs to activators of PPAR. These results raise the possibility of convergence of the PPAR and retinoid-dependent signaling pathways on promoters containing PPRE-like responsive elements.
Interactions between Vaccinia Virus IEV Membrane Proteins and Their Roles in IEV Assembly and Actin Tail Formation (1999)

The intracellular enveloped form of vaccinia virus (IEV) induces the formation of actin tails that are strikingly similar to those seen in Listeria and Shigella infections. In contrast to the case for Listeria and Shigella, the vaccinia virus protein(s) responsible for directly initiating actin tail formation remains obscure. However, previous studies with recombinant vaccinia virus strains have suggested that the IEV-specific proteins A33R, A34R, A36R, B5R, and F13L play an undefined role in actin tail formation. In this study we have sought to understand how these proteins, all of which are predicted to have small cytoplasmic domains, are involved in IEV assembly and actin tail formation. Our data reveal that while deletion of A34R, B5R, or F13L resulted in a severe reduction in IEV particle assembly, IEVs formed by the DeltaB5R and DeltaF13L deletion strains, but not DeltaA34R, were still able to induce actin tails. The DeltaA36R deletion strain produced normal amounts of IEV particles, although these were unable to induce actin tails. Using several different approaches, we demonstrated that A36R is a type Ib membrane protein with a large, 195-amino-acid cytoplasmic domain exposed on the surface of IEV particles. Finally, coimmunoprecipitation experiments demonstrated that A36R interacts with A33R and A34R but not with B5R and that B5R forms a complex with A34R but not with A33R or A36R. Using extracts from DeltaA34R- and DeltaA36R-infected cells, we found that the interaction of A36R with A33R and that of A34R with B5R are independent of A34R and A36R, respectively. We conclude from our observations that multiple interactions between IEV membrane proteins exist which have important implications for IEV assembly and actin tail formation. Furthermore, these data suggest that while A34R is involved in IEV assembly and organization, A36R is critical for actin tail formation.
A Review of Parameters for the Bioelectrical Characterization of Breast Tissue (1999)

In the data set collected by the authors in freshly excised breast tissue, the admittance loci generally differed from circular arcs, rendering the calculation of the usual set of parameters impossible. Alternative parameters were used for the analysis of these data. The present study consists of the definition and evaluation of a set of such parameters aimed at the characterization and differentiation of breast tissues. These parameters were defined so that their calculation does not require the fit of circular arcs to the experimental points and is independent of any equivalent circuit model. The results of the statistical analysis showed significant differences between most of the tissue groups, especially between cancerous tissue and all the other groups, which confirmed that impedance spectroscopy can be considered as potentially suitable for breast cancer detection.
Sacral neuromodulation in urological indications: The Finnish experience (2010)

The difference in gender distribution compared with earlier published series may be explained by a selection bias due to the limited referrals of female patients from gynaecologists. The results favour the use of a tined lead device because of the shorter operating room time. Furthermore, the outcome seems to be more favourable among patients with a staged implant procedure compared with a one-stage operation with a tined lead device.
Efficient subpixel image registration algorithms (2008)

Three new algorithms for 2D translation image registration to within a small fraction of a pixel that use nonlinear optimization and matrix-multiply discrete Fourier transforms are compared. These algorithms can achieve registration with an accuracy equivalent to that of the conventional fast Fourier transform upsampling approach in a small fraction of the computation time and with greatly reduced memory requirements. Their accuracy and computation time are compared for the purpose of evaluating a translation-invariant error metric.
Extremely Low Bit Neural Network: Squeeze the Last Bit Out With ADMM (2018)

Although deep learning models are highly effective for various learning tasks, their high computational costs prohibit the deployment to scenarios where either memory or computational resources are limited. In this paper, we focus on compressing and accelerating deep models with network weights represented by very small numbers of bits, referred to as extremely low bit neural network. We model this problem as a discretely constrained optimization problem. Borrowing the idea from Alternating Direction Method of Multipliers (ADMM), we decouple the continuous parameters from the discrete constraints of network, and cast the original hard problem into several subproblems. We propose to solve these subproblems using extragradient and iterative quantization algorithms that lead to considerably faster convergency compared to conventional optimization methods. Extensive experiments on image recognition and object detection verify that the proposed algorithm is more effective than state-of-the-art approaches when coming to extremely low bit neural network.
Segmentation, Content Extraction and Visualization of Broadcast News Video using Multistream Analysis (1997)

This paper reports the development of a broadcast news video corpora and novel techniques to automatically segment stories, extract proper names, and visualize associated metadata. We report story segmentation and proper name xtraction results using an information retrieval inspired evaluation methodology, measuring the precision and recall performance of our techniques. We briefly describe our implementation of a Broadcast News Analysis(BNA’~) system and an associated viewer, Broadcast News Navigator (BNNTM). We point to current efforts toward more robust processing using multistream analysis on imagery, audio, and closed-caption streams and future efforts in automatic video summarization and user-tailored presentation generation. 1. Problem and Related Research Content based video access is a valuable capability for several important applications including video teleconference archiving, video mail access, and individualized video news program generation. The current state of the art for commercial video archives focuses on manual annotation (Davis 1991), which suffers from problems of accuracy, consistency (when performed by more than one operator), timeliness, scalability, and cost. Just as information retrieval techniques are required to manage large text collections, video sources require similar indexing and storage facilities to support real-time profiling as well as retrospective search. Within the imagery stream, techniques performing in the ninety plus percent accuracy range have been developed to index video based on visual transitions (e.g., dissolve, fade, cut) and shot classification (e.g., anchor versus story shots (Zhang et al. 1994). Others have investigated linguistic streams associated with video
Versatile cosmid vectors for the isolation, expression, and rescue of gene sequences: studies with the human alpha-globin gene cluster. (1983)

We have developed a series of cosmids that can be used as vectors for genomic recombinant DNA library preparations, as expression vectors in mammalian cells for both transient and stable transformations, and as shuttle vectors between bacteria and mammalian cells. These cosmids were constructed by inserting one of the SV2-derived selectable gene markers--SV2-gpt, SV2-DHFR, and SV2-neo--in cosmid pJB8. High efficiency of genomic cloning was obtained with these cosmids and the size of the inserts was 30-42 kilobases. We isolated recombinant cosmids containing the human alpha-globin gene cluster from these genomic libraries. The simian virus 40 DNA in these selectable gene markers provides the origin of replication and enhancer sequences necessary for replication in permissive cells such as COS 7 cells and thereby allows transient expression of alpha-globin genes in these cells. These cosmids and their recombinants could also be stably transformed into mammalian cells by using the respective selection systems. Both of the adult alpha-globin genes were more actively expressed than the embryonic zeta-globin genes in these transformed cell lines. Because of the presence of the cohesive ends of the Charon 4A phage in the cosmids, the transforming DNA sequences could readily be rescued from these stably transformed cells into bacteria by in vitro packaging of total cellular DNA. Thus, these cosmid vectors are potentially useful for direct isolation of structural genes.